Chevron Catalog

GENERAL

General Concepts

chevron is a collection of functions to creates tables, listings, and graphs following Roche standards for clinical trials reporting. After loading the R packages and the trial data, the output is to be created by the main function run(...) . Two arguments object= and adam_db= are always expected in the function. object= specifies which Roche Standard Template ID to use. adam_db= specifies the input dataset. Other mandatory and optional arguments within the run function vary depending on which template ID is called. To access which arguments are required and what functions are used in each template, simply try ?template (e.g. ?aet01) to see more detailed descriptions and instructions.

1. Input dataset and dataset names

The input dataset expected by the argument adam_db= in the run(...) function is a collection of ADaM datasets as a list object. Each ADaM dataset is expected to be an object of data frame. If the ADaM datasets are read in individually, user will need to combine them into a list object and provide the name of the list to adam_db=. Also, each element in the list are expected to have corresponding ADaM dataset names. Conventional ADaM dataset names, including adsl,adex, adae, adlb,advs,adeg,adcm,admh,adrs, and adtte, can be picked up by chevron with one exception.

std_data <- list(adsl = adsl, adae = adae)
run(object = aet01_nollt, adam_db = std_data)

2. Expected variables in input analysis dataset

By default, chevron does not pull any subject-level information from either adsl or adsub and merge into the analysis dataset in the underlying preprocessing steps. The analysis dataset fed into adam_db= is expected to have all variables required for analysis available.

3. Character vs Factor

In the output generation, we often need to specify a particular sorting order of a variable at the time of display. In chevron, a character variable needs to be factorized with pre-specified levels to display in order. When encountering cases, for instance, "ARM A" has an Asian group only while "ARM B" has both Asian and White groups, it is not able to produce outputs like the demographic table unless "RACE" is factorized to provide access to the same level attribute of the variable "RACE" after the arm split. It is noted that the feature comes from rtables instead of chevron.

proc_data <- syn_data
proc_data$adsl <- proc_data$adsl %>%
  mutate(RACE = case_when(
    ARMCD == "ARM A" ~ "ASIAN",
    ARMCD == "ARM B" & !.data$RACE %in% c("WHITE", "ASIAN") ~ "ASIAN",
    TRUE ~ RACE
  ))

Having "RACE" as a character variable rather than a factor leads to error message showing up as “Error: Error applying analysis function (var - RACE): Number of rows generated by analysis function do not match across all columns,” and it is recommended to convert analysis variable "RACE" to a factor.

run(dmt01, proc_data)

To resolve this issue, simply try factorizing the variable "RACE":

proc_data$adsl$RACE <- as.factor(proc_data$adsl$RACE)
run(dmt01, proc_data)
#>                                        A: Drug X    B: Placebo   C: Combination   All Patients
#>                                          (N=15)       (N=15)         (N=15)          (N=45)   
#>   ————————————————————————————————————————————————————————————————————————————————————————————
#>   Age (yr)                                                                                    
#>     n                                      15           15             15              45     
#>     Mean (SD)                          31.3 (5.3)   35.1 (9.0)     36.6 (6.4)      34.3 (7.3) 
#>     Median                                31.0         35.0           35.0            34.0    
#>     Min - Max                           24 - 40      24 - 57        24 - 49         24 - 57   
#>   Age Group                                                                                   
#>     n                                      15           15             15              45     
#>     <65                                15 (100%)    15 (100%)      15 (100%)       45 (100%)  
#>   Sex                                                                                         
#>     n                                      15           15             15              45     
#>     Male                               3 (20.0%)    7 (46.7%)      5 (33.3%)       15 (33.3%) 
#>     Female                             12 (80.0%)   8 (53.3%)      10 (66.7%)      30 (66.7%) 
#>   Ethnicity                                                                                   
#>     n                                      15           15             15              45     
#>     NOT REPORTED                           0            0          2 (13.3%)        2 (4.4%)  
#>     HISPANIC OR LATINO                 2 (13.3%)        0              0            2 (4.4%)  
#>     NOT HISPANIC OR LATINO             13 (86.7%)   15 (100%)      13 (86.7%)      41 (91.1%) 
#>   RACE                                                                                        
#>     n                                      15           15             15              45     
#>     AMERICAN INDIAN OR ALASKA NATIVE       0            0           1 (6.7%)        1 (2.2%)  
#>     ASIAN                              15 (100%)    13 (86.7%)     8 (53.3%)       36 (80.0%) 
#>     BLACK OR AFRICAN AMERICAN              0            0          4 (26.7%)        4 (8.9%)  
#>     WHITE                                  0        2 (13.3%)      2 (13.3%)        4 (8.9%)

4. Testing the codes for plot generation

The run function when calling a Graphics Template ID returns a gTree object which will be used in the downstream workflow for output generation. There are two alternative approaches to rendering the plot: (1) having draw = TRUE in the run function to enable the generated plot to be automatically created and viewed via the Plots tab, and (2) calling the function grid.draw from the package grid which can be utilized to render the plot for viewing and testing purpose. See example below:

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")

# method 1
run(kmg01, proc_data, dataset = "adtte", draw = TRUE)

# method 2
res <- run(kmg01, proc_data, dataset = "adtte")
grid::grid.newpage()
grid::grid.draw(res)

General Control Arguments

1. lbl_overall: Column of Total

The generic argument lbl_overall controls whether the column of total will be produced or not. lbl_overall = NULL suppresses the total, lbl_overall = "All Patients" produces the total.

2. Column counts: N=xxx

Column counts are displayed by default. There is no generic argument controlling whether the count of unique number of subjects (N=xxx) will be displayed in the column header or not. Users are allowed to customize the display of N=xxx by forcing display_columncounts = FALSE to wipe column counts away during the postprocessing (with precautions and it is not recommended).

tbl <- run(dmt01, syn_data) # table with column counts
tbl@col_info@display_columncounts <- FALSE
tbl # no column counts now
#>                                        A: Drug X    B: Placebo   C: Combination   All Patients
#>   ————————————————————————————————————————————————————————————————————————————————————————————
#>   Age (yr)                                                                                    
#>     n                                      15           15             15              45     
#>     Mean (SD)                          31.3 (5.3)   35.1 (9.0)     36.6 (6.4)      34.3 (7.3) 
#>     Median                                31.0         35.0           35.0            34.0    
#>     Min - Max                           24 - 40      24 - 57        24 - 49         24 - 57   
#>   Age Group                                                                                   
#>     n                                      15           15             15              45     
#>     <65                                15 (100%)    15 (100%)      15 (100%)       45 (100%)  
#>   Sex                                                                                         
#>     n                                      15           15             15              45     
#>     Male                               3 (20.0%)    7 (46.7%)      5 (33.3%)       15 (33.3%) 
#>     Female                             12 (80.0%)   8 (53.3%)      10 (66.7%)      30 (66.7%) 
#>   Ethnicity                                                                                   
#>     n                                      15           15             15              45     
#>     NOT REPORTED                           0            0          2 (13.3%)        2 (4.4%)  
#>     HISPANIC OR LATINO                 2 (13.3%)        0              0            2 (4.4%)  
#>     NOT HISPANIC OR LATINO             13 (86.7%)   15 (100%)      13 (86.7%)      41 (91.1%) 
#>   RACE                                                                                        
#>     n                                      15           15             15              45     
#>     AMERICAN INDIAN OR ALASKA NATIVE       0        2 (13.3%)       1 (6.7%)        3 (6.7%)  
#>     ASIAN                              8 (53.3%)    10 (66.7%)     8 (53.3%)       26 (57.8%) 
#>     BLACK OR AFRICAN AMERICAN          4 (26.7%)     1 (6.7%)      4 (26.7%)       9 (20.0%)  
#>     WHITE                              3 (20.0%)    2 (13.3%)      2 (13.3%)       7 (15.6%)

TABLES

Safety Summary (AET01)

1. Safety Summary

The aet01 template produces the standard safety summary.

run(aet01, syn_data, arm_var = "ARM")
#>                                                                A: Drug X    B: Placebo   C: Combination
#>                                                                  (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one AE                13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of AEs                                              58           59             99      
#>   Total number of deaths                                       2 (13.3%)    4 (26.7%)      3 (20.0%)   
#>   Total number of patients withdrawn from study due to an AE       0            0           1 (6.7%)   
#>   Total number of patients with at least one                                                           
#>     AE with fatal outcome                                      8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>     Serious AE                                                 12 (80.0%)   12 (80.0%)     11 (73.3%)  
#>     Serious AE leading to withdrawal from treatment                0            0          2 (13.3%)   
#>     Serious AE leading to dose modification/interruption       4 (26.7%)    3 (20.0%)      4 (26.7%)   
#>     Related Serious AE                                         8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>     AE leading to withdrawal from treatment                    2 (13.3%)    3 (20.0%)      3 (20.0%)   
#>     AE leading to dose modification/interruption               6 (40.0%)    9 (60.0%)      11 (73.3%)  
#>     Related AE                                                 11 (73.3%)   10 (66.7%)     13 (86.7%)  
#>     Related AE leading to withdrawal from treatment                0        3 (20.0%)          0       
#>     Related AE leading to dose modification/interruption        1 (6.7%)    4 (26.7%)      9 (60.0%)   
#>     Severe AE (at greatest intensity)                          11 (73.3%)   10 (66.7%)     12 (80.0%)

2. Safety Summary with Modified Rows

Analyses under “Total number of patients with at least one” can be removed, added, or modified by editing the parameter anl_vars. An analysis here is an abbreviated name of the analysis of interest, and supported by a variable in ADAE derived under the condition of interest. The defined analyses currently include "FATAL", "SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", and "SEV". When modification is made, analyses must all be listed in the argument anl_vars. The example below shows adding the customized analysis "RELCTC35".

proc_data <- syn_data
proc_data$adae <- proc_data$adae %>%
  filter(.data$ANL01FL == "Y") %>%
  mutate(
    FATAL = with_label(.data$AESDTH == "Y", "AE with fatal outcome"),
    SER = with_label(.data$AESER == "Y", "Serious AE"),
    SEV = with_label(.data$ASEV == "SEVERE", "Severe AE (at greatest intensity)"),
    REL = with_label(.data$AREL == "Y", "Related AE"),
    WD = with_label(.data$AEACN == "DRUG WITHDRAWN", "AE leading to withdrawal from treatment"),
    DSM = with_label(
      .data$AEACN %in% c("DRUG INTERRUPTED", "DOSE INCREASED", "DOSE REDUCED"),
      "AE leading to dose modification/interruption"
    ),
    SERWD = with_label(.data$SER & .data$WD, "Serious AE leading to withdrawal from treatment"),
    SERDSM = with_label(.data$SER & .data$DSM, "Serious AE leading to dose modification/interruption"),
    RELSER = with_label(.data$SER & .data$REL, "Related Serious AE"),
    RELWD = with_label(.data$REL & .data$WD, "Related AE leading to withdrawal from treatment"),
    RELDSM = with_label(.data$REL & .data$DSM, "Related AE leading to dose modification/interruption"),
    CTC35 = with_label(.data$ATOXGR %in% c("3", "4", "5"), "Grade 3-5 AE"),
    CTC45 = with_label(.data$ATOXGR %in% c("4", "5"), "Grade 4/5 AE"),
    RELCTC35 = with_label(.data$ATOXGR %in% c("3", "4", "5") & .data$AEREL == "Y", "Related Grade 3-5")
  )

proc_data$adsl <- proc_data$adsl %>%
  mutate(DCSREAS = reformat(.data$DCSREAS, missing_rule))

run(aet01, proc_data, anl_vars = list(safety_var = c("FATAL", "SER", "RELSER", "RELCTC35")), auto_pre = FALSE)
#>                                                                A: Drug X    B: Placebo   C: Combination
#>                                                                  (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one AE                13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of AEs                                              58           59             99      
#>   Total number of deaths                                       2 (13.3%)    4 (26.7%)      3 (20.0%)   
#>   Total number of patients withdrawn from study due to an AE       0            0           1 (6.7%)   
#>   Total number of patients with at least one                                                           
#>     AE with fatal outcome                                      8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>     Serious AE                                                 12 (80.0%)   12 (80.0%)     11 (73.3%)  
#>     Related Serious AE                                         8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>     Related Grade 3-5                                          11 (73.3%)   10 (66.7%)     12 (80.0%)

Safety Summary (Adverse Events of Special Interest) (AET01_AESI)

1. Safety Summary (Adverse Events of Special Interest)

The aet01_aesi template produces the standard safety summary for adverse events of special interest.

run(aet01_aesi, syn_data)
#>                                                                                   A: Drug X    B: Placebo   C: Combination
#>                                                                                     (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one AE                                   13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of AEs                                                                 58           59             99      
#>   Total number of patients with at least one AE by worst grade                                                            
#>     Grade 1                                                                           0         1 (6.7%)       1 (6.7%)   
#>     Grade 2                                                                        1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>     Grade 3                                                                        1 (6.7%)    2 (13.3%)       1 (6.7%)   
#>     Grade 4                                                                       3 (20.0%)    2 (13.3%)      2 (13.3%)   
#>     Grade 5 (fatal outcome)                                                       8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>   Total number of patients with study drug withdrawn due to AE                    2 (13.3%)    3 (20.0%)      3 (20.0%)   
#>   Total number of patients with dose modified/interrupted due to AE               6 (40.0%)    9 (60.0%)      11 (73.3%)  
#>   Total number of patients with treatment received for AE                         10 (66.7%)   10 (66.7%)     14 (93.3%)  
#>   Total number of patients with all non-fatal AEs resolved                        9 (60.0%)    10 (66.7%)     12 (80.0%)  
#>   Total number of patients with at least one unresolved or ongoing non-fatal AE   10 (66.7%)   9 (60.0%)      14 (93.3%)  
#>   Total number of patients with at least one serious AE                           12 (80.0%)   12 (80.0%)     11 (73.3%)  
#>   Total number of patients with at least one related AE                           11 (73.3%)   10 (66.7%)     13 (86.7%)

2. Safety Summary (Adverse Events of Special Interest) (optional lines)

Additional analyses can be added with the argument aesi_vars, please type ?aet01_aesi in console to find out the list of all pre-defined optional analyses in the HELP.

run(aet01_aesi, syn_data, aesi_vars = c("RESLWD", "RELSER"))
#>                                                                                   A: Drug X    B: Placebo   C: Combination
#>                                                                                     (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one AE                                   13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of AEs                                                                 58           59             99      
#>   Total number of patients with at least one AE by worst grade                                                            
#>     Grade 1                                                                           0         1 (6.7%)       1 (6.7%)   
#>     Grade 2                                                                        1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>     Grade 3                                                                        1 (6.7%)    2 (13.3%)       1 (6.7%)   
#>     Grade 4                                                                       3 (20.0%)    2 (13.3%)      2 (13.3%)   
#>     Grade 5 (fatal outcome)                                                       8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>   Total number of patients with study drug withdrawn due to AE                    2 (13.3%)    3 (20.0%)      3 (20.0%)   
#>   Total number of patients with dose modified/interrupted due to AE               6 (40.0%)    9 (60.0%)      11 (73.3%)  
#>   Total number of patients with treatment received for AE                         10 (66.7%)   10 (66.7%)     14 (93.3%)  
#>   Total number of patients with all non-fatal AEs resolved                        9 (60.0%)    10 (66.7%)     12 (80.0%)  
#>   Total number of patients with at least one unresolved or ongoing non-fatal AE   10 (66.7%)   9 (60.0%)      14 (93.3%)  
#>   Total number of patients with at least one serious AE                           12 (80.0%)   12 (80.0%)     11 (73.3%)  
#>   Total number of patients with at least one related AE                           11 (73.3%)   10 (66.7%)     13 (86.7%)  
#>     No. of patients with serious, related AE                                      8 (53.3%)    8 (53.3%)      10 (66.7%)

3. Safety Summary (Adverse Events of Special Interest) (for studies with multiple drugs)

For studies with more than one study drug, users need to define the analyses in adae and add to the argument aesi_vars following the example above. No pre-defined analysis is available at this moment.

Adverse Events (AET02)

1. Adverse Events

  1. The template aet02 produces the standard adverse event summary by MedDRA system organ class and preferred term.
  2. The template does not include the column of total as default. The ‘All Patients’ column can be added with the argument lbl_overall = "All Patients".
  3. Missing values in "AEBODSYS", and "AEDECOD" are labeled as No Coding Available.
run(aet02, syn_data)
#>   MedDRA System Organ Class                                    A: Drug X    B: Placebo   C: Combination
#>     MedDRA Preferred Term                                        (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one adverse event     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Overall total number of events                                   58           59             99      
#>   cl B.2                                                                                               
#>     Total number of patients with at least one adverse event   11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>     Total number of events                                         18           15             20      
#>     dcd B.2.2.3.1                                              8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>     dcd B.2.1.2.1                                              5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   cl D.1                                                                                               
#>     Total number of patients with at least one adverse event   9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>     Total number of events                                         13           9              19      
#>     dcd D.1.1.1.1                                              4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.4.2                                              6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>   cl A.1                                                                                               
#>     Total number of patients with at least one adverse event   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>     Total number of events                                         8            11             16      
#>     dcd A.1.1.1.2                                              5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.1                                              3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>   cl B.1                                                                                               
#>     Total number of patients with at least one adverse event   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     Total number of events                                         6            6              12      
#>     dcd B.1.1.1.1                                              5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                                                               
#>     Total number of patients with at least one adverse event   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     Total number of events                                         6            4              12      
#>     dcd C.2.1.2.1                                              6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>   cl D.2                                                                                               
#>     Total number of patients with at least one adverse event   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>     Total number of events                                         3            5              10      
#>     dcd D.2.1.5.3                                              2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>   cl C.1                                                                                               
#>     Total number of patients with at least one adverse event   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>     Total number of events                                         4            9              10      
#>     dcd C.1.1.1.3                                              4 (26.7%)    4 (26.7%)      5 (33.3%)

2. Adverse Events (with High-level Term)

The syntax below displays adverse events by MedDRA system organ class, high-level term and preferred term.

run(aet02, syn_data, row_split_var = c("AEBODSYS", "AEHLT"))
#>   MedDRA System Organ Class                                                                              
#>     High Level Term                                              A: Drug X    B: Placebo   C: Combination
#>       MedDRA Preferred Term                                        (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one adverse event       13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Overall total number of events                                     58           59             99      
#>   cl B.2                                                                                                 
#>     Total number of patients with at least one adverse event     11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>     Total number of events                                           18           15             20      
#>     hlt B.2.2.3                                                                                          
#>       Total number of patients with at least one adverse event   8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>       Total number of events                                         9            7              13      
#>       dcd B.2.2.3.1                                              8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>     hlt B.2.1.2                                                                                          
#>       Total number of patients with at least one adverse event   5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>       Total number of events                                         9            8              7       
#>       dcd B.2.1.2.1                                              5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   cl D.1                                                                                                 
#>     Total number of patients with at least one adverse event     9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>     Total number of events                                           13           9              19      
#>     hlt D.1.1.1                                                                                          
#>       Total number of patients with at least one adverse event   4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>       Total number of events                                         5            7              11      
#>       dcd D.1.1.1.1                                              4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     hlt D.1.1.4                                                                                          
#>       Total number of patients with at least one adverse event   6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>       Total number of events                                         8            2              8       
#>       dcd D.1.1.4.2                                              6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>   cl A.1                                                                                                 
#>     Total number of patients with at least one adverse event     7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>     Total number of events                                           8            11             16      
#>     hlt A.1.1.1                                                                                          
#>       Total number of patients with at least one adverse event   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>       Total number of events                                         8            11             16      
#>       dcd A.1.1.1.2                                              5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>       dcd A.1.1.1.1                                              3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>   cl B.1                                                                                                 
#>     Total number of patients with at least one adverse event     5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     Total number of events                                           6            6              12      
#>     hlt B.1.1.1                                                                                          
#>       Total number of patients with at least one adverse event   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>       Total number of events                                         6            6              12      
#>       dcd B.1.1.1.1                                              5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                                                                 
#>     Total number of patients with at least one adverse event     6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     Total number of events                                           6            4              12      
#>     hlt C.2.1.2                                                                                          
#>       Total number of patients with at least one adverse event   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>       Total number of events                                         6            4              12      
#>       dcd C.2.1.2.1                                              6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>   cl D.2                                                                                                 
#>     Total number of patients with at least one adverse event     2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>     Total number of events                                           3            5              10      
#>     hlt D.2.1.5                                                                                          
#>       Total number of patients with at least one adverse event   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>       Total number of events                                         3            5              10      
#>       dcd D.2.1.5.3                                              2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>   cl C.1                                                                                                 
#>     Total number of patients with at least one adverse event     4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>     Total number of events                                           4            9              10      
#>     hlt C.1.1.1                                                                                          
#>       Total number of patients with at least one adverse event   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>       Total number of events                                         4            9              10      
#>       dcd C.1.1.1.3                                              4 (26.7%)    4 (26.7%)      5 (33.3%)

3. Adverse Events (Preferred Terms only)

The syntax below displays adverse events by preferred term only.

run(aet02, syn_data, row_split_var = NULL)
#>                                                              A: Drug X    B: Placebo   C: Combination
#>   MedDRA Preferred Term                                        (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one adverse event   13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Overall total number of events                                 58           59             99      
#>   dcd B.2.2.3.1                                              8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>   dcd B.1.1.1.1                                              5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   dcd C.2.1.2.1                                              6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>   dcd A.1.1.1.2                                              5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>   dcd B.2.1.2.1                                              5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   dcd D.1.1.1.1                                              4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>   dcd D.1.1.4.2                                              6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>   dcd D.2.1.5.3                                              2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>   dcd C.1.1.1.3                                              4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>   dcd A.1.1.1.1                                              3 (20.0%)     1 (6.7%)      6 (40.0%)

Adverse Events by Greatest Intensity(AET03)

1. Adverse Events by Greatest Intensity

This aet03 template produces the standard adverse event by greatest intensity summary

run(aet03, syn_data)
#>   MedDRA System Organ Class   A: Drug X    B: Placebo   C: Combination
#>     MedDRA Preferred Term       (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————
#>   - Any Intensity -           13 (86.7%)   14 (93.3%)     15 (100%)   
#>   MILD                            0         1 (6.7%)       1 (6.7%)   
#>   MODERATE                    2 (13.3%)    3 (20.0%)      2 (13.3%)   
#>   SEVERE                      11 (73.3%)   10 (66.7%)     12 (80.0%)  
#>   cl B.2                                                              
#>     - Any Intensity -         11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>     MILD                      6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>     MODERATE                  5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>     dcd B.2.2.3.1                                                     
#>       - Any Intensity -       8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>       MILD                    8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>     dcd B.2.1.2.1                                                     
#>       - Any Intensity -       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>       MODERATE                5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   cl D.1                                                              
#>     - Any Intensity -         9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>     MODERATE                  5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>     SEVERE                    4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.1.1                                                     
#>       - Any Intensity -       4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>       SEVERE                  4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.4.2                                                     
#>       - Any Intensity -       6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>       MODERATE                6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>   cl A.1                                                              
#>     - Any Intensity -         7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>     MILD                      2 (13.3%)        0          4 (26.7%)   
#>     MODERATE                  5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.2                                                     
#>       - Any Intensity -       5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>       MODERATE                5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.1                                                     
#>       - Any Intensity -       3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>       MILD                    3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>   cl B.1                                                              
#>     - Any Intensity -         5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     SEVERE                    5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     dcd B.1.1.1.1                                                     
#>       - Any Intensity -       5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>       SEVERE                  5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                              
#>     - Any Intensity -         6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     MODERATE                  6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     dcd C.2.1.2.1                                                     
#>       - Any Intensity -       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>       MODERATE                6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>   cl D.2                                                              
#>     - Any Intensity -         2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>     MILD                      2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>     dcd D.2.1.5.3                                                     
#>       - Any Intensity -       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>       MILD                    2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>   cl C.1                                                              
#>     - Any Intensity -         4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>     SEVERE                    4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>     dcd C.1.1.1.3                                                     
#>       - Any Intensity -       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>       SEVERE                  4 (26.7%)    4 (26.7%)      5 (33.3%)

Adverse Events by Highest NCI CTCAE Grade (AET04)

1. Adverse Events by Highest NCI CTCAE Grade

  1. The aet04 template produces the standard adverse event by highest NCI CTCAE grade summary.
  2. By default, this template includes the grouped grades of ‘Grade 1-2’ and ‘Grade 3-4’.
  3. By default this template removes the rows with 0 count.
  4. If a treatment group does not have any adverse event, the treatment group is automatically displayed providing that it is defined in ADSL.
run(aet04, syn_data)
#>   MedDRA System Organ Class                                                           
#>     MedDRA Preferred Term                     A: Drug X    B: Placebo   C: Combination
#>                               Grade             (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————
#>   - Any adverse events -                                                              
#>                               - Any Grade -   13 (86.7%)   14 (93.3%)     15 (100%)   
#>                               Grade 1-2        1 (6.7%)    2 (13.3%)      2 (13.3%)   
#>                               1                   0         1 (6.7%)       1 (6.7%)   
#>                               2                1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      3 (20.0%)   
#>                               3                1 (6.7%)    2 (13.3%)       1 (6.7%)   
#>                               4               3 (20.0%)    2 (13.3%)      2 (13.3%)   
#>                               Grade 5         8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>   cl B.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>                               Grade 1-2       6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               1               6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               Grade 3-4       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>     dcd B.2.2.3.1                                                                     
#>                               - Any Grade -   8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               Grade 1-2       8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               1               8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>     dcd B.2.1.2.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               Grade 3-4       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   cl D.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>                               Grade 3-4       5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>                               3               5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>                               Grade 5         4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.1.1                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>                               Grade 5         4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.4.2                                                                     
#>                               - Any Grade -   6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               Grade 3-4       6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               3               6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>   cl A.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               Grade 1-2       7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               1               2 (13.3%)        0          4 (26.7%)   
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.2                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 1-2       5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.1                                                                     
#>                               - Any Grade -   3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               Grade 1-2       3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               1               3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>   cl B.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 5         5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     dcd B.1.1.1.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 5         5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     dcd C.2.1.2.1                                                                     
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>   cl D.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>     dcd D.2.1.5.3                                                                     
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>   cl C.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>     dcd C.1.1.1.3                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)

2. Adverse Events by Highest NCI CTCAE Grade (Fill in of Grades)

If, for some preferred terms, not all grades occur but all grades should be displayed, this can be achieved by specifying the argument prune_0 = FALSE.

run(aet04, syn_data, prune_0 = FALSE)
#>   MedDRA System Organ Class                                                           
#>     MedDRA Preferred Term                     A: Drug X    B: Placebo   C: Combination
#>                               Grade             (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————
#>   - Any adverse events -                                                              
#>                               - Any Grade -   13 (86.7%)   14 (93.3%)     15 (100%)   
#>                               Grade 1-2        1 (6.7%)    2 (13.3%)      2 (13.3%)   
#>                               1                   0         1 (6.7%)       1 (6.7%)   
#>                               2                1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      3 (20.0%)   
#>                               3                1 (6.7%)    2 (13.3%)       1 (6.7%)   
#>                               4               3 (20.0%)    2 (13.3%)      2 (13.3%)   
#>                               Grade 5         8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>   cl B.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>                               Grade 1-2       6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               1               6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               2                   0            0              0       
#>                               Grade 3-4       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd B.2.2.3.1                                                                     
#>                               - Any Grade -   8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               Grade 1-2       8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               1               8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd B.2.1.2.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>   cl D.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4       5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>                               3               5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>                               4                   0            0              0       
#>                               Grade 5         4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.1.1                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5         4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.4.2                                                                     
#>                               - Any Grade -   6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4       6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               3               6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>   cl A.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               Grade 1-2       7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               1               2 (13.3%)        0          4 (26.7%)   
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd A.1.1.1.2                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 1-2       5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               1                   0            0              0       
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd A.1.1.1.1                                                                     
#>                               - Any Grade -   3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               Grade 1-2       3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               1               3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>   cl B.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5         5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     dcd B.1.1.1.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5         5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               1                   0            0              0       
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd C.2.1.2.1                                                                     
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               1                   0            0              0       
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>   cl D.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>     dcd D.2.1.5.3                                                                     
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-4           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               Grade 5             0            0              0       
#>   cl C.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               3                   0            0              0       
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 5             0            0              0       
#>     dcd C.1.1.1.3                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-4       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               3                   0            0              0       
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 5             0            0              0

3. Adverse Events by Highest NCI CTCAE Grade with modified grouping of grade

Collapsing grade 3-4 with grade 5, can be achieved by modifying the definition of grade groups in the argument grade_groups.

grade_groups <- list(
  "Grade 1-2" = c("1", "2"),
  "Grade 3-5" = c("3", "4", "5")
)

run(aet04, syn_data, grade_groups = grade_groups, prune_0 = FALSE)
#>   MedDRA System Organ Class                                                           
#>     MedDRA Preferred Term                     A: Drug X    B: Placebo   C: Combination
#>                               Grade             (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————
#>   - Any adverse events -                                                              
#>                               - Any Grade -   13 (86.7%)   14 (93.3%)     15 (100%)   
#>                               Grade 1-2        1 (6.7%)    2 (13.3%)      2 (13.3%)   
#>                               1                   0         1 (6.7%)       1 (6.7%)   
#>                               2                1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>                               Grade 3-5       12 (80.0%)   12 (80.0%)     13 (86.7%)  
#>                               3                1 (6.7%)    2 (13.3%)       1 (6.7%)   
#>                               4               3 (20.0%)    2 (13.3%)      2 (13.3%)   
#>                               5               8 (53.3%)    8 (53.3%)      10 (66.7%)  
#>   cl B.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   11 (73.3%)   8 (53.3%)      10 (66.7%)  
#>                               Grade 1-2       6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               1               6 (40.0%)    2 (13.3%)      5 (33.3%)   
#>                               2                   0            0              0       
#>                               Grade 3-5       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd B.2.2.3.1                                                                     
#>                               - Any Grade -   8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               Grade 1-2       8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               1               8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd B.2.1.2.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               3               5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>   cl D.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       9 (60.0%)    5 (33.3%)      11 (73.3%)  
#>                               3               5 (33.3%)     1 (6.7%)      4 (26.7%)   
#>                               4                   0            0              0       
#>                               5               4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.1.1                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5               4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     dcd D.1.1.4.2                                                                     
#>                               - Any Grade -   6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               3               6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>   cl A.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               Grade 1-2       7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>                               1               2 (13.3%)        0          4 (26.7%)   
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd A.1.1.1.2                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 1-2       5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               1                   0            0              0       
#>                               2               5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd A.1.1.1.1                                                                     
#>                               - Any Grade -   3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               Grade 1-2       3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               1               3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>                               2                   0            0              0       
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>   cl B.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5               5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     dcd B.1.1.1.1                                                                     
#>                               - Any Grade -   5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5               5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>   cl C.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               1                   0            0              0       
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd C.2.1.2.1                                                                     
#>                               - Any Grade -   6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 1-2       6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               1                   0            0              0       
#>                               2               6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>   cl D.2                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>     dcd D.2.1.5.3                                                                     
#>                               - Any Grade -   2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               Grade 1-2       2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               1               2 (13.3%)    5 (33.3%)      7 (46.7%)   
#>                               2                   0            0              0       
#>                               Grade 3-5           0            0              0       
#>                               3                   0            0              0       
#>                               4                   0            0              0       
#>                               5                   0            0              0       
#>   cl C.1                                                                              
#>     - Overall -                                                                       
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               3                   0            0              0       
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               5                   0            0              0       
#>     dcd C.1.1.1.3                                                                     
#>                               - Any Grade -   4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               Grade 1-2           0            0              0       
#>                               1                   0            0              0       
#>                               2                   0            0              0       
#>                               Grade 3-5       4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               3                   0            0              0       
#>                               4               4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>                               5                   0            0              0

Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence (AET05)

1. Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence

  1. The aet05 template produces the standard adverse event rate adjusted for patient-years at risk summary considering first occurrence only.
  2. By default, all adsaftte parameter codes containing the string "TTE" are included in the output. Users are expected to filter the parameter(s) of interest from input safety time-to-event dataset in pre-processing if needed.
  3. In the input safety time-to-event dataset, in the censoring variable CNSR, 0 indicates the occurrence of an event of interest and 1 denotes censoring.
proc_data <- log_filter(syn_data, PARAMCD == "AETTE1", "adsaftte")

run(aet05, proc_data)
#>                                                     A: Drug X       B: Placebo      C: Combination
#>                                                      (N=15)           (N=15)            (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————————————————————————
#>   Time to first occurrence of any adverse event                                                   
#>     Total patient-years at risk                       31.0              9.0              22.0     
#>     Number of adverse events observed                   5               13                8       
#>     AE rate per 100 patient-years                     16.13           143.84            36.30     
#>     95% CI                                        (1.99, 30.27)   (65.65, 222.03)   (11.15, 61.46)

2. Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence (setting type of confidence interval)

  1. The type of the confidence interval for rate can be specified by the argument conf_type. Options include normal (default), normal_log and exact.
  2. The confidence interval can be adjusted by the argument conf_level.
run(aet05, syn_data, conf_level = 0.90, conf_type = "exact")
#>                                                              A: Drug X         B: Placebo      C: Combination 
#>                                                               (N=15)             (N=15)            (N=15)     
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Time to first occurrence of a grade 3-5 adverse event                                                       
#>     Total patient-years at risk                                10.3               6.3                8.3      
#>     Number of adverse events observed                           12                 14                13       
#>     AE rate per 100 patient-years                             116.36             223.84            156.98     
#>     90% CI                                                (67.14, 188.53)   (135.32, 349.93)   (92.86, 249.59)
#>   Time to first occurrence of any adverse event                                                               
#>     Total patient-years at risk                                31.0               9.0               22.0      
#>     Number of adverse events observed                            5                 13                 8       
#>     AE rate per 100 patient-years                              16.13             143.84             36.30     
#>     90% CI                                                 (6.36, 33.91)    (85.08, 228.69)    (18.07, 65.51) 
#>   Time to first occurrence of any serious adverse event                                                       
#>     Total patient-years at risk                                32.9               7.6                9.4      
#>     Number of adverse events observed                            4                 14                13       
#>     AE rate per 100 patient-years                              12.15             183.83            137.79     
#>     90% CI                                                 (4.15, 27.80)    (111.14, 287.38)   (81.50, 219.06)

Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences (AET05_ALL)

1. Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences

  1. The aet05_all template produces the standard adverse event rate adjusted for patient-years at risk summary considering all occurrences.
  2. By default, all adsaftte parameter codes containing the string "TOT" and the parameter code "AEREPTTE" are required. "TOT" parameters store the number of occurrences of adverse event of interests. Parameter code "AEREPTTE" stores the time to end of adverse event reporting period in years that contribute to the summary of “total patient-years at risk” in the output. Users are expected to filter parameters of interest from input analysis dataset in pre-processing, if needed.
  3. In the input safety time-to-event dataset, in the censoring variable CNSR, 0 indicates the occurrence of an event of interest and 1 denotes censoring.
proc_data <- log_filter(syn_data, PARAMCD == "AETOT1" | PARAMCD == "AEREPTTE", "adsaftte")

run(aet05_all, proc_data)
#>                                                  A: Drug X        B: Placebo      C: Combination 
#>                                                    (N=15)           (N=15)            (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————————————————————
#>   Number of occurrences of any adverse event                                                     
#>     Total patient-years at risk                     44.4             44.2              44.4      
#>     Number of adverse events observed                29               49                56       
#>     AE rate per 100 patient-years                  65.32            110.78            126.16     
#>     95% CI                                     (41.55, 89.09)   (79.76, 141.79)   (93.12, 159.20)

2. Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences (setting type of confidence interval)

  1. The type of the confidence interval for rate can be specified by the argument conf_type. Options include normal (default), normal_log, exact, and byar.
  2. The confidence interval can be adjusted by the argument conf_level.
run(aet05_all, syn_data, conf_level = 0.90, conf_type = "exact")
#>                                                           A: Drug X         B: Placebo       C: Combination 
#>                                                             (N=15)            (N=15)             (N=15)     
#>   ——————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Number of occurrences of a grade 3-5 adverse event                                                        
#>     Total patient-years at risk                              44.4              44.2               44.4      
#>     Number of adverse events observed                         65                54                 95       
#>     AE rate per 100 patient-years                           146.41            122.08             214.02     
#>     90% CI                                             (117.87, 179.98)   (96.10, 153.14)   (179.23, 253.81)
#>   Number of occurrences of any adverse event                                                                
#>     Total patient-years at risk                              44.4              44.2               44.4      
#>     Number of adverse events observed                         29                49                 56       
#>     AE rate per 100 patient-years                           65.32             110.78             126.16     
#>     90% CI                                              (46.73, 89.06)    (86.09, 140.55)   (99.77, 157.61) 
#>   Number of occurrences of any serious adverse event                                                        
#>     Total patient-years at risk                              44.4              44.2               44.4      
#>     Number of adverse events observed                         9                 36                 60       
#>     AE rate per 100 patient-years                           20.27              81.39             135.17     
#>     90% CI                                              (10.58, 35.37)    (60.43, 107.48)   (107.80, 167.59)

Most Common (>=5%) Adverse Events (AET10)

1. Most Common (>=5%) Adverse Events

  1. The aet10 template produces the standard most common adverse events occurring with relative frequency >=5% output.
run(aet10, syn_data)
#>                           A: Drug X   B: Placebo   C: Combination
#>   MedDRA Preferred Term    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————
#>   dcd B.2.2.3.1           8 (53.3%)   6 (40.0%)      7 (46.7%)   
#>   dcd B.1.1.1.1           5 (33.3%)   6 (40.0%)      8 (53.3%)   
#>   dcd C.2.1.2.1           6 (40.0%)   4 (26.7%)      8 (53.3%)   
#>   dcd A.1.1.1.2           5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>   dcd B.2.1.2.1           5 (33.3%)   6 (40.0%)      5 (33.3%)   
#>   dcd D.1.1.1.1           4 (26.7%)   4 (26.7%)      7 (46.7%)   
#>   dcd D.1.1.4.2           6 (40.0%)   2 (13.3%)      7 (46.7%)   
#>   dcd D.2.1.5.3           2 (13.3%)   5 (33.3%)      7 (46.7%)   
#>   dcd C.1.1.1.3           4 (26.7%)   4 (26.7%)      5 (33.3%)   
#>   dcd A.1.1.1.1           3 (20.0%)    1 (6.7%)      6 (40.0%)

2. Most Common (>=8%) Adverse Events (setting threshold)

To modify the threshold for displaying preferred terms, this can be achieved by providing the threshold to the argument atleast.

run(aet10, syn_data, atleast = 0.08)
#>                           A: Drug X   B: Placebo   C: Combination
#>   MedDRA Preferred Term    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————
#>   dcd B.2.2.3.1           8 (53.3%)   6 (40.0%)      7 (46.7%)   
#>   dcd B.1.1.1.1           5 (33.3%)   6 (40.0%)      8 (53.3%)   
#>   dcd C.2.1.2.1           6 (40.0%)   4 (26.7%)      8 (53.3%)   
#>   dcd A.1.1.1.2           5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>   dcd B.2.1.2.1           5 (33.3%)   6 (40.0%)      5 (33.3%)   
#>   dcd D.1.1.1.1           4 (26.7%)   4 (26.7%)      7 (46.7%)   
#>   dcd D.1.1.4.2           6 (40.0%)   2 (13.3%)      7 (46.7%)   
#>   dcd D.2.1.5.3           2 (13.3%)   5 (33.3%)      7 (46.7%)   
#>   dcd C.1.1.1.3           4 (26.7%)   4 (26.7%)      5 (33.3%)   
#>   dcd A.1.1.1.1           3 (20.0%)    1 (6.7%)      6 (40.0%)

Concomitant Medications by Medication Class and Preferred Name (CMT01A)

1. Concomitant Medications by Medication Class and Preferred Name

  1. The cmt01a template displays concomitant medications by ATC Level 2 and Preferred Name by default.
  2. The template does not include the column of total by default.
  3. The template sort medication class and preferred name by alphabetical order by default.
run(cmt01a, syn_data)
#>   ATC Level 2 Text                                         A: Drug X    B: Placebo   C: Combination
#>     Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of treatments                                   58           59             99      
#>   ATCCLAS2 A                                                                                       
#>     Total number of patients with at least one treatment   10 (66.7%)   11 (73.3%)     12 (80.0%)  
#>     Total number of treatments                                 15           21             28      
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>     medname A_1/3                                          4 (26.7%)    3 (20.0%)      8 (53.3%)   
#>   ATCCLAS2 A p2                                                                                    
#>     Total number of patients with at least one treatment   5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     Total number of treatments                                 6            8              8       
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   ATCCLAS2 B                                                                                       
#>     Total number of patients with at least one treatment   12 (80.0%)   10 (66.7%)     14 (93.3%)  
#>     Total number of treatments                                 30           30             52      
#>     medname B_3/4                                          8 (53.3%)    6 (40.0%)      8 (53.3%)   
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   ATCCLAS2 B p2                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 B p3                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 C                                                                                       
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p2                                                                                    
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p3                                                                                    
#>     Total number of patients with at least one treatment   4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     Total number of treatments                                 5            5              12      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)

2. Concomitant Medications by Medication Class and Preferred Name (changing ATC class level)

run(cmt01a, syn_data, row_split_var = "ATC1")
#>   ATC Level 1 Text                                         A: Drug X    B: Placebo   C: Combination
#>     Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of treatments                                   58           59             99      
#>   ATCCLAS1 A                                                                                       
#>     Total number of patients with at least one treatment   10 (66.7%)   11 (73.3%)     12 (80.0%)  
#>     Total number of treatments                                 15           21             28      
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>     medname A_1/3                                          4 (26.7%)    3 (20.0%)      8 (53.3%)   
#>   ATCCLAS1 A p2                                                                                    
#>     Total number of patients with at least one treatment   5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     Total number of treatments                                 6            8              8       
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   ATCCLAS1 B                                                                                       
#>     Total number of patients with at least one treatment   12 (80.0%)   10 (66.7%)     14 (93.3%)  
#>     Total number of treatments                                 30           30             52      
#>     medname B_3/4                                          8 (53.3%)    6 (40.0%)      8 (53.3%)   
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   ATCCLAS1 B p2                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS1 B p3                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS1 C                                                                                       
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS1 C p2                                                                                    
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS1 C p3                                                                                    
#>     Total number of patients with at least one treatment   4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     Total number of treatments                                 5            5              12      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)

3. Concomitant Medications by Medication Class and Preferred Name (classes sorted by frequency)

The argument sort_by_freq = TRUE sort medication class by frequency.

run(cmt01a, syn_data, sort_by_freq = TRUE)
#>   ATC Level 2 Text                                         A: Drug X    B: Placebo   C: Combination
#>     Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of treatments                                   58           59             99      
#>   ATCCLAS2 B                                                                                       
#>     Total number of patients with at least one treatment   12 (80.0%)   10 (66.7%)     14 (93.3%)  
#>     Total number of treatments                                 30           30             52      
#>     medname B_3/4                                          8 (53.3%)    6 (40.0%)      8 (53.3%)   
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   ATCCLAS2 A                                                                                       
#>     Total number of patients with at least one treatment   10 (66.7%)   11 (73.3%)     12 (80.0%)  
#>     Total number of treatments                                 15           21             28      
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>     medname A_1/3                                          4 (26.7%)    3 (20.0%)      8 (53.3%)   
#>   ATCCLAS2 B p2                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 B p3                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     Total number of treatments                                 18           17             25      
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 C                                                                                       
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p2                                                                                    
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 A p2                                                                                    
#>     Total number of patients with at least one treatment   5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     Total number of treatments                                 6            8              8       
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   ATCCLAS2 C p3                                                                                    
#>     Total number of patients with at least one treatment   4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     Total number of treatments                                 5            5              12      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)

4. Concomitant Medications by Medication Class and Preferred Name (total number of treatments per medication class suppressed)

The cmt01a template includes the analysis of ‘total number of treatments’ by default, modify the argument summary_labels to change it.

run(cmt01a, syn_data, summary_labels = list(TOTAL = cmt01_label, ATC2 = cmt01_label[1]))
#>   ATC Level 2 Text                                         A: Drug X    B: Placebo   C: Combination
#>     Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of treatments                                   58           59             99      
#>   ATCCLAS2 A                                                                                       
#>     Total number of patients with at least one treatment   10 (66.7%)   11 (73.3%)     12 (80.0%)  
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>     medname A_1/3                                          4 (26.7%)    3 (20.0%)      8 (53.3%)   
#>   ATCCLAS2 A p2                                                                                    
#>     Total number of patients with at least one treatment   5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   ATCCLAS2 B                                                                                       
#>     Total number of patients with at least one treatment   12 (80.0%)   10 (66.7%)     14 (93.3%)  
#>     medname B_3/4                                          8 (53.3%)    6 (40.0%)      8 (53.3%)   
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   ATCCLAS2 B p2                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 B p3                                                                                    
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      12 (80.0%)  
#>     medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 C                                                                                       
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p2                                                                                    
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p3                                                                                    
#>     Total number of patients with at least one treatment   4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)

Concomitant Medications by Preferred Name (CMT02_PT)

1. Concomitant Medications by Preferred Name

  1. The cmt02_pt template displays concomitant medications by Preferred Name by default.
  2. The template does not include the column of total by default.
  3. The template sorts preferred name by alphabetical order by default. Set the argument sort_by_freq = TRUE to sort preferred names by frequency.
run(cmt02_pt, syn_data)
#>                                                          A: Drug X    B: Placebo   C: Combination
#>   Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment   13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of treatments                                 58           59             99      
#>   medname B_3/4                                          8 (53.3%)    6 (40.0%)      8 (53.3%)   
#>   medname B_2/4                                          6 (40.0%)    5 (33.3%)      10 (66.7%)  
#>   medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>   medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>   medname A_1/3                                          4 (26.7%)    3 (20.0%)      8 (53.3%)   
#>   medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)

Cox Regression (COXT01)

1. Cox Regression

  1. The coxt01 template produces the standard Cox regression output.
  2. Users are expected to pre-process the input analysis data by selecting a time-to-event parameter to be analyzed. The example below is based on the time-to-event parameter “Duration of Confirmed Response by Investigator”.
  3. The time variable in the model is specified through the time_var argument. By default, time_var is set to "AVAL", which comes from ADTTE.AVAL.
  4. The event variable in the model is specified through the event_var argument. By default, event_var is set to "EVENT", which is derived based on the censoring indicator ADTTE.CNSR in the pre-processing function coxt01_pre.
  5. If there are more than two treatment groups present in the input analysis data, users are also expected to select only two treatment groups. The example below is based on treatment groups "Arm A" and "Arm B".
proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
proc_data <- log_filter(proc_data, ARMCD != "ARM C", "adsl")
run(coxt01, proc_data, time_var = "AVAL", event_var = "EVENT")
#>                                                Treatment Effect Adjusted for Covariate     
#>   Effect/Covariate Included in the Model    n      Hazard Ratio       95% CI       p-value 
#>   —————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                               
#>     B: Placebo vs control (A: Drug X)       30         1.56        (0.61, 3.95)     0.3501 
#>   Covariate:                                                                               
#>     Sex                                     30         1.29        (0.48, 3.49)     0.6164 
#>     RACE                                    30         1.32        (0.49, 3.56)     0.5836 
#>     Age (yr)                                30         1.56        (0.61, 3.95)     0.3501

2. Cox Regression (with interaction term)

To add the interaction term to the model, interaction = TRUE, which is passed to tern::control_coxreg(), needs to be specified.

run(coxt01, proc_data, covariates = "AAGE", interaction = TRUE)
#>                                                        Treatment Effect Adjusted for Covariate             
#>   Effect/Covariate Included in the Model   n    Hazard Ratio      95% CI      p-value   Interaction p-value
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                               
#>     B: Placebo vs control (A: Drug X)      30       1.56       (0.61, 3.95)   0.3501                       
#>   Covariate:                                                                                               
#>     Age (yr)                               30                                                 0.0973       
#>       32                                            1.50       (0.57, 3.97)

3. Cox Regression (specifying covariates)

  1. By default, "SEX", "RACE" and "AAGE" are used as the covariates for the model.
  2. Users can specify a different set of covariates through the covariates argument. In the example below, "RACE" and "AAGE" are used as covariates.
run(coxt01, proc_data, covariates = c("RACE", "AAGE"))
#>                                                Treatment Effect Adjusted for Covariate     
#>   Effect/Covariate Included in the Model    n      Hazard Ratio       95% CI       p-value 
#>   —————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                               
#>     B: Placebo vs control (A: Drug X)       30         1.56        (0.61, 3.95)     0.3501 
#>   Covariate:                                                                               
#>     RACE                                    30         1.32        (0.49, 3.56)     0.5836 
#>     Age (yr)                                30         1.56        (0.61, 3.95)     0.3501

4. Cox Regression (setting strata, ties, and alpha level)

  1. By default, strata = NULL (no stratification), ties = "exact" (equivalent to DISCRETE in SAS), and conf_level = 0.95 are applied.
  2. Users can specify one or more stratification variables via the strata argument.
  3. Other tie handling methods, i.e., "efron" or "breslow", can be specified in the tie argument, which is passed to tern::control_coxreg().
  4. Users can also customize the alpha level for the confidence intervals through the conf_level argument, which is passed to tern::control_coxreg().
run(coxt01, proc_data, covariates = c("SEX", "AAGE"), strata = c("RACE"), conf_level = 0.90)
#>                                                Treatment Effect Adjusted for Covariate     
#>   Effect/Covariate Included in the Model    n      Hazard Ratio       90% CI       p-value 
#>   —————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                               
#>     B: Placebo vs control (A: Drug X)       30         1.28        (0.55, 2.97)     0.6338 
#>   Covariate:                                                                               
#>     Sex                                     30         1.19        (0.50, 2.84)     0.7360 
#>     Age (yr)                                30         1.28        (0.55, 2.97)     0.6337

Multi-variable Cox Regression (COXT02)

1. Multi-variable Cox Regression

  1. The coxt02 template produces the standard multi-variable cox regression output.
  2. Users are expected to pre-process the input analysis data by selecting a time-to-event parameter to be analyzed. The example below is based on the time-to-event parameter “Duration of Confirmed Response by Investigator”.
  3. The time variable in the model is specified through the time_var argument. By default, time_var is set to "AVAL", which comes from ADTTE.AVAL.
  4. The event variable in the model is specified through the event_var argument. By default, event_var is set to "EVENT", which is derived based on the censoring indicator ADTTE.CNSR in the pre-processing function coxt01_pre.
proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(coxt02, proc_data, time_var = "AVAL", event_var = "EVENT")
#>   Effect/Covariate Included in the Model                  Hazard Ratio      95% CI      p-value
#>   —————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                   
#>     Description of Planned Arm (reference = A: Drug X)                                  0.2152 
#>       B: Placebo                                              1.21       (0.45, 3.23)   0.7038 
#>       C: Combination                                          2.24       (0.86, 5.88)   0.0998 
#>   Covariate:                                                                                   
#>     Sex (reference = F)                                                                        
#>       M                                                       1.44       (0.63, 3.28)   0.3903 
#>     RACE (reference = AMERICAN INDIAN OR ALASKA NATIVE)                                 0.6113 
#>       ASIAN                                                   0.42       (0.11, 1.57)   0.1972 
#>       BLACK OR AFRICAN AMERICAN                               0.39       (0.08, 2.01)   0.2627 
#>       WHITE                                                   0.38       (0.07, 1.99)   0.2517 
#>     Age (yr)                                                                                   
#>       All                                                     1.02       (0.96, 1.07)   0.6043

2. Multi-variable Cox Regression (specifying covariates)

  1. By default, "SEX", "RACE" and "AAGE" are used as the covariates for the model.
  2. Users can specify a different set of covariates through the covariates argument. In the example below, "RACE" and "AAGE" are used as covariates.
run(coxt02, proc_data, covariates = c("RACE", "AAGE"))
#>   Effect/Covariate Included in the Model                  Hazard Ratio      95% CI      p-value
#>   —————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                   
#>     Description of Planned Arm (reference = A: Drug X)                                  0.1508 
#>       B: Placebo                                              1.36       (0.53, 3.49)   0.5207 
#>       C: Combination                                          2.51       (0.97, 6.49)   0.0574 
#>   Covariate:                                                                                   
#>     RACE (reference = AMERICAN INDIAN OR ALASKA NATIVE)                                 0.6453 
#>       ASIAN                                                   0.45       (0.12, 1.65)   0.2294 
#>       BLACK OR AFRICAN AMERICAN                               0.39       (0.08, 1.94)   0.2487 
#>       WHITE                                                   0.42       (0.08, 2.17)   0.2986 
#>     Age (yr)                                                                                   
#>       All                                                     1.02       (0.97, 1.08)   0.4836

3. Multi-variable Cox Regression (setting strata, ties, and alpha level)

  1. By default, strata = NULL (no stratification), ties = "exact" (equivalent to DISCRETE in SAS), and conf_level = 0.95 are applied.
  2. Users can specify one or more stratification variables via the strata argument.
  3. Other tie handling methods, i.e., "efron" or "breslow", can be specified in the tie argument, which is passed to tern::control_coxreg().
  4. Users can also customize the alpha level for the confidence intervals through the conf_level argument, which is passed to tern::control_coxreg().
run(coxt02, proc_data, covariates = c("SEX", "AAGE"), strata = c("RACE"), conf_level = 0.90, ties = "efron")
#>   Effect/Covariate Included in the Model                 Hazard Ratio      90% CI      p-value
#>   ————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                  
#>     Description of Planned Arm (reference = A: Drug X)                                 0.1066 
#>       B: Placebo                                             1.28       (0.55, 3.00)   0.6265 
#>       C: Combination                                         2.84       (1.21, 6.69)   0.0447 
#>   Covariate:                                                                                  
#>     Sex (reference = F)                                                                       
#>       M                                                      1.25       (0.61, 2.56)   0.6168 
#>     Age (yr)                                                                                  
#>       All                                                    1.01       (0.96, 1.06)   0.7637

Demographics and Baseline Characteristics (DMT01)

1. Demographics and Baseline Characteristics with All Patients

  1. The dmt01 template produces the standard demographics and baseline characteristics summary.
  2. This template includes the column of total by default.
run(dmt01, syn_data)
#>                                        A: Drug X    B: Placebo   C: Combination   All Patients
#>                                          (N=15)       (N=15)         (N=15)          (N=45)   
#>   ————————————————————————————————————————————————————————————————————————————————————————————
#>   Age (yr)                                                                                    
#>     n                                      15           15             15              45     
#>     Mean (SD)                          31.3 (5.3)   35.1 (9.0)     36.6 (6.4)      34.3 (7.3) 
#>     Median                                31.0         35.0           35.0            34.0    
#>     Min - Max                           24 - 40      24 - 57        24 - 49         24 - 57   
#>   Age Group                                                                                   
#>     n                                      15           15             15              45     
#>     <65                                15 (100%)    15 (100%)      15 (100%)       45 (100%)  
#>   Sex                                                                                         
#>     n                                      15           15             15              45     
#>     Male                               3 (20.0%)    7 (46.7%)      5 (33.3%)       15 (33.3%) 
#>     Female                             12 (80.0%)   8 (53.3%)      10 (66.7%)      30 (66.7%) 
#>   Ethnicity                                                                                   
#>     n                                      15           15             15              45     
#>     NOT REPORTED                           0            0          2 (13.3%)        2 (4.4%)  
#>     HISPANIC OR LATINO                 2 (13.3%)        0              0            2 (4.4%)  
#>     NOT HISPANIC OR LATINO             13 (86.7%)   15 (100%)      13 (86.7%)      41 (91.1%) 
#>   RACE                                                                                        
#>     n                                      15           15             15              45     
#>     AMERICAN INDIAN OR ALASKA NATIVE       0        2 (13.3%)       1 (6.7%)        3 (6.7%)  
#>     ASIAN                              8 (53.3%)    10 (66.7%)     8 (53.3%)       26 (57.8%) 
#>     BLACK OR AFRICAN AMERICAN          4 (26.7%)     1 (6.7%)      4 (26.7%)       9 (20.0%)  
#>     WHITE                              3 (20.0%)    2 (13.3%)      2 (13.3%)       7 (15.6%)

2. Demographics and Baseline Characteristics without All Patients

To remove the column of total, set the argument lbl_overall to NULL.

run(dmt01, syn_data, lbl_overall = NULL)
#>                                        A: Drug X    B: Placebo   C: Combination
#>                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————
#>   Age (yr)                                                                     
#>     n                                      15           15             15      
#>     Mean (SD)                          31.3 (5.3)   35.1 (9.0)     36.6 (6.4)  
#>     Median                                31.0         35.0           35.0     
#>     Min - Max                           24 - 40      24 - 57        24 - 49    
#>   Age Group                                                                    
#>     n                                      15           15             15      
#>     <65                                15 (100%)    15 (100%)      15 (100%)   
#>   Sex                                                                          
#>     n                                      15           15             15      
#>     Male                               3 (20.0%)    7 (46.7%)      5 (33.3%)   
#>     Female                             12 (80.0%)   8 (53.3%)      10 (66.7%)  
#>   Ethnicity                                                                    
#>     n                                      15           15             15      
#>     NOT REPORTED                           0            0          2 (13.3%)   
#>     HISPANIC OR LATINO                 2 (13.3%)        0              0       
#>     NOT HISPANIC OR LATINO             13 (86.7%)   15 (100%)      13 (86.7%)  
#>   RACE                                                                         
#>     n                                      15           15             15      
#>     AMERICAN INDIAN OR ALASKA NATIVE       0        2 (13.3%)       1 (6.7%)   
#>     ASIAN                              8 (53.3%)    10 (66.7%)     8 (53.3%)   
#>     BLACK OR AFRICAN AMERICAN          4 (26.7%)     1 (6.7%)      4 (26.7%)   
#>     WHITE                              3 (20.0%)    2 (13.3%)      2 (13.3%)

3. Demographics and Baseline Characteristics with an additional study specific continuous variable

  1. Study specific continuous variables can be added to the standard demographics and baseline characteristics summary by editing the argument summaryvars. To add or remove analyses, you need to pass all variables you would like to include to the argument.
  2. CHEVRON performs the analysis based on the type of variable as defined in the input data.
run(dmt01, syn_data, summaryvars = c("AGE", "AGEGR1", "SEX", "ETHNIC", "RACE", "BBMISI"), lbl_overall = NULL)
#>                                          A: Drug X      B: Placebo     C: Combination
#>                                           (N=15)          (N=15)           (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   Age                                                                                
#>     n                                       15              15               15      
#>     Mean (SD)                           31.3 (5.3)      35.1 (9.0)       36.6 (6.4)  
#>     Median                                 31.0            35.0             35.0     
#>     Min - Max                             24 - 40         24 - 57         24 - 49    
#>   Age Group                                                                          
#>     n                                       15              15               15      
#>     <65                                  15 (100%)       15 (100%)       15 (100%)   
#>   Sex                                                                                
#>     n                                       15              15               15      
#>     Male                                 3 (20.0%)       7 (46.7%)       5 (33.3%)   
#>     Female                              12 (80.0%)       8 (53.3%)       10 (66.7%)  
#>   Ethnicity                                                                          
#>     n                                       15              15               15      
#>     NOT REPORTED                             0               0           2 (13.3%)   
#>     HISPANIC OR LATINO                   2 (13.3%)           0               0       
#>     NOT HISPANIC OR LATINO              13 (86.7%)       15 (100%)       13 (86.7%)  
#>   RACE                                                                               
#>     n                                       15              15               15      
#>     AMERICAN INDIAN OR ALASKA NATIVE         0           2 (13.3%)        1 (6.7%)   
#>     ASIAN                                8 (53.3%)      10 (66.7%)       8 (53.3%)   
#>     BLACK OR AFRICAN AMERICAN            4 (26.7%)       1 (6.7%)        4 (26.7%)   
#>     WHITE                                3 (20.0%)       2 (13.3%)       2 (13.3%)   
#>   Baseline BMI                                                                       
#>     n                                       15              15               15      
#>     Mean (SD)                          29.75 (15.10)   41.08 (26.65)   33.90 (15.39) 
#>     Median                                 37.00           33.70           37.80     
#>     Min - Max                           6.4 - 47.9      5.3 - 117.9     -3.5 - 59.0

4. Demographics and Baseline Characteristics with an additional study specific categorical variable

  1. Study specific categorical variables can be added to the standard demographics and baseline characteristics summary by editing the argument summaryvars.
  2. To display the values within a categorical variable in pre-specified order, the categorical variable need to be factorized with pre-specified order provided as levels.
proc_data <- syn_data
proc_data$adsl <- proc_data$adsl %>%
  mutate(
    SEX = reformat(.data$SEX, rule(Male = "M", Female = "F")),
    BBMIGR1 = factor(case_when(
      BBMISI < 15 ~ "Very severely underweight",
      BBMISI >= 15 & BBMISI < 16 ~ "Severely underweight",
      BBMISI >= 16 & BBMISI < 18.5 ~ "Underweight",
      BBMISI >= 18.5 & BBMISI < 25 ~ "Normal (healthy weight)",
      BBMISI >= 25 & BBMISI < 30 ~ "Overweight",
      BBMISI >= 30 & BBMISI < 35 ~ "Obese Class I (Moderately obese)",
      BBMISI >= 35 & BBMISI < 40 ~ "Obese Class II (Severely obese)",
      BBMISI >= 40 ~ "Obese Class III (Very severely obese)"
    ), levels = c(
      "Very severely underweight",
      "Severely underweight",
      "Underweight",
      "Normal (healthy weight)",
      "Overweight",
      "Obese Class I (Moderately obese)",
      "Obese Class II (Severely obese)",
      "Obese Class III (Very severely obese)"
    ))
  )

run(dmt01, proc_data, summaryvars = c("AGE", "AGEGR1", "SEX", "ETHNIC", "RACE", "BBMIGR1"), auto_pre = FALSE)
#>                                             A: Drug X    B: Placebo   C: Combination   All Patients
#>                                               (N=15)       (N=15)         (N=15)          (N=45)   
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Age                                                                                              
#>     n                                           15           15             15              45     
#>     Mean (SD)                               31.3 (5.3)   35.1 (9.0)     36.6 (6.4)      34.3 (7.3) 
#>     Median                                     31.0         35.0           35.0            34.0    
#>     Min - Max                                24 - 40      24 - 57        24 - 49         24 - 57   
#>   Age Group                                                                                        
#>     n                                           15           15             15              45     
#>     <65                                     15 (100%)    15 (100%)      15 (100%)       45 (100%)  
#>   Sex                                                                                              
#>     n                                           15           15             15              45     
#>     Male                                    3 (20.0%)    7 (46.7%)      5 (33.3%)       15 (33.3%) 
#>     Female                                  12 (80.0%)   8 (53.3%)      10 (66.7%)      30 (66.7%) 
#>   Ethnicity                                                                                        
#>     n                                           15           15             15              45     
#>     NOT REPORTED                                0            0          2 (13.3%)        2 (4.4%)  
#>     HISPANIC OR LATINO                      2 (13.3%)        0              0            2 (4.4%)  
#>     NOT HISPANIC OR LATINO                  13 (86.7%)   15 (100%)      13 (86.7%)      41 (91.1%) 
#>   RACE                                                                                             
#>     n                                           15           15             15              45     
#>     AMERICAN INDIAN OR ALASKA NATIVE            0        2 (13.3%)       1 (6.7%)        3 (6.7%)  
#>     ASIAN                                   8 (53.3%)    10 (66.7%)     8 (53.3%)       26 (57.8%) 
#>     BLACK OR AFRICAN AMERICAN               4 (26.7%)     1 (6.7%)      4 (26.7%)       9 (20.0%)  
#>     WHITE                                   3 (20.0%)    2 (13.3%)      2 (13.3%)       7 (15.6%)  
#>   BBMIGR1                                                                                          
#>     n                                           15           15             15              45     
#>     Very severely underweight               4 (26.7%)     1 (6.7%)       1 (6.7%)       6 (13.3%)  
#>     Underweight                              1 (6.7%)        0              0            1 (2.2%)  
#>     Normal (healthy weight)                  1 (6.7%)    3 (20.0%)      4 (26.7%)       8 (17.8%)  
#>     Overweight                                  0         1 (6.7%)       1 (6.7%)        2 (4.4%)  
#>     Obese Class I (Moderately obese)            0        3 (20.0%)          0            3 (6.7%)  
#>     Obese Class II (Severely obese)         4 (26.7%)     1 (6.7%)      3 (20.0%)       8 (17.8%)  
#>     Obese Class III (Very severely obese)   5 (33.3%)    6 (40.0%)      6 (40.0%)       17 (37.8%)

5. Demographics and Baseline Characteristics with additional vital signs baseline values from ADVS or ADSUB

To add baseline vital signs or other baseline characteristics to the demographics and baseline characteristics summary, manual preprocess of input adsl dataset is expected and merge the vital signs baseline values from advs (where ADVS.ABLFL == "Y") or adsub with adsl by unique subject identifier.

proc_data <- syn_data
diabpbl <- proc_data$advs %>%
  filter(ABLFL == "Y" & PARAMCD == "DIABP") %>%
  mutate(DIABPBL = AVAL) %>%
  select("STUDYID", "USUBJID", "DIABPBL")

proc_data$adsl <- proc_data$adsl %>%
  mutate(SEX = reformat(.data$SEX, rule(Male = "M", Female = "F"))) %>%
  left_join(diabpbl, by = c("STUDYID", "USUBJID"))

run(dmt01, proc_data, summaryvars = c("AGE", "AGEGR1", "SEX", "ETHNIC", "RACE", "DIABPBL"), auto_pre = FALSE)
#>                                             A: Drug X              B: Placebo           C: Combination          All Patients    
#>                                               (N=15)                 (N=15)                 (N=15)                 (N=45)       
#>   ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Age                                                                                                                           
#>     n                                           15                     15                     15                     45         
#>     Mean (SD)                               31.3 (5.3)             35.1 (9.0)             36.6 (6.4)             34.3 (7.3)     
#>     Median                                     31.0                   35.0                   35.0                   34.0        
#>     Min - Max                                24 - 40                24 - 57                24 - 49                24 - 57       
#>   Age Group                                                                                                                     
#>     n                                           15                     15                     15                     45         
#>     <65                                     15 (100%)              15 (100%)              15 (100%)              45 (100%)      
#>   Sex                                                                                                                           
#>     n                                           15                     15                     15                     45         
#>     Male                                    3 (20.0%)              7 (46.7%)              5 (33.3%)              15 (33.3%)     
#>     Female                                  12 (80.0%)             8 (53.3%)              10 (66.7%)             30 (66.7%)     
#>   Ethnicity                                                                                                                     
#>     n                                           15                     15                     15                     45         
#>     NOT REPORTED                                0                      0                  2 (13.3%)               2 (4.4%)      
#>     HISPANIC OR LATINO                      2 (13.3%)                  0                      0                   2 (4.4%)      
#>     NOT HISPANIC OR LATINO                  13 (86.7%)             15 (100%)              13 (86.7%)             41 (91.1%)     
#>   RACE                                                                                                                          
#>     n                                           15                     15                     15                     45         
#>     AMERICAN INDIAN OR ALASKA NATIVE            0                  2 (13.3%)               1 (6.7%)               3 (6.7%)      
#>     ASIAN                                   8 (53.3%)              10 (66.7%)             8 (53.3%)              26 (57.8%)     
#>     BLACK OR AFRICAN AMERICAN               4 (26.7%)               1 (6.7%)              4 (26.7%)              9 (20.0%)      
#>     WHITE                                   3 (20.0%)              2 (13.3%)              2 (13.3%)              7 (15.6%)      
#>   Analysis Value                                                                                                                
#>     n                                           15                     15                     15                     45         
#>     Mean (SD)                          48.453004 (8.983282)   53.244378 (6.029780)   51.259527 (7.900675)   50.985636 (7.813978)
#>     Median                                  47.331328              53.580543              51.139608              50.958451      
#>     Min - Max                          34.23396 - 64.63737    43.37711 - 62.64600    36.42089 - 64.62102    34.23396 - 64.63737

Patient Disposition (DST01)

1. Patient Disposition

  1. The dst01 template produces the standard patient disposition summary.
  2. The template includes the column of total by default. Use lbl_overall = NULL to suppress the default.
run(dst01, syn_data, lbl_overall = NULL)
#>                                     A: Drug X    B: Placebo   C: Combination
#>                                       (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————
#>   Completed                         10 (66.7%)   10 (66.7%)     10 (66.7%)  
#>   Discontinued                      5 (33.3%)    5 (33.3%)      5 (33.3%)   
#>     ADVERSE EVENT                       0            0           1 (6.7%)   
#>     DEATH                           2 (13.3%)    4 (26.7%)      3 (20.0%)   
#>     LACK OF EFFICACY                2 (13.3%)        0              0       
#>     PHYSICIAN DECISION                  0            0           1 (6.7%)   
#>     PROTOCOL VIOLATION                  0         1 (6.7%)          0       
#>     WITHDRAWAL BY PARENT/GUARDIAN    1 (6.7%)        0              0

2. Patient Disposition (with grouping of reasons)

  1. The syntax below produces the standard patient disposition summary with grouping of the discontinuation reasons.
  2. The variable [ADSL.DCSREASGP] that groups the discontinuation reasons needs to be derived manually and provided in the input adsl dataset.
run(dst01, syn_data, detail_vars = list(Discontinued = c("DCSREASGP", "DCSREAS")), lbl_overall = NULL)
#>                                       A: Drug X    B: Placebo   C: Combination
#>                                         (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————————————————
#>   Completed                           10 (66.7%)   10 (66.7%)     10 (66.7%)  
#>   Discontinued                        5 (33.3%)    5 (33.3%)      5 (33.3%)   
#>     Safety                                                                    
#>       ADVERSE EVENT                       0            0           1 (6.7%)   
#>       DEATH                           2 (13.3%)    4 (26.7%)      3 (20.0%)   
#>     Non-Safety                                                                
#>       LACK OF EFFICACY                2 (13.3%)        0              0       
#>       PHYSICIAN DECISION                  0            0           1 (6.7%)   
#>       PROTOCOL VIOLATION                  0         1 (6.7%)          0       
#>       WITHDRAWAL BY PARENT/GUARDIAN    1 (6.7%)        0              0

3. Patient Disposition (adding end of treatment status)

The syntax below adds the end of treatment status to the standard patient disposition summary by providing the end of treatment status variable to the argument trt_status_var.

run(dst01, syn_data, trt_status_var = "EOTSTT", lbl_overall = NULL)
#>                                     A: Drug X    B: Placebo   C: Combination
#>                                       (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————
#>   Completed                         10 (66.7%)   10 (66.7%)     10 (66.7%)  
#>   Discontinued                      5 (33.3%)    5 (33.3%)      5 (33.3%)   
#>     ADVERSE EVENT                       0            0           1 (6.7%)   
#>     DEATH                           2 (13.3%)    4 (26.7%)      3 (20.0%)   
#>     LACK OF EFFICACY                2 (13.3%)        0              0       
#>     PHYSICIAN DECISION                  0            0           1 (6.7%)   
#>     PROTOCOL VIOLATION                  0         1 (6.7%)          0       
#>     WITHDRAWAL BY PARENT/GUARDIAN    1 (6.7%)        0              0       
#>   Completed Treatment               8 (53.3%)    4 (26.7%)      5 (33.3%)   
#>   Ongoing Treatment                 4 (26.7%)    6 (40.0%)      4 (26.7%)   
#>   Discontinued Treatment            3 (20.0%)    5 (33.3%)      6 (40.0%)

4. Patient Disposition (adding details of study ongoing status)

The syntax adds the details of study ongoing/alive status to the standard patient disposition summary by modifying the argument detail_vars.

run(dst01, syn_data, detail_vars = list(Discontinued = "DCSREAS", Ongoing = "STDONS"))
#>                                     A: Drug X    B: Placebo   C: Combination   All Patients
#>                                       (N=15)       (N=15)         (N=15)          (N=45)   
#>   —————————————————————————————————————————————————————————————————————————————————————————
#>   Completed                         10 (66.7%)   10 (66.7%)     10 (66.7%)      30 (66.7%) 
#>   Discontinued                      5 (33.3%)    5 (33.3%)      5 (33.3%)       15 (33.3%) 
#>     ADVERSE EVENT                       0            0           1 (6.7%)        1 (2.2%)  
#>     DEATH                           2 (13.3%)    4 (26.7%)      3 (20.0%)       9 (20.0%)  
#>     LACK OF EFFICACY                2 (13.3%)        0              0            2 (4.4%)  
#>     PHYSICIAN DECISION                  0            0           1 (6.7%)        1 (2.2%)  
#>     PROTOCOL VIOLATION                  0         1 (6.7%)          0            1 (2.2%)  
#>     WITHDRAWAL BY PARENT/GUARDIAN    1 (6.7%)        0              0            1 (2.2%)

Deaths (DTHT01)

1. Deaths

The dtht01 template produces the standard deaths output.

run(dst01, syn_data)
#>                                     A: Drug X    B: Placebo   C: Combination   All Patients
#>                                       (N=15)       (N=15)         (N=15)          (N=45)   
#>   —————————————————————————————————————————————————————————————————————————————————————————
#>   Completed                         10 (66.7%)   10 (66.7%)     10 (66.7%)      30 (66.7%) 
#>   Discontinued                      5 (33.3%)    5 (33.3%)      5 (33.3%)       15 (33.3%) 
#>     ADVERSE EVENT                       0            0           1 (6.7%)        1 (2.2%)  
#>     DEATH                           2 (13.3%)    4 (26.7%)      3 (20.0%)       9 (20.0%)  
#>     LACK OF EFFICACY                2 (13.3%)        0              0            2 (4.4%)  
#>     PHYSICIAN DECISION                  0            0           1 (6.7%)        1 (2.2%)  
#>     PROTOCOL VIOLATION                  0         1 (6.7%)          0            1 (2.2%)  
#>     WITHDRAWAL BY PARENT/GUARDIAN    1 (6.7%)        0              0            1 (2.2%)

2. Deaths (adding “Primary Cause of Death” details for ‘Other’ category)

run(dtht01, syn_data, other_category = TRUE)
#>                            A: Drug X   B: Placebo   C: Combination
#>                             (N=15)       (N=15)         (N=15)    
#>   ————————————————————————————————————————————————————————————————
#>   Total number of deaths   2 (13.3%)   4 (26.7%)      3 (20.0%)   
#>   Primary Cause of Death                                          
#>     n                          2           4              3       
#>     Adverse Event          1 (50.0%)   2 (50.0%)      1 (33.3%)   
#>     Progressive Disease    1 (50.0%)       0          2 (66.7%)   
#>     Other                      0       2 (50.0%)          0       
#>       LOST TO FOLLOW UP        0        1 (50%)           0       
#>       SUICIDE                  0        1 (50%)           0

NOTE: In order to avoid the warning above and display ‘Other’ as the last category under “Primary Cause of Death” right above the detailed reasons for “Other”, the user is expected to manually provide levels to ADSL.DTHCAT based on categories available in the dataset.

3. Deaths (adding summary by days from last study drug administration)

Setting time_since_last_dose to TRUE, the syntax produces the count of deaths by days from last study drug administration as well as the count of deaths by primary cause and days from last study drug administration.

run(dtht01, syn_data, time_since_last_dose = TRUE)
#>                                                               A: Drug X   B: Placebo   C: Combination
#>                                                                (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of deaths                                      2 (13.3%)   4 (26.7%)      3 (20.0%)   
#>   Days from last drug administration                                                                 
#>     n                                                             2           4              3       
#>     <=30                                                      2 (100%)    1 (25.0%)      2 (66.7%)   
#>     >30                                                           0       3 (75.0%)      1 (33.3%)   
#>   Primary cause by days from last study drug administration                                          
#>     <=30                                                                                             
#>       n                                                           2           1              2       
#>       Adverse Event                                           1 (50.0%)       0          1 (50.0%)   
#>       Progressive Disease                                     1 (50.0%)       0          1 (50.0%)   
#>       Other                                                       0        1 (100%)          0       
#>     >30                                                                                              
#>       n                                                           0           3              1       
#>       Adverse Event                                               0       2 (66.7%)          0       
#>       Progressive Disease                                         0           0           1 (100%)   
#>       Other                                                       0       1 (33.3%)          0

ECG Results and Change from Baseline by Visit (EGT01)

1. ECG Results and Change from Baseline by Visit

The egt01 template produces the standard ECG results and change from baseline by visit summary.

run(egt01, syn_data)
#>                                    A: Drug X                                B: Placebo                             C: Combination             
#>                                             Change from                               Change from                              Change from    
#>                       Value at Visit          Baseline          Value at Visit         Baseline          Value at Visit          Baseline     
#>   Analysis Visit          (N=15)               (N=15)               (N=15)              (N=15)               (N=15)               (N=15)      
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Heart Rate                                                                                                                                  
#>     BASELINE                                                                                                                                  
#>       n                     15                                        15                                       15                             
#>       Mean (SD)      76.594 (17.889)                           69.899 (18.788)                          70.492 (18.175)                       
#>       Median              77.531                                    77.174                                   74.111                           
#>       Min - Max       46.50 - 106.68                            26.42 - 97.69                            45.37 - 115.49                       
#>     WEEK 1 DAY 8                                                                                                                              
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      71.140 (23.441)      -5.454 (25.128)      70.958 (14.877)      1.059 (23.345)      67.450 (18.932)      -3.043 (23.753)  
#>       Median              77.210               -2.152               70.033              -8.403               68.471               0.181       
#>       Min - Max       8.53 - 102.63        -50.97 - 36.54       44.85 - 93.79       -25.34 - 60.50       38.90 - 100.05       -52.20 - 33.13  
#>     WEEK 2 DAY 15                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      69.350 (16.083)      -7.244 (28.960)      76.096 (14.958)      6.198 (29.319)      63.694 (12.920)      -6.799 (23.949)  
#>       Median              65.746              -11.369               75.323               0.255               61.076               -4.954      
#>       Min - Max       47.22 - 101.44       -49.59 - 42.91       47.50 - 111.40      -37.51 - 69.34       43.25 - 86.13        -52.70 - 40.76  
#>     WEEK 3 DAY 22                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      73.894 (24.576)      -2.700 (32.079)      67.635 (19.114)      -2.263 (29.989)     72.054 (19.308)       1.562 (27.494)  
#>       Median              69.296               5.492                68.468              -2.093               68.686               -5.848      
#>       Min - Max       44.15 - 131.73       -62.53 - 38.19       31.89 - 108.87      -52.26 - 66.81       32.16 - 109.86       -49.61 - 35.23  
#>     WEEK 4 DAY 29                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      73.241 (19.256)      -3.353 (29.170)      66.524 (25.487)      -3.374 (36.024)     66.600 (22.839)      -3.892 (24.140)  
#>       Median              68.689               0.232                66.397              -11.730              64.969               -6.827      
#>       Min - Max       33.71 - 111.54       -55.14 - 65.04       19.66 - 111.29      -60.39 - 61.00       10.35 - 100.88       -50.72 - 26.77  
#>     WEEK 5 DAY 36                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      61.690 (22.182)      -14.904 (30.330)     60.712 (20.025)      -9.187 (24.587)     72.683 (23.495)       2.191 (26.654)  
#>       Median              57.925              -12.660               60.454              -16.100              77.585               14.635      
#>       Min - Max       23.89 - 103.74       -60.00 - 57.24       32.53 - 102.02      -52.56 - 50.96       31.21 - 105.05       -42.90 - 34.64  
#>   QT Duration                                                                                                                                 
#>     BASELINE                                                                                                                                  
#>       n                     15                                        15                                       15                             
#>       Mean (SD)     335.294 (123.231)                          363.104 (68.160)                         347.311 (86.236)                      
#>       Median             372.731                                   386.316                                  348.254                           
#>       Min - Max      121.28 - 554.97                           214.65 - 445.53                          170.80 - 508.54                       
#>     WEEK 1 DAY 8                                                                                                                              
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      357.361 (85.688)     22.067 (144.166)    415.225 (105.425)    52.121 (144.259)    321.078 (107.553)    -26.233 (129.135) 
#>       Median             344.797               49.432              421.950              62.762              307.962              -17.006      
#>       Min - Max      241.22 - 517.39      -207.23 - 245.36     234.11 - 604.72     -190.70 - 364.94     118.36 - 480.29      -363.11 - 163.67 
#>     WEEK 2 DAY 15                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     344.883 (106.793)     9.589 (174.797)      370.548 (80.862)     7.444 (91.301)      354.129 (95.133)     6.818 (142.397)  
#>       Median             312.236               -9.264              388.515              -9.429              365.292               39.930      
#>       Min - Max      187.77 - 501.87      -278.91 - 372.71     204.55 - 514.43     -190.58 - 173.87     200.19 - 493.40      -279.46 - 265.56 
#>     WEEK 3 DAY 22                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      342.062 (92.568)     6.768 (151.505)     326.684 (116.421)    -36.420 (145.415)    366.245 (99.106)     18.935 (168.417) 
#>       Median             352.930              -22.771              298.353              -78.409             329.688              -21.584      
#>       Min - Max      199.40 - 476.04      -230.25 - 303.00     151.05 - 561.23     -205.30 - 293.76     249.42 - 580.81      -252.73 - 410.01 
#>     WEEK 4 DAY 29                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)      371.650 (44.805)     36.356 (139.308)    333.697 (110.377)    -29.407 (125.592)    333.181 (96.466)    -14.130 (107.622) 
#>       Median             375.412               58.958              308.020              -40.987             330.911              -25.820      
#>       Min - Max      302.32 - 451.62      -214.07 - 258.04     183.09 - 531.08     -241.72 - 134.12     126.95 - 488.57      -234.92 - 152.49 
#>     WEEK 5 DAY 36                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     345.504 (130.543)     10.210 (198.224)     309.919 (84.624)    -53.185 (105.730)    322.931 (67.801)    -24.380 (117.331) 
#>       Median             355.730              -23.213              306.219              -12.373             341.988              -26.952      
#>       Min - Max       88.38 - 661.12      -271.06 - 539.84     189.01 - 448.58      -256.52 - 91.57     217.51 - 427.16      -291.03 - 171.19 
#>   RR Duration                                                                                                                                 
#>     BASELINE                                                                                                                                  
#>       n                     15                                        15                                       15                             
#>       Mean (SD)     1086.908 (363.811)                        1050.034 (390.444)                       1102.659 (310.359)                     
#>       Median             1116.849                                  1089.193                                 1250.037                          
#>       Min - Max      626.19 - 1653.12                          414.61 - 1721.89                         385.51 - 1430.81                      
#>     WEEK 1 DAY 8                                                                                                                              
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     968.499 (287.811)    -118.409 (546.796)   1041.186 (211.201)   -8.848 (435.281)    948.491 (213.746)    -154.168 (442.882)
#>       Median             961.296              -147.460             1013.786             24.754              965.429              -224.054     
#>       Min - Max      358.92 - 1593.51    -1014.82 - 911.82     714.44 - 1417.52    -618.80 - 847.31     513.35 - 1229.09     -736.69 - 843.58 
#>     WEEK 2 DAY 15                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     932.717 (259.634)    -154.191 (331.884)   1139.332 (454.231)   89.298 (582.750)    1021.283 (233.529)   -81.376 (415.781) 
#>       Median             950.533              -205.949             1068.007             -5.449              964.616              -142.180     
#>       Min - Max      409.68 - 1269.35     -649.69 - 473.09     486.51 - 2048.73    -846.72 - 1148.61    667.36 - 1367.25     -647.47 - 616.15 
#>     WEEK 3 DAY 22                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     1068.865 (319.540)   -18.043 (513.412)    1110.882 (259.523)   60.848 (432.700)    1105.918 (306.185)    3.259 (516.734)  
#>       Median             1201.998             -65.085              1163.690             51.200              1187.130              30.318      
#>       Min - Max      380.49 - 1551.65     -832.86 - 703.74     621.41 - 1453.29    -887.06 - 822.18     446.02 - 1648.32     -984.79 - 816.30 
#>     WEEK 4 DAY 29                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     1087.915 (205.940)    1.008 (403.039)     1161.681 (293.257)   111.647 (460.979)   992.134 (283.177)    -110.525 (334.932)
#>       Median             1084.658             146.611              1055.223             191.008             1028.997             -112.599     
#>       Min - Max      697.59 - 1499.17     -801.16 - 402.97     722.35 - 1762.04    -528.27 - 1191.83    497.14 - 1382.12     -597.95 - 757.99 
#>     WEEK 5 DAY 36                                                                                                                             
#>       n                     15                   15                   15                  15                   15                   15        
#>       Mean (SD)     1016.880 (424.428)   -70.027 (505.078)    1135.131 (224.684)   85.097 (497.679)    1089.527 (238.909)   -13.132 (362.606) 
#>       Median             962.584              -142.925             1158.815             -9.553              1081.015              16.706      
#>       Min - Max      352.97 - 1843.86    -894.83 - 1162.79     714.34 - 1436.68    -843.41 - 992.34     699.72 - 1611.38     -696.03 - 561.53

ECG Abnormalities (Regardless of Abnormality at Baseline) (EGT02_1)

1. ECG Abnormalities (Regardless of Abnormality at Baseline)

The egt02_1 template produces the standard ECG abnormalities summary where the abnormalities are summarized regardless of the abnormality at baseline.

run(egt02_1, syn_data)
#>   Assessment      A: Drug X      B: Placebo    C: Combination
#>    Abnormality      (N=15)         (N=15)          (N=15)    
#>   ———————————————————————————————————————————————————————————
#>   Heart Rate                                                 
#>     Low          4/15 (26.7%)    6/15 (40%)     4/15 (26.7%) 
#>     High         5/15 (33.3%)    3/15 (20%)     4/15 (26.7%) 
#>   QT Duration                                                
#>     Low          5/15 (33.3%)    6/15 (40%)     4/15 (26.7%) 
#>     High         4/15 (26.7%)    6/15 (40%)      3/15 (20%)  
#>   RR Duration                                                
#>     Low           9/15 (60%)    5/15 (33.3%)     6/15 (40%)  
#>     High          6/15 (40%)    7/15 (46.7%)     3/15 (20%)

ECG Abnormalities (Among Subject Without Abnormality at Baseline) (EGT02_2)

1. ECG Abnormalities (Among Subject Without Abnormality at Baseline)

The egt02_2 template produces the standard ECG abnormalities summary where the abnormalities are summarized among subject without abnormality at baseline.

run(egt02_2, syn_data)
#>   Assessment      A: Drug X      B: Placebo    C: Combination
#>    Abnormality      (N=15)         (N=15)          (N=15)    
#>   ———————————————————————————————————————————————————————————
#>   Heart Rate                                                 
#>     Low          4/15 (26.7%)   5/14 (35.7%)    4/15 (26.7%) 
#>     High         3/13 (23.1%)    3/15 (20%)     3/14 (21.4%) 
#>   QT Duration                                                
#>     Low          2/12 (16.7%)    6/15 (40%)     3/14 (21.4%) 
#>     High         3/14 (21.4%)    6/15 (40%)     2/14 (14.3%) 
#>   RR Duration                                                
#>     Low           9/15 (60%)    3/13 (23.1%)    5/14 (35.7%) 
#>     High         4/13 (30.8%)   5/13 (38.5%)     3/15 (20%)

Shift Table of ECG Interval Data - Baseline versus Minimum/Maximum Post-Baseline (EGT03)

1. Shift Table of ECG Interval Data - Baseline versus Minimum Post-Baseline

The egt03 template produces the standard shift table of ECG interval data - baseline versus minimum post-baseline summary.

proc_data <- log_filter(syn_data, PARAMCD == "HR", "adeg")
run(egt03, proc_data)
#>   Actual Arm Code                            Minimum Post-Baseline Assessment     
#>     Baseline Reference Range Indicator      LOW         NORMAL      HIGH   Missing
#>   ————————————————————————————————————————————————————————————————————————————————
#>   Heart Rate                                                                      
#>     ARM A (N=15)                                                                  
#>       LOW                                    0             0         0        0   
#>       NORMAL                             4 (26.7%)     9 (60.0%)     0        0   
#>       HIGH                                   0         2 (13.3%)     0        0   
#>       Missing                                0             0         0        0   
#>     ARM B (N=15)                                                                  
#>       LOW                                    0         1 (6.7%)      0        0   
#>       NORMAL                             4 (26.7%)    10 (66.7%)     0        0   
#>       HIGH                                   0             0         0        0   
#>       Missing                                0             0         0        0   
#>     ARM C (N=15)                                                                  
#>       LOW                                    0             0         0        0   
#>       NORMAL                             4 (26.7%)    10 (66.7%)     0        0   
#>       HIGH                                   0         1 (6.7%)      0        0   
#>       Missing                                0             0         0        0

2. Shift Table of ECG Interval Data - Baseline versus Maximum Post-Baseline

To produce the standard shift table of ECG interval data - baseline versus maximum post-baseline summary….TBA

ECG Actual Values and Changes from Baseline by Visit (EGT05_QTCAT)

1. ECG Actual Values and Changes from Baseline by Visit

The egt05_qtcat template produces the standard ECG actual values and changes from baseline by visit summary.

run(egt05_qtcat, syn_data)
#>   Parameter                                                          
#>     Analysis Visit           A: Drug X    B: Placebo   C: Combination
#>       Category                 (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————
#>   QT Duration                                                        
#>     BASELINE                                                         
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           13 (86.7%)   15 (100%)      13 (86.7%)  
#>         >450 to <=480 msec    1 (6.7%)        0              0       
#>         >480 to <=500 msec       0            0           1 (6.7%)   
#>         >500 msec             1 (6.7%)        0           1 (6.7%)   
#>     WEEK 1 DAY 8                                                     
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           12 (80.0%)   9 (60.0%)      13 (86.7%)  
#>         >450 to <=480 msec    1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>         >480 to <=500 msec    1 (6.7%)    3 (20.0%)       1 (6.7%)   
#>         >500 msec             1 (6.7%)    2 (13.3%)          0       
#>       Change from Baseline                                           
#>         n                        15           15             15      
#>         <=30 msec            7 (46.7%)    6 (40.0%)      9 (60.0%)   
#>         >30 to <=60 msec     2 (13.3%)     1 (6.7%)       1 (6.7%)   
#>         >60 msec             6 (40.0%)    8 (53.3%)      5 (33.3%)   
#>     WEEK 2 DAY 15                                                    
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           11 (73.3%)   14 (93.3%)     12 (80.0%)  
#>         >450 to <=480 msec   2 (13.3%)        0          2 (13.3%)   
#>         >480 to <=500 msec    1 (6.7%)        0           1 (6.7%)   
#>         >500 msec             1 (6.7%)     1 (6.7%)          0       
#>       Change from Baseline                                           
#>         n                        15           15             15      
#>         <=30 msec            9 (60.0%)    12 (80.0%)     7 (46.7%)   
#>         >30 to <=60 msec     2 (13.3%)        0          3 (20.0%)   
#>         >60 msec             4 (26.7%)    3 (20.0%)      5 (33.3%)   
#>     WEEK 3 DAY 22                                                    
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           12 (80.0%)   12 (80.0%)     12 (80.0%)  
#>         >450 to <=480 msec   3 (20.0%)     1 (6.7%)       1 (6.7%)   
#>         >500 msec                0        2 (13.3%)      2 (13.3%)   
#>       Change from Baseline                                           
#>         n                        15           15             15      
#>         <=30 msec            9 (60.0%)    11 (73.3%)     9 (60.0%)   
#>         >30 to <=60 msec      1 (6.7%)     1 (6.7%)          0       
#>         >60 msec             5 (33.3%)    3 (20.0%)      6 (40.0%)   
#>     WEEK 4 DAY 29                                                    
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           14 (93.3%)   12 (80.0%)     13 (86.7%)  
#>         >450 to <=480 msec    1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>         >480 to <=500 msec       0            0           1 (6.7%)   
#>         >500 msec                0        2 (13.3%)          0       
#>       Change from Baseline                                           
#>         n                        15           15             15      
#>         <=30 msec            6 (40.0%)    9 (60.0%)      9 (60.0%)   
#>         >30 to <=60 msec     2 (13.3%)     1 (6.7%)      2 (13.3%)   
#>         >60 msec             7 (46.7%)    5 (33.3%)      4 (26.7%)   
#>     WEEK 5 DAY 36                                                    
#>       Value at Visit                                                 
#>         n                        15           15             15      
#>         <=450 msec           12 (80.0%)   15 (100%)      15 (100%)   
#>         >450 to <=480 msec   2 (13.3%)        0              0       
#>         >500 msec             1 (6.7%)        0              0       
#>       Change from Baseline                                           
#>         n                        15           15             15      
#>         <=30 msec            9 (60.0%)    11 (73.3%)     9 (60.0%)   
#>         >30 to <=60 msec         0        3 (20.0%)      2 (13.3%)   
#>         >60 msec             6 (40.0%)     1 (6.7%)      4 (26.7%)

2. ECG Actual Values and Changes from Baseline by Visit (removing default analyses)

The template have two default analyses of ADEG.AVALCAT1 and ADEG.CHGCAT1. To keep only the analyses needed, this can be achieved by modifying the parameter summaryvars.

run(egt05_qtcat, syn_data, summaryvars = c("AVALCAT1"))
#>   Parameter                                                        
#>     Analysis Visit         A: Drug X    B: Placebo   C: Combination
#>       Category               (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————
#>   QT Duration                                                      
#>     BASELINE                                                       
#>       n                        15           15             15      
#>       <=450 msec           13 (86.7%)   15 (100%)      13 (86.7%)  
#>       >450 to <=480 msec    1 (6.7%)        0              0       
#>       >480 to <=500 msec       0            0           1 (6.7%)   
#>       >500 msec             1 (6.7%)        0           1 (6.7%)   
#>     WEEK 1 DAY 8                                                   
#>       n                        15           15             15      
#>       <=450 msec           12 (80.0%)   9 (60.0%)      13 (86.7%)  
#>       >450 to <=480 msec    1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>       >480 to <=500 msec    1 (6.7%)    3 (20.0%)       1 (6.7%)   
#>       >500 msec             1 (6.7%)    2 (13.3%)          0       
#>     WEEK 2 DAY 15                                                  
#>       n                        15           15             15      
#>       <=450 msec           11 (73.3%)   14 (93.3%)     12 (80.0%)  
#>       >450 to <=480 msec   2 (13.3%)        0          2 (13.3%)   
#>       >480 to <=500 msec    1 (6.7%)        0           1 (6.7%)   
#>       >500 msec             1 (6.7%)     1 (6.7%)          0       
#>     WEEK 3 DAY 22                                                  
#>       n                        15           15             15      
#>       <=450 msec           12 (80.0%)   12 (80.0%)     12 (80.0%)  
#>       >450 to <=480 msec   3 (20.0%)     1 (6.7%)       1 (6.7%)   
#>       >500 msec                0        2 (13.3%)      2 (13.3%)   
#>     WEEK 4 DAY 29                                                  
#>       n                        15           15             15      
#>       <=450 msec           14 (93.3%)   12 (80.0%)     13 (86.7%)  
#>       >450 to <=480 msec    1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>       >480 to <=500 msec       0            0           1 (6.7%)   
#>       >500 msec                0        2 (13.3%)          0       
#>     WEEK 5 DAY 36                                                  
#>       n                        15           15             15      
#>       <=450 msec           12 (80.0%)   15 (100%)      15 (100%)   
#>       >450 to <=480 msec   2 (13.3%)        0              0       
#>       >500 msec             1 (6.7%)        0              0

Study Drug Exposure (EXT01)

1. Study Drug Exposure

  1. The ext01 template displays total number of doses administered and total dose administered by default
  2. The template does not include the column of total by default
run(ext01, syn_data)
#>                                  A: Drug X        B: Placebo      C: Combination 
#>   PARCAT2                         (N=15)            (N=15)            (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Drug A                                                                         
#>     Overall duration (days)                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)                157.5 (67.4)      115.4 (62.8)       98.6 (68.8)  
#>       Median                       174.0             119.0             89.0      
#>       Min - Max                53.0 - 239.0      22.0 - 219.0       1.0 - 182.0  
#>     Total dose administered                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)               6567.3 (1127.1)   7028.6 (1626.1)   6377.1 (863.7) 
#>       Median                      6720.0            7200.0            6480.0     
#>       Min - Max               4800.0 - 8400.0   5280.0 - 9360.0   5280.0 - 7440.0
#>   Drug B                                                                         
#>     Overall duration (days)                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)                142.2 (100.3)     105.9 (60.0)      158.2 (96.2)  
#>       Median                       160.0             95.0              203.0     
#>       Min - Max                17.0 - 232.0      37.0 - 211.0      27.0 - 249.0  
#>     Total dose administered                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)               7020.0 (1148.9)   5250.0 (864.7)    5940.0 (1187.9)
#>       Median                      6960.0            5160.0            5880.0     
#>       Min - Max               5760.0 - 8400.0   4080.0 - 6480.0   4320.0 - 7680.0

Laboratory Test Results and Change from Baseline by Visit (LBT01)

1. Laboratory Test Results and Change from Baseline by Visit

  1. The lbt01 template produces the standard laboratory test results and change from baseline by visit.
  2. To select the SI/CV/LS results and the panel (chemistry/hematology/urinalysis/coagulation etc.) to display, user defines individual filters and apply to input datasets prior to running CHEVRON.
t_lb_chg <- run(lbt01, syn_data)
head(t_lb_chg, 20)
#>                                                     A: Drug X                        B: Placebo                     C: Combination         
#>                                                            Change from                       Change from                      Change from  
#>                                          Value at Visit      Baseline      Value at Visit     Baseline      Value at Visit      Baseline   
#>                                              (N=15)           (N=15)           (N=15)          (N=15)           (N=15)           (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                                                                                     
#>     BASELINE                                                                                                                               
#>       n                                        15                                15                               15                       
#>       Mean (SD)                          20.262 (4.982)                    19.371 (4.687)                   21.724 (3.857)                 
#>       Median                                 19.216                            19.781                           22.900                     
#>       Min - Max                          13.77 - 30.43                     11.58 - 25.59                    12.57 - 27.69                  
#>     WEEK 1 DAY 8                                                                                                                           
#>       n                                        15               15               15              15               15               15      
#>       Mean (SD)                          19.227 (4.492)   -1.036 (7.113)   21.622 (3.015)   2.251 (6.830)   20.630 (3.950)   -1.094 (4.425)
#>       Median                                 18.666           -2.148           21.790           2.901           20.570           -0.398    
#>       Min - Max                          12.12 - 27.32    -12.07 - 9.07    16.69 - 26.32    -6.73 - 14.36   13.21 - 27.31     -7.84 - 7.84 
#>     WEEK 2 DAY 15                                                                                                                          
#>       n                                        15               15               15              15               15               15      
#>       Mean (SD)                          19.458 (4.211)   -0.804 (6.309)   21.103 (3.831)   1.732 (5.981)   17.164 (3.089)   -4.559 (4.438)
#>       Median                                 18.988           -2.571           20.200           2.499           16.740           -3.463    
#>       Min - Max                          12.96 - 26.92    -12.00 - 13.14   13.42 - 29.93    -9.97 - 14.39   12.94 - 22.80    -10.95 - 1.01 
#>     WEEK 3 DAY 22                                                                                                                          
#>       n                                        15               15               15              15               15               15      
#>       Mean (SD)                          19.795 (4.272)   -0.467 (6.304)   20.822 (3.234)   1.451 (6.839)   20.165 (3.805)   -1.559 (4.042)
#>       Median                                 18.489           0.542            21.541           2.138           20.612           -2.878

2. Laboratory Test Results and Change from Baseline by Visit (customized precision)

TBA

Laboratory Abnormalities (LBT04)

1. Laboratory Abnormalities

  1. The lbt04 template produces the standard laboratory abnormalities summary.
  2. The template subsets to SI results by default.
  3. The laboratory tests and directions of abnormality in this template is data-driven. Table entries provide the number of patients with a during treatment laboratory value abnormality in the direction specified among patients without this abnormality at baseline.
run(lbt04, syn_data)
#>   Laboratory Test                           A: Drug X    B: Placebo    C: Combination
#>       Direction of Abnormality               (N=15)        (N=15)          (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   CHEMISTRY                                                                          
#>     Alanine Aminotransferase Measurement                                             
#>       Low                                  1/7 (14.3%)   1/3 (33.3%)        0/8      
#>       High                                 2/7 (28.6%)       0/2        1/9 (11.1%)  
#>     C-Reactive Protein Measurement                                                   
#>       Low                                      0/8           0/2        2/7 (28.6%)  
#>       High                                     0/8           0/3            0/7      
#>     Immunoglobulin A Measurement                                                     
#>       Low                                  2/5 (40.0%)   1/8 (12.5%)    1/6 (16.7%)  
#>       High                                 2/5 (40.0%)   1/9 (11.1%)        0/6      
#>   COAGULATION                                                                        
#>     Alanine Aminotransferase Measurement                                             
#>       Low                                      0/5       1/5 (20.0%)        0/5      
#>       High                                     0/6       1/6 (16.7%)    1/5 (20.0%)  
#>     C-Reactive Protein Measurement                                                   
#>       Low                                  1/6 (16.7%)       0/5        1/4 (25.0%)  
#>       High                                 1/5 (20.0%)   1/6 (16.7%)        0/3      
#>     Immunoglobulin A Measurement                                                     
#>       Low                                      0/7           0/9            0/7      
#>       High                                 1/7 (14.3%)      0/10            0/6      
#>   HEMATOLOGY                                                                         
#>     Alanine Aminotransferase Measurement                                             
#>       Low                                  1/5 (20.0%)   1/5 (20.0%)        0/4      
#>       High                                     0/5           0/4            0/4      
#>     C-Reactive Protein Measurement                                                   
#>       Low                                  1/4 (25.0%)       0/2        3/9 (33.3%)  
#>       High                                     0/4           0/5            0/9      
#>     Immunoglobulin A Measurement                                                     
#>       Low                                      0/2           0/3        2/8 (25.0%)  
#>       High                                     0/4       1/4 (25.0%)        0/7

Laboratory Abnormalities with Single and Replicated Marked (LBT05)

1. Laboratory Abnormalities with Single and Replicated Marked

  1. The lbt05 template produces the standard laboratory abnormalities summary for marked abnormalities.
  2. The laboratory tests and directions of abnormality in this template is currently data-driven. The standard metadata for Safety Lab Standardization will be incorporated in future release.
run(lbt05, syn_data)
#>   Laboratory Test                            A: Drug X   B: Placebo   C: Combination
#>       Direction of Abnormality                (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement (n)      15           12             13      
#>     Low                                                                             
#>       Single, not last                       1 (6.7%)        0           1 (7.7%)   
#>       Last or replicated                         0       2 (16.7%)          0       
#>       Any Abnormality                        1 (6.7%)    2 (16.7%)       1 (7.7%)   
#>     High                                                                            
#>       Single, not last                           0        1 (8.3%)          0       
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0        1 (8.3%)          0       
#>   C-Reactive Protein Measurement (n)            12           14             15      
#>     Low                                                                             
#>       Single, not last                           0           0           1 (6.7%)   
#>       Last or replicated                     1 (8.3%)        0              0       
#>       Any Abnormality                        1 (8.3%)        0           1 (6.7%)   
#>     High                                                                            
#>       Single, not last                       1 (8.3%)        0           1 (6.7%)   
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                        1 (8.3%)        0           1 (6.7%)   
#>   Immunoglobulin A Measurement (n)              11           14             13      
#>     Low                                                                             
#>       Single, not last                           0        1 (7.1%)       1 (7.7%)   
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0        1 (7.1%)       1 (7.7%)   
#>     High                                                                            
#>       Single, not last                           0           0              0       
#>       Last or replicated                     1 (9.1%)        0              0       
#>       Any Abnormality                        1 (9.1%)        0              0

2. Laboratory Abnormalities with Single and Replicated Marked showing all categories

3. Laboratory Abnormalities with Single and Replicated Marked with study specific MLAs

Laboratory Abnormalities by Visit and Baseline Status (LBT06)

1. Laboratory Abnormalities by Visit and Baseline Status

  1. The lbt06 template produces the standard laboratory abnormalities by visit and baseline status summary.
run(lbt06, syn_data)
#>   Visit                                                                            
#>     Abnormality at Visit                  A: Drug X    B: Placebo    C: Combination
#>               Baseline Status              (N=15)        (N=15)          (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                             
#>     WEEK 1 DAY 8                                                                   
#>       Low                                                                          
#>                 Not low                      0/3       1/6 (16.7%)        0/3      
#>                 Low                          0/0           0/1            0/0      
#>                 Total                        0/3       1/7 (14.3%)        0/3      
#>       High                                                                         
#>                 Not high                     0/3           0/6            0/3      
#>                 High                         0/0           0/1            0/0      
#>                 Total                        0/3           0/7            0/3      
#>     WEEK 2 DAY 15                                                                  
#>       Low                                                                          
#>                 Not low                  1/3 (33.3%)       0/2            0/3      
#>                 Low                          0/0           0/0            0/0      
#>                 Total                    1/3 (33.3%)       0/2            0/3      
#>       High                                                                         
#>                 Not high                     0/3           0/2        1/3 (33.3%)  
#>                 High                         0/0           0/0            0/0      
#>                 Total                        0/3           0/2        1/3 (33.3%)  
#>     WEEK 3 DAY 22                                                                  
#>       Low                                                                          
#>                 Not low                      0/5       1/3 (33.3%)        0/6      
#>                 Low                      1/1 (100%)        0/0            0/0      
#>                 Total                    1/6 (16.7%)   1/3 (33.3%)        0/6      
#>       High                                                                         
#>                 Not high                  1/5 (20%)    1/3 (33.3%)        0/6      
#>                 High                     1/1 (100%)        0/0            0/0      
#>                 Total                    2/6 (33.3%)   1/3 (33.3%)        0/6      
#>     WEEK 4 DAY 29                                                                  
#>       Low                                                                          
#>                 Not low                   1/5 (20%)        0/3            0/2      
#>                 Low                          0/1           0/1            0/0      
#>                 Total                    1/6 (16.7%)       0/4            0/2      
#>       High                                                                         
#>                 Not high                  1/5 (20%)        0/3         1/2 (50%)   
#>                 High                         0/1           0/1            0/0      
#>                 Total                    1/6 (16.7%)       0/4         1/2 (50%)   
#>     WEEK 5 DAY 36                                                                  
#>       Low                                                                          
#>                 Not low                      0/3        1/2 (50%)         0/5      
#>                 Low                      1/1 (100%)        0/1            0/1      
#>                 Total                     1/4 (25%)    1/3 (33.3%)        0/6      
#>       High                                                                         
#>                 Not high                     0/4           0/1            0/6      
#>                 High                         0/0           0/2            0/0      
#>                 Total                        0/4           0/3            0/6      
#>   C-Reactive Protein Measurement                                                   
#>     WEEK 1 DAY 8                                                                   
#>       Low                                                                          
#>                 Not low                  1/7 (14.3%)       0/4        1/6 (16.7%)  
#>                 Low                          0/1           0/0            0/0      
#>                 Total                    1/8 (12.5%)       0/4        1/6 (16.7%)  
#>       High                                                                         
#>                 Not high                 1/7 (14.3%)       0/4            0/5      
#>                 High                         0/1           0/0            0/1      
#>                 Total                    1/8 (12.5%)       0/4            0/6      
#>     WEEK 2 DAY 15                                                                  
#>       Low                                                                          
#>                 Not low                      0/7           0/0        1/3 (33.3%)  
#>                 Low                          0/0           0/2            0/0      
#>                 Total                        0/7           0/2        1/3 (33.3%)  
#>       High                                                                         
#>                 Not high                     0/5        1/2 (50%)         0/2      
#>                 High                         0/2           0/0            0/1      
#>                 Total                        0/7        1/2 (50%)         0/3      
#>     WEEK 3 DAY 22                                                                  
#>       Low                                                                          
#>                 Not low                      0/4           0/4        2/7 (28.6%)  
#>                 Low                          0/1           0/2            0/1      
#>                 Total                        0/5           0/6         2/8 (25%)   
#>       High                                                                         
#>                 Not high                     0/5        1/5 (20%)         0/6      
#>                 High                         0/0           0/1            0/2      
#>                 Total                        0/5       1/6 (16.7%)        0/8      
#>     WEEK 4 DAY 29                                                                  
#>       Low                                                                          
#>                 Not low                   1/2 (50%)        0/1            0/2      
#>                 Low                          0/0           0/1            0/1      
#>                 Total                     1/2 (50%)        0/2            0/3      
#>       High                                                                         
#>                 Not high                     0/2           0/2            0/3      
#>                 High                         0/0           0/0            0/0      
#>                 Total                        0/2           0/2            0/3      
#>     WEEK 5 DAY 36                                                                  
#>       Low                                                                          
#>                 Not low                      0/2           0/2        2/6 (33.3%)  
#>                 Low                          0/1           0/2            0/0      
#>                 Total                        0/3           0/4        2/6 (33.3%)  
#>       High                                                                         
#>                 Not high                     0/3           0/4            0/6      
#>                 High                         0/0           0/0            0/0      
#>                 Total                        0/3           0/4            0/6      
#>   Immunoglobulin A Measurement                                                     
#>     WEEK 1 DAY 8                                                                   
#>       Low                                                                          
#>                 Not low                      0/4           0/6            0/3      
#>                 Low                          0/2       1/1 (100%)         0/0      
#>                 Total                        0/6       1/7 (14.3%)        0/3      
#>       High                                                                         
#>                 Not high                 1/6 (16.7%)       0/7            0/2      
#>                 High                         0/0           0/0            0/1      
#>                 Total                    1/6 (16.7%)       0/7            0/3      
#>     WEEK 2 DAY 15                                                                  
#>       Low                                                                          
#>                 Not low                      0/4       1/6 (16.7%)        0/4      
#>                 Low                          0/0           0/1            0/0      
#>                 Total                        0/4       1/7 (14.3%)        0/4      
#>       High                                                                         
#>                 Not high                  1/4 (25%)        0/7            0/4      
#>                 High                         0/0           0/0            0/0      
#>                 Total                     1/4 (25%)        0/7            0/4      
#>     WEEK 3 DAY 22                                                                  
#>       Low                                                                          
#>                 Not low                      0/4           0/5            0/8      
#>                 Low                          0/1           0/1         1/1 (100%)  
#>                 Total                        0/5           0/6        1/9 (11.1%)  
#>       High                                                                         
#>                 Not high                     0/4       1/6 (16.7%)        0/7      
#>                 High                         0/1           0/0            0/2      
#>                 Total                        0/5       1/6 (16.7%)        0/9      
#>     WEEK 4 DAY 29                                                                  
#>       Low                                                                          
#>                 Not low                      0/1           0/5         2/4 (50%)   
#>                 Low                          0/1           0/1            0/0      
#>                 Total                        0/2           0/6         2/4 (50%)   
#>       High                                                                         
#>                 Not high                 1/1 (100%)    1/6 (16.7%)        0/4      
#>                 High                         0/1           0/0            0/0      
#>                 Total                     1/2 (50%)    1/6 (16.7%)        0/4      
#>     WEEK 5 DAY 36                                                                  
#>       Low                                                                          
#>                 Not low                  2/7 (28.6%)       0/4        1/6 (16.7%)  
#>                 Low                          0/0           0/1            0/0      
#>                 Total                    2/7 (28.6%)       0/5        1/6 (16.7%)  
#>       High                                                                         
#>                 Not high                     0/5           0/5            0/6      
#>                 High                         0/2           0/0            0/0      
#>                 Total                        0/7           0/5            0/6

Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline (LBT07)

1. Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline

  1. The lbt07 template produces the standard laboratory test results with highest NCI CTCAE grade post-baseline summary.
  2. The laboratory tests and grades in this template is currently data-driven. The standard metadata for possible lab tests and corresponding NCI CTCAE grade will be incorporated in future release.
run(lbt07, syn_data)
#>   Parameter                                                                         
#>     Direction of Abnormality                 A: Drug X   B: Placebo   C: Combination
#>               Highest NCI CTCAE Grade         (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement (n)      15           15             15      
#>     LOW                                                                             
#>               1                              3 (20.0%)   2 (13.3%)      2 (13.3%)   
#>               2                                  0        1 (6.7%)       1 (6.7%)   
#>               3                              5 (33.3%)   3 (20.0%)      2 (13.3%)   
#>               4                              1 (6.7%)    2 (13.3%)          0       
#>               Any                            9 (60.0%)   8 (53.3%)      5 (33.3%)   
#>     HIGH                                                                            
#>               1                              3 (20.0%)   2 (13.3%)      3 (20.0%)   
#>               2                              2 (13.3%)       0          4 (26.7%)   
#>               3                              1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>               4                                  0        1 (6.7%)          0       
#>               Any                            6 (40.0%)   4 (26.7%)      8 (53.3%)   
#>   C-Reactive Protein Measurement (n)            15           15             15      
#>     LOW                                                                             
#>               1                              2 (13.3%)    1 (6.7%)      3 (20.0%)   
#>               2                                  0       2 (13.3%)      2 (13.3%)   
#>               3                              2 (13.3%)       0          4 (26.7%)   
#>               4                              1 (6.7%)        0           1 (6.7%)   
#>               Any                            5 (33.3%)   3 (20.0%)      10 (66.7%)  
#>     HIGH                                                                            
#>               1                              1 (6.7%)        0              0       
#>               2                              3 (20.0%)       0              0       
#>               3                              1 (6.7%)        0           1 (6.7%)   
#>               4                              1 (6.7%)     1 (6.7%)          0       
#>               Any                            6 (40.0%)    1 (6.7%)       1 (6.7%)   
#>   Immunoglobulin A Measurement (n)              15           15             15      
#>     LOW                                                                             
#>               1                              2 (13.3%)    1 (6.7%)          0       
#>               2                              1 (6.7%)     1 (6.7%)      2 (13.3%)   
#>               3                              2 (13.3%)    1 (6.7%)      4 (26.7%)   
#>               4                              1 (6.7%)    2 (13.3%)      2 (13.3%)   
#>               Any                            6 (40.0%)   5 (33.3%)      8 (53.3%)   
#>     HIGH                                                                            
#>               1                              4 (26.7%)   2 (13.3%)          0       
#>               2                              1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>               3                              1 (6.7%)     1 (6.7%)          0       
#>               4                                  0        1 (6.7%)       1 (6.7%)   
#>               Any                            6 (40.0%)   5 (33.3%)      2 (13.3%)

Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (LBT14)

1. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (High)

To produce the standard laboratory test results shift table - highest NCI-CTCAE grade post-baseline by baseline NCI-CTCAE grade summary for high abnormalities, use the lbt14 template and set the parameter direction to high.

run(lbt14, syn_data, direction = "high")
#>   Baseline Toxicity Grade                 A: Drug X   B: Placebo   C: Combination
#>           Post-baseline NCI-CTCAE Grade    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                           
#>     Not High                                 14           13             15      
#>             Not High                      9 (60.0%)   9 (60.0%)      7 (46.7%)   
#>             1                             2 (13.3%)   2 (13.3%)      3 (20.0%)   
#>             2                             2 (13.3%)       0          4 (26.7%)   
#>             3                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             4                                 0        1 (6.7%)          0       
#>     1                                         1           0              0       
#>             1                             1 (6.7%)        0              0       
#>     2                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>     3                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>   C-Reactive Protein Measurement                                                 
#>     Not High                                 13           13             13      
#>             Not High                      7 (46.7%)   12 (80.0%)     12 (80.0%)  
#>             1                             1 (6.7%)        0              0       
#>             2                             3 (20.0%)       0              0       
#>             3                             1 (6.7%)        0           1 (6.7%)   
#>             4                             1 (6.7%)     1 (6.7%)          0       
#>     1                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>     2                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>   Immunoglobulin A Measurement                                                   
#>     Not High                                 12           15             13      
#>             Not High                      6 (40.0%)   10 (66.7%)     11 (73.3%)  
#>             1                             4 (26.7%)   2 (13.3%)          0       
#>             2                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             3                             1 (6.7%)     1 (6.7%)          0       
#>             4                                 0        1 (6.7%)       1 (6.7%)   
#>     1                                         1           0              2       
#>             Not High                      1 (6.7%)        0          2 (13.3%)   
#>     3                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0       
#>     4                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0

2. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (Low)

To produce the standard laboratory test results shift table - highest NCI-CTCAE grade post-baseline by baseline NCI-CTCAE grade summary for high abnormalities, use the lbt14 template and the argument direction is low by default.

run(lbt14, syn_data)
#>   Baseline Toxicity Grade                 A: Drug X   B: Placebo   C: Combination
#>           Post-baseline NCI-CTCAE Grade    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                           
#>     Not Low                                  13           13             14      
#>             Not Low                       6 (40.0%)   5 (33.3%)      9 (60.0%)   
#>             1                             3 (20.0%)   2 (13.3%)      2 (13.3%)   
#>             2                                 0        1 (6.7%)       1 (6.7%)   
#>             3                             3 (20.0%)   3 (20.0%)      2 (13.3%)   
#>             4                             1 (6.7%)    2 (13.3%)          0       
#>     1                                         1           1              0       
#>             Not Low                           0        1 (6.7%)          0       
#>             3                             1 (6.7%)        0              0       
#>     2                                         0           0              1       
#>             Not Low                           0           0           1 (6.7%)   
#>     3                                         0           1              0       
#>             Not Low                           0        1 (6.7%)          0       
#>     4                                         1           0              0       
#>             3                             1 (6.7%)        0              0       
#>   C-Reactive Protein Measurement                                                 
#>     Not Low                                  14           11             13      
#>             Not Low                       9 (60.0%)   9 (60.0%)      4 (26.7%)   
#>             1                             2 (13.3%)    1 (6.7%)      3 (20.0%)   
#>             2                                 0        1 (6.7%)      2 (13.3%)   
#>             3                             2 (13.3%)       0          3 (20.0%)   
#>             4                             1 (6.7%)        0           1 (6.7%)   
#>     1                                         0           1              0       
#>             Not Low                           0        1 (6.7%)          0       
#>     2                                         0           1              0       
#>             2                                 0        1 (6.7%)          0       
#>     3                                         1           1              1       
#>             Not Low                       1 (6.7%)     1 (6.7%)          0       
#>             3                                 0           0           1 (6.7%)   
#>     4                                         0           1              1       
#>             Not Low                           0        1 (6.7%)       1 (6.7%)   
#>   Immunoglobulin A Measurement                                                   
#>     Not Low                                  13           14             13      
#>             Not Low                       7 (46.7%)   10 (66.7%)     7 (46.7%)   
#>             1                             2 (13.3%)    1 (6.7%)          0       
#>             2                             1 (6.7%)        0          2 (13.3%)   
#>             3                             2 (13.3%)    1 (6.7%)      4 (26.7%)   
#>             4                             1 (6.7%)    2 (13.3%)          0       
#>     1                                         1           1              0       
#>             Not Low                       1 (6.7%)        0              0       
#>             2                                 0        1 (6.7%)          0       
#>     3                                         1           0              1       
#>             Not Low                       1 (6.7%)        0              0       
#>             4                                 0           0           1 (6.7%)   
#>     4                                         0           0              1       
#>             4                                 0           0           1 (6.7%)

3. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (High) Without Patients with Missing Baseline

To exclude patients with missing baseline grade, set the argument gr_missing to excl.

run(lbt14, syn_data, direction = "high", gr_missing = "excl")
#>   Baseline Toxicity Grade                 A: Drug X   B: Placebo   C: Combination
#>           Post-baseline NCI-CTCAE Grade    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                           
#>     Not High                                 14           13             15      
#>             Not High                      9 (60.0%)   9 (60.0%)      7 (46.7%)   
#>             1                             2 (13.3%)   2 (13.3%)      3 (20.0%)   
#>             2                             2 (13.3%)       0          4 (26.7%)   
#>             3                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             4                                 0        1 (6.7%)          0       
#>     1                                         1           0              0       
#>             1                             1 (6.7%)        0              0       
#>     2                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>     3                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>   C-Reactive Protein Measurement                                                 
#>     Not High                                 13           13             13      
#>             Not High                      7 (46.7%)   12 (80.0%)     12 (80.0%)  
#>             1                             1 (6.7%)        0              0       
#>             2                             3 (20.0%)       0              0       
#>             3                             1 (6.7%)        0           1 (6.7%)   
#>             4                             1 (6.7%)     1 (6.7%)          0       
#>     1                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>     2                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>   Immunoglobulin A Measurement                                                   
#>     Not High                                 12           15             13      
#>             Not High                      6 (40.0%)   10 (66.7%)     11 (73.3%)  
#>             1                             4 (26.7%)   2 (13.3%)          0       
#>             2                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             3                             1 (6.7%)     1 (6.7%)          0       
#>             4                                 0        1 (6.7%)       1 (6.7%)   
#>     1                                         1           0              2       
#>             Not High                      1 (6.7%)        0          2 (13.3%)   
#>     3                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0       
#>     4                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0

4. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (Low) with Missing Baseline Considered as Grade 0

To count patients with missing baseline grade as grade 0, set the argument gr_missing to gr_0.

run(lbt14, syn_data, gr_missing = "gr_0")
#>   Baseline Toxicity Grade                 A: Drug X   B: Placebo   C: Combination
#>           Post-baseline NCI-CTCAE Grade    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                           
#>     1                                         1           1              0       
#>             Not Low                           0        1 (6.7%)          0       
#>             3                             1 (6.7%)        0              0       
#>     2                                         0           0              1       
#>             1                                 0           0           1 (6.7%)   
#>     3                                         0           1              0       
#>             1                                 0        1 (6.7%)          0       
#>     4                                         1           0              0       
#>             3                             1 (6.7%)        0              0       
#>     Not Low                                  13           13             14      
#>             Not Low                       6 (40.0%)   5 (33.3%)      9 (60.0%)   
#>             1                             3 (20.0%)   2 (13.3%)      2 (13.3%)   
#>             2                                 0        1 (6.7%)       1 (6.7%)   
#>             3                             3 (20.0%)   3 (20.0%)      2 (13.3%)   
#>             4                             1 (6.7%)    2 (13.3%)          0       
#>   C-Reactive Protein Measurement                                                 
#>     1                                         0           1              0       
#>             1                                 0        1 (6.7%)          0       
#>     2                                         0           1              0       
#>             3                                 0        1 (6.7%)          0       
#>     3                                         1           1              1       
#>             Not Low                       1 (6.7%)     1 (6.7%)          0       
#>             3                                 0           0           1 (6.7%)   
#>     4                                         0           1              1       
#>             1                                 0        1 (6.7%)       1 (6.7%)   
#>     Not Low                                  14           11             13      
#>             Not Low                       9 (60.0%)   9 (60.0%)      4 (26.7%)   
#>             1                             2 (13.3%)    1 (6.7%)      3 (20.0%)   
#>             2                                 0        1 (6.7%)      2 (13.3%)   
#>             3                             2 (13.3%)       0          3 (20.0%)   
#>             4                             1 (6.7%)        0           1 (6.7%)   
#>   Immunoglobulin A Measurement                                                   
#>     1                                         1           1              0       
#>             Not Low                       1 (6.7%)        0              0       
#>             2                                 0        1 (6.7%)          0       
#>     3                                         1           0              1       
#>             Not Low                       1 (6.7%)        0              0       
#>             4                                 0           0           1 (6.7%)   
#>     4                                         0           0              1       
#>             Not Low                           0           0           1 (6.7%)   
#>     Not Low                                  13           14             13      
#>             Not Low                       7 (46.7%)   10 (66.7%)     7 (46.7%)   
#>             1                             2 (13.3%)    1 (6.7%)          0       
#>             2                             1 (6.7%)        0          2 (13.3%)   
#>             3                             2 (13.3%)    1 (6.7%)      4 (26.7%)   
#>             4                             1 (6.7%)    2 (13.3%)          0

4. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (with fill in of grades)

To display all possible grades even if they do not occur in the data, set the argument prune_0 to FALSE.

run(lbt14, syn_data, direction = "high", prune_0 = FALSE)
#>   Baseline Toxicity Grade                 A: Drug X   B: Placebo   C: Combination
#>           Post-baseline NCI-CTCAE Grade    (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                           
#>     Not High                                 14           13             15      
#>             Not High                      9 (60.0%)   9 (60.0%)      7 (46.7%)   
#>             1                             2 (13.3%)   2 (13.3%)      3 (20.0%)   
#>             2                             2 (13.3%)       0          4 (26.7%)   
#>             3                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             4                                 0        1 (6.7%)          0       
#>             Missing                           0           0              0       
#>     1                                         1           0              0       
#>             Not High                          0           0              0       
#>             1                             1 (6.7%)        0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     2                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     3                                         0           1              0       
#>             Not High                          0        1 (6.7%)          0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     4                                         0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     Missing                                   0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>   C-Reactive Protein Measurement                                                 
#>     Not High                                 13           13             13      
#>             Not High                      7 (46.7%)   12 (80.0%)     12 (80.0%)  
#>             1                             1 (6.7%)        0              0       
#>             2                             3 (20.0%)       0              0       
#>             3                             1 (6.7%)        0           1 (6.7%)   
#>             4                             1 (6.7%)     1 (6.7%)          0       
#>             Missing                           0           0              0       
#>     1                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     2                                         1           1              1       
#>             Not High                      1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     3                                         0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     4                                         0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     Missing                                   0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>   Immunoglobulin A Measurement                                                   
#>     Not High                                 12           15             13      
#>             Not High                      6 (40.0%)   10 (66.7%)     11 (73.3%)  
#>             1                             4 (26.7%)   2 (13.3%)          0       
#>             2                             1 (6.7%)     1 (6.7%)       1 (6.7%)   
#>             3                             1 (6.7%)     1 (6.7%)          0       
#>             4                                 0        1 (6.7%)       1 (6.7%)   
#>             Missing                           0           0              0       
#>     1                                         1           0              2       
#>             Not High                      1 (6.7%)        0          2 (13.3%)   
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     2                                         0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     3                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     4                                         1           0              0       
#>             Not High                      1 (6.7%)        0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0       
#>     Missing                                   0           0              0       
#>             Not High                          0           0              0       
#>             1                                 0           0              0       
#>             2                                 0           0              0       
#>             3                                 0           0              0       
#>             4                                 0           0              0       
#>             Missing                           0           0              0

Medical History (MHT01)

1. Medical History

  1. The mht01 template displays medical conditions by MedDRA system organ class and Preferred Name by default.
  2. The default treatment variable is "ADSL.ARM".
  3. The user is expected to use filter to subset medical conditions prior to or on entering study.
  4. By default, the template produces the overall ‘total number of conditions’ as well as the ‘total number of conditions’ per body system after the summary of patients. 5）This template currently does not support sorting MedDRA system organ class and preferred names by order of frequency.
run(mht01, syn_data)
#>   MedDRA System Organ Class                                A: Drug X    B: Placebo   C: Combination
#>     MedDRA Preferred Term                                    (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one condition     13 (86.7%)   14 (93.3%)     15 (100%)   
#>   Total number of conditions                                   58           59             99      
#>   cl A                                                                                             
#>     Total number of patients with at least one condition   7 (46.7%)    6 (40.0%)      10 (66.7%)  
#>     Total number of conditions                                 8            11             16      
#>     trm A_2/2                                              5 (33.3%)    6 (40.0%)      6 (40.0%)   
#>     trm A_1/2                                              3 (20.0%)     1 (6.7%)      6 (40.0%)   
#>   cl B                                                                                             
#>     Total number of patients with at least one condition   12 (80.0%)   11 (73.3%)     12 (80.0%)  
#>     Total number of conditions                                 24           21             32      
#>     trm B_3/3                                              8 (53.3%)    6 (40.0%)      7 (46.7%)   
#>     trm B_1/3                                              5 (33.3%)    6 (40.0%)      8 (53.3%)   
#>     trm B_2/3                                              5 (33.3%)    6 (40.0%)      5 (33.3%)   
#>   cl C                                                                                             
#>     Total number of patients with at least one condition   8 (53.3%)    6 (40.0%)      11 (73.3%)  
#>     Total number of conditions                                 10           13             22      
#>     trm C_2/2                                              6 (40.0%)    4 (26.7%)      8 (53.3%)   
#>     trm C_1/2                                              4 (26.7%)    4 (26.7%)      5 (33.3%)   
#>   cl D                                                                                             
#>     Total number of patients with at least one condition   10 (66.7%)   7 (46.7%)      13 (86.7%)  
#>     Total number of conditions                                 16           14             29      
#>     trm D_1/3                                              4 (26.7%)    4 (26.7%)      7 (46.7%)   
#>     trm D_2/3                                              6 (40.0%)    2 (13.3%)      7 (46.7%)   
#>     trm D_3/3                                              2 (13.3%)    5 (33.3%)      7 (46.7%)

2. Medical History showing additional column ‘All Patients’

run(mht01, syn_data, lbl_overall = "All Patients")
#>   MedDRA System Organ Class                                A: Drug X    B: Placebo   C: Combination   All Patients
#>     MedDRA Preferred Term                                    (N=15)       (N=15)         (N=15)          (N=45)   
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one condition     13 (86.7%)   14 (93.3%)     15 (100%)       42 (93.3%) 
#>   Total number of conditions                                   58           59             99             216     
#>   cl A                                                                                                            
#>     Total number of patients with at least one condition   7 (46.7%)    6 (40.0%)      10 (66.7%)      23 (51.1%) 
#>     Total number of conditions                                 8            11             16              35     
#>     trm A_2/2                                              5 (33.3%)    6 (40.0%)      6 (40.0%)       17 (37.8%) 
#>     trm A_1/2                                              3 (20.0%)     1 (6.7%)      6 (40.0%)       10 (22.2%) 
#>   cl B                                                                                                            
#>     Total number of patients with at least one condition   12 (80.0%)   11 (73.3%)     12 (80.0%)      35 (77.8%) 
#>     Total number of conditions                                 24           21             32              77     
#>     trm B_3/3                                              8 (53.3%)    6 (40.0%)      7 (46.7%)       21 (46.7%) 
#>     trm B_1/3                                              5 (33.3%)    6 (40.0%)      8 (53.3%)       19 (42.2%) 
#>     trm B_2/3                                              5 (33.3%)    6 (40.0%)      5 (33.3%)       16 (35.6%) 
#>   cl C                                                                                                            
#>     Total number of patients with at least one condition   8 (53.3%)    6 (40.0%)      11 (73.3%)      25 (55.6%) 
#>     Total number of conditions                                 10           13             22              45     
#>     trm C_2/2                                              6 (40.0%)    4 (26.7%)      8 (53.3%)       18 (40.0%) 
#>     trm C_1/2                                              4 (26.7%)    4 (26.7%)      5 (33.3%)       13 (28.9%) 
#>   cl D                                                                                                            
#>     Total number of patients with at least one condition   10 (66.7%)   7 (46.7%)      13 (86.7%)      30 (66.7%) 
#>     Total number of conditions                                 16           14             29              59     
#>     trm D_1/3                                              4 (26.7%)    4 (26.7%)      7 (46.7%)       15 (33.3%) 
#>     trm D_2/3                                              6 (40.0%)    2 (13.3%)      7 (46.7%)       15 (33.3%) 
#>     trm D_3/3                                              2 (13.3%)    5 (33.3%)      7 (46.7%)       14 (31.1%)

Major Protocol Deviations (PDT01)

1. Major Protocol Deviations

  1. The pdt01 template produces the standard major protocol deviations output.
  2. Users are expected to filter addv to only include records where DVCAT == "MAJOR" in pre-processing.
proc_data <- syn_data
proc_data$addv <- proc_data$addv %>%
  filter(DVCAT == "MAJOR")

run(pdt01, proc_data)
#>   Category                                                              A: Drug X   B: Placebo   C: Combination
#>     Description                                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one major protocol deviation   3 (20.0%)   3 (20.0%)          0       
#>   Total number of major protocol deviations                                 3           4              0       
#>   EXCLUSION CRITERIA                                                                                           
#>     Active or untreated or other excluded cns metastases                    0        1 (6.7%)          0       
#>     Pregnancy criteria                                                      0        1 (6.7%)          0       
#>   INCLUSION CRITERIA                                                                                           
#>     Ineligible cancer type or current cancer stage                      2 (13.3%)       0              0       
#>   MEDICATION                                                                                                   
#>     Received prohibited concomitant medication                              0        1 (6.7%)          0       
#>   PROCEDURAL                                                                                                   
#>     Eligibility-related test not done/out of window                         0        1 (6.7%)          0       
#>     Failure to sign updated ICF within two visits                       1 (6.7%)        0              0

Duration of Exposure for Risk Management Plan (RMPT01)

1. Duration of Exposure for Risk Management Plan

The rmpt01 template produces the standard duration of exposure output for the Risk Management Plan (RMP).

Person time is the sum of exposure across all patients in days.

run(rmpt01, syn_data)
#>                                        Patients     Person time
#>   Duration of exposure                  (N=45)        (N=45)   
#>   —————————————————————————————————————————————————————————————
#>   < 1 month                            4 (8.9%)         67     
#>   1 to <3 months                      13 (28.9%)        837    
#>   3 to <6 months                      13 (28.9%)       1728    
#>   >=6 months                          15 (33.3%)       3281    
#>   Total patients number/person time   45 (100.0%)      5913

Extent of Exposure by Age Group and Gender for Risk Management Plan (RMPT03)

1. Extent of Exposure by Age Group and Gender for Risk Management Plan

The rmpt03 template produces the standard extent of exposure by age group and gender output for the Risk Management Plan (RMP).

By default, the AGEGR1 variable is used as the age group. If AGEGR1 is available in ADSL only but not in ADEX, it needs to be added to ADEX first.

proc_data <- syn_data
proc_data <- propagate(proc_data, "adsl", "AGEGR1", "USUBJID")
#> 
#> Updating: adae with: AGEGR1
#> Updating: adsaftte with: AGEGR1
#> Updating: adcm with: AGEGR1
#> Updating: addv with: AGEGR1
#> Updating: adeg with: AGEGR1
#> Updating: adex with: AGEGR1
#> Updating: adlb with: AGEGR1
#> Updating: admh with: AGEGR1
#> Skipping: adrs
#> Updating: adsub with: AGEGR1
#> Skipping: adtte
#> Updating: advs with: AGEGR1
run(rmpt03, proc_data)
#>                                                   F                           M                      All Genders       
#>                                        Patients     Person time    Patients     Person time    Patients     Person time
#>   Age Group                             (N=30)        (N=30)        (N=15)        (N=15)        (N=45)        (N=45)   
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   <65                                 30 (100.0%)      4088       15 (100.0%)      1825       45 (100.0%)      5913    
#>   Total patients number/person time   30 (100.0%)      4088       15 (100.0%)      1825       45 (100.0%)      5913

Any other study specific age group can be used by editing the parameter summaryvars. For all RMP tables, if the variable specified per summaryvars is unavailable in ADEX, it needs to be added to ADEX first.

proc_data <- syn_data
proc_data$adsl <- proc_data$adsl %>%
  mutate(
    AGEGR2 = with_label(
      factor(case_when(
        AAGE < 18 ~ "<18",
        AAGE >= 18 & AAGE <= 65 ~ "18 - 65",
        AAGE > 65 ~ ">65",
      ), levels = c("<18", "18 - 65", ">65")),
      "Age Group 2"
    )
  )
proc_data <- propagate(proc_data, "adsl", "AGEGR2", "USUBJID")
#> 
#> Updating: adae with: AGEGR2
#> Updating: adsaftte with: AGEGR2
#> Updating: adcm with: AGEGR2
#> Updating: addv with: AGEGR2
#> Updating: adeg with: AGEGR2
#> Updating: adex with: AGEGR2
#> Updating: adlb with: AGEGR2
#> Updating: admh with: AGEGR2
#> Updating: adrs with: AGEGR2
#> Updating: adsub with: AGEGR2
#> Updating: adtte with: AGEGR2
#> Updating: advs with: AGEGR2
run(rmpt03, proc_data, summaryvars = "AGEGR2")
#>                                                   F                           M                      All Genders       
#>                                        Patients     Person time    Patients     Person time    Patients     Person time
#>   Age Group 2                           (N=30)        (N=30)        (N=15)        (N=15)        (N=45)        (N=45)   
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   18 - 65                             30 (100.0%)      4088       15 (100.0%)      1825       45 (100.0%)      5913    
#>   Total patients number/person time   30 (100.0%)      4088       15 (100.0%)      1825       45 (100.0%)      5913

Extent of Exposure by Ethnic Origin for Risk Management Plan (RMPT04)

1. Extent of Exposure by Ethnic Origin for Risk Management Plan

The rmpt04 template produces the standard extent of exposure by ethnic origin output for the Risk Management Plan (RMP).

run(rmpt04, syn_data)
#>                                        Patients     Person time
#>   ETHNIC                                (N=45)        (N=45)   
#>   —————————————————————————————————————————————————————————————
#>   NOT REPORTED                         2 (4.4%)         49     
#>   HISPANIC OR LATINO                   2 (4.4%)         309    
#>   NOT HISPANIC OR LATINO              41 (91.1%)       5555    
#>   Total patients number/person time   45 (100.0%)      5913

Extent of Exposure by Race for Risk Management Plan (RMPT05)

1. Extent of Exposure by Race for Risk Management Plan

The rmpt05 template produces the standard extent of exposure by race output for the Risk Management Plan (RMP).

run(rmpt05, syn_data)
#>                                        Patients     Person time
#>   RACE                                  (N=45)        (N=45)   
#>   —————————————————————————————————————————————————————————————
#>   ASIAN                               26 (57.8%)       3309    
#>   BLACK OR AFRICAN AMERICAN            9 (20.0%)       1139    
#>   WHITE                                7 (15.6%)       1231    
#>   AMERICAN INDIAN OR ALASKA NATIVE     3 (6.7%)         234    
#>   Total patients number/person time   45 (100.0%)      5913

Best Overall Response (RSPT01)

1. Best Overall Response

  1. The rspt01 template produces the standard best overall response output.
  2. The template syntax is built based on RECIST 1.1. By default, the subjects with response results of "CR" or "PR" are considered as responders.
  3. Users are expected to pre-process the input analysis data and select the parameter to be analyzed, i.e., best overall response by investigator or best overall response by BICR.
  4. Unstratified analysis is provided by default.
proc_data <- log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")

run(rspt01, proc_data, ref_group = NULL, perform_analysis = "unstrat", strata = NULL)
#> Warning in stats::prop.test(tbl, correct = FALSE): Chi-squared approximation
#> may be incorrect
#>                                          A: Drug X          B: Placebo         C: Combination  
#>                                            (N=15)             (N=15)               (N=15)      
#>   —————————————————————————————————————————————————————————————————————————————————————————————
#>   Responders                             10 (66.7%)         9 (60.0%)            11 (73.3%)    
#>   95% CI (Wald, with correction)        (39.5, 93.9)       (31.9, 88.1)         (47.6, 99.0)   
#>   Unstratified Analysis                                                                        
#>     Difference in Response rate (%)                            -6.7                 6.7        
#>       95% CI (Wald, with correction)                      (-47.7, 34.4)        (-32.7, 46.0)   
#>     p-value (Chi-Squared Test)                                0.7048               0.6903      
#>   Odds Ratio (95% CI)                                   0.75 (0.17 - 3.33)   1.37 (0.29 - 6.60)
#>   Complete Response (CR)                 4 (26.7%)          4 (26.7%)            7 (46.7%)     
#>     95% CI (Wald, with correction)     (0.95, 52.38)      (0.95, 52.38)        (18.09, 75.25)  
#>   Partial Response (PR)                  6 (40.0%)          5 (33.3%)            4 (26.7%)     
#>     95% CI (Wald, with correction)     (11.87, 68.13)     (6.14, 60.52)        (0.95, 52.38)   
#>   Stable Disease (SD)                    5 (33.3%)          6 (40.0%)            4 (26.7%)     
#>     95% CI (Wald, with correction)     (6.14, 60.52)      (11.87, 68.13)       (0.95, 52.38)

2. Best Overall Response (Ordering of treatment groups) {#1}

  1. By default, the first level or value of arm_var (default to "ADSL.ARM" unless specified) is treated as the reference group without specification.
  2. To apply user-defined reference group, please provide the value from the treatment variable to the argument ref_group, e.g., ref_group = "PLACEBO".
  3. Since rtables displays the reference group at the very left column, the order of displayed treatment groups may not be exactly the same as the order factorized, depending on which group is selected as the reference group. See below for examples:
Factorized trt order ref_group Displayed trt order Reference group used in analysis
ARM C, ARM B, ARM A NULL ARM C, ARM B, ARM A ARM C
NULL ARM B ARM B, ARM A, ARM C ARM B
ARM C, ARM B, ARM A ARM B ARM B, ARM C, ARM A ARM B

3. Best Overall Response (selecting sections to display)

  1. The section of Odds Ratio can be suppressed with the argument odds_ratio = FALSE.
  2. The section of Difference in response rate can be suppressed with the argument perform_analysis = NULL.
proc_data <- log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")

run(rspt01, proc_data, odds_ratio = FALSE, perform_analysis = NULL)
#>                                        A: Drug X        B: Placebo     C: Combination
#>                                          (N=15)           (N=15)           (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   Responders                           10 (66.7%)       9 (60.0%)        11 (73.3%)  
#>   95% CI (Wald, with correction)      (39.5, 93.9)     (31.9, 88.1)     (47.6, 99.0) 
#>   Complete Response (CR)               4 (26.7%)        4 (26.7%)        7 (46.7%)   
#>     95% CI (Wald, with correction)   (0.95, 52.38)    (0.95, 52.38)    (18.09, 75.25)
#>   Partial Response (PR)                6 (40.0%)        5 (33.3%)        4 (26.7%)   
#>     95% CI (Wald, with correction)   (11.87, 68.13)   (6.14, 60.52)    (0.95, 52.38) 
#>   Stable Disease (SD)                  5 (33.3%)        6 (40.0%)        4 (26.7%)   
#>     95% CI (Wald, with correction)   (6.14, 60.52)    (11.87, 68.13)   (0.95, 52.38)

4. Best Overall Response (with stratified analysis)

  1. A stratified analysis can be added by specifying the argument perform_analysis = "strat" and providing the stratification variable to the argument strata . The argument strata is expected if perform_analysis is set to include stratified analysis.
  2. The stratification variables are expected to be available in adrs.
  3. If both unstratified and stratified analysis are required, use perform_analysis = c("unstrat", "strat")
proc_data <- log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")

run(rspt01, proc_data, perform_analysis = "strat", strata = c("STRATA1", "STRATA2"))
#> Warning in prop_diff_cmh(rsp, grp, strata, conf_level): Less than 5
#> observations in some strata.

#> Warning in prop_diff_cmh(rsp, grp, strata, conf_level): Less than 5
#> observations in some strata.
#> Warning in prop_cmh(tbl): <5 data points in some strata. CMH test may be
#> incorrect.

#> Warning in prop_cmh(tbl): <5 data points in some strata. CMH test may be
#> incorrect.
#>                                                A: Drug X          B: Placebo         C: Combination  
#>                                                  (N=15)             (N=15)               (N=15)      
#>   ———————————————————————————————————————————————————————————————————————————————————————————————————
#>   Responders                                   10 (66.7%)         9 (60.0%)            11 (73.3%)    
#>   95% CI (Wald, with correction)              (39.5, 93.9)       (31.9, 88.1)         (47.6, 99.0)   
#>   Stratified Analysis                                                                                
#>     Difference in Response rate (%)                                 -11.0                 22.5       
#>       95% CI (CMH, without correction)                          (-42.7, 20.7)         (-3.5, 48.5)   
#>     p-value (Cochran-Mantel-Haenszel Test)                          0.5731               0.3088      
#>   Odds Ratio (95% CI)                                         0.75 (0.17 - 3.33)   1.37 (0.29 - 6.60)
#>   Complete Response (CR)                       4 (26.7%)          4 (26.7%)            7 (46.7%)     
#>     95% CI (Wald, with correction)           (0.95, 52.38)      (0.95, 52.38)        (18.09, 75.25)  
#>   Partial Response (PR)                        6 (40.0%)          5 (33.3%)            4 (26.7%)     
#>     95% CI (Wald, with correction)           (11.87, 68.13)     (6.14, 60.52)        (0.95, 52.38)   
#>   Stable Disease (SD)                          5 (33.3%)          6 (40.0%)            4 (26.7%)     
#>     95% CI (Wald, with correction)           (6.14, 60.52)      (11.87, 68.13)       (0.95, 52.38)

5. Best Overall Response (modifying analysis details like type of confidence interval, alpha level, test for p-value)

  1. The level of the confidence intervals is defined by the argument conf_level.
  2. The methods to construct confidence interval and p-value are controlled by the argument methods. It is a named list with five optional sub-arguments. For example, methods = list(prop_conf_method = "wald", diff_conf_method = "wald", strat_diff_conf_method = "ha", diff_pval_method = "fisher", strat_diff_pval_method = "schouten")

See table below for what each argument controls and the available method options:

Arguments Methods Controlled Methods Options
prop_conf_method proportion confidence interval "waldcc" (default), "wald", etc.
diff_conf_method unstratified difference confidence interval "waldcc" (default), "wald", etc.
diff_pval_method unstratified p-value for odds ratio "chisq" (default), "fisher"
strat_diff_conf_method stratified difference confidence interval "cmh" (default), "ha"
strat_diff_pval_method stratified p-value for odds ratio "cmh" (default), "schouten"

See in the table below the method options for estimates of proportions and the associated statistical methods:

Method Options Statistical Methods
"clopper-pearson" Clopper-Pearson
"wald" Wald, without correction
"waldcc" Wald, with correction
"wilson" Wilson, without correction
"strat_wilson" Stratified Wilson, without correction
"wilsonc" Wilson, with correction
"strat_wilsonc" Stratified Wilson, with correction
"agresti-coull" Agresti-Coull
"jeffreys" Jeffreys

See in the table below the method options for estimates of proportion difference and the associated statistical methods:

Method Options Statistical Methods
"cmh" CMH, without correction
"wald" Wald, with correction
"waldcc" Wald, without correction
"ha" Anderson-Hauck
"newcombe" Newcombe, without correction
"newcombecc" Newcombe, with correction
"strat_wilsonc" Stratified Wilson, with correction
"strat_newcombe" Stratified Newcombe, without correction
"strat_newcombecc" Stratified Newcombe, with correction

See in the table below the method options for testing proportion difference and the associated statistical methods:

Method Options Statistical Methods
"chisq" Chi-Squared test
"fisher" the Fisher’s exact test
"cmh" stratified Cochran-Mantel-Haenszel test
"shouten" Chi-Squared test with Schouten correction

An example:

proc_data <- log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")

run(rspt01, proc_data,
  conf_level = 0.90,
  methods = list(
    prop_conf_method = "wald",
    diff_conf_method = "wald",
    diff_pval_method = "fisher"
  )
)
#>                                             A: Drug X          B: Placebo         C: Combination  
#>                                               (N=15)             (N=15)               (N=15)      
#>   ————————————————————————————————————————————————————————————————————————————————————————————————
#>   Responders                                10 (66.7%)         9 (60.0%)            11 (73.3%)    
#>   90% CI (Wald, without correction)        (46.6, 86.7)       (39.2, 80.8)         (54.6, 92.1)   
#>   Unstratified Analysis                                                                           
#>     Difference in Response rate (%)                               -6.7                 6.7        
#>       90% CI (Wald, without correction)                      (-35.5, 22.2)        (-20.8, 34.1)   
#>     p-value (Fisher's Exact Test)                                1.0000               1.0000      
#>   Odds Ratio (95% CI)                                      0.75 (0.17 - 3.33)   1.37 (0.29 - 6.60)
#>   Complete Response (CR)                    4 (26.7%)          4 (26.7%)            7 (46.7%)     
#>     90% CI (Wald, without correction)     (7.89, 45.45)      (7.89, 45.45)        (25.48, 67.85)  
#>   Partial Response (PR)                     6 (40.0%)          5 (33.3%)            4 (26.7%)     
#>     90% CI (Wald, without correction)     (19.19, 60.81)     (13.31, 53.35)       (7.89, 45.45)   
#>   Stable Disease (SD)                       5 (33.3%)          6 (40.0%)            4 (26.7%)     
#>     90% CI (Wald, without correction)     (13.31, 53.35)     (19.19, 60.81)       (7.89, 45.45)

6. Best Overall Response (modifying the definition of overall response)

The following example shows how to customize the definition of responder, e.g, consider only complete response as response.

proc_data <- log_filter(syn_data, PARAMCD == "BESRSPI", "adrs")

preprocess(rspt01) <- function(adam_db, ...) {
  adam_db$adrs <- adam_db$adrs %>%
    mutate(RSP_LAB = tern::d_onco_rsp_label(.data$AVALC)) %>%
    mutate(IS_RSP = .data$AVALC %in% c("CR"))
  adam_db
}

run(rspt01, proc_data)
#> Warning in stats::prop.test(tbl, correct = FALSE): Chi-squared approximation
#> may be incorrect
#>                                          A: Drug X          B: Placebo         C: Combination   
#>                                            (N=15)             (N=15)               (N=15)       
#>   ——————————————————————————————————————————————————————————————————————————————————————————————
#>   Responders                             4 (26.7%)          4 (26.7%)             7 (46.7%)     
#>   95% CI (Wald, with correction)        (1.0, 52.4)        (1.0, 52.4)          (18.1, 75.2)    
#>   Unstratified Analysis                                                                         
#>     Difference in Response rate (%)                            0.0                  20.0        
#>       95% CI (Wald, with correction)                      (-38.3, 38.3)         (-20.4, 60.4)   
#>     p-value (Chi-Squared Test)                                1.0000               0.2557       
#>   Odds Ratio (95% CI)                                   1.00 (0.20 - 5.04)   2.41 (0.52 - 11.10)
#>   Complete Response (CR)                 4 (26.7%)          4 (26.7%)             7 (46.7%)     
#>     95% CI (Wald, with correction)     (0.95, 52.38)      (0.95, 52.38)        (18.09, 75.25)   
#>   Partial Response (PR)                  6 (40.0%)          5 (33.3%)             4 (26.7%)     
#>     95% CI (Wald, with correction)     (11.87, 68.13)     (6.14, 60.52)         (0.95, 52.38)   
#>   Stable Disease (SD)                    5 (33.3%)          6 (40.0%)             4 (26.7%)     
#>     95% CI (Wald, with correction)     (6.14, 60.52)      (11.87, 68.13)        (0.95, 52.38)

Time-to-event Summary (TTET01)

1. Time-to-event Summary

  1. The ttet01 template produces the standard time-to-event summary.
  2. Users are expected to subset the parameter of interest (e.g. PARAMCD == "PFS") in pre-processing.
  3. Please see the section of Best Overall Response (Ordering of treatment groups) to find out more about the ordering of treatment groups and reference group.
  4. Unstratified analysis is provided by default.
  5. Survival estimations and difference in survival are both provided by default.
proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data)
#>                                        A: Drug X        B: Placebo      C: Combination 
#>                                         (N=15)            (N=15)            (N=15)     
#>   —————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>     Earliest contributing event                                                        
#>       Death                                5                 6                 4       
#>       Disease Progression                  5                 5                 7       
#>   Patients without event (%)           5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                               
#>     Median                               17.2              18.1              12.6      
#>       95% CI                         (11.9, 24.4)       (6.5, 34.1)       (7.1, 15.6)  
#>     25% and 75%-ile                   11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                           1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Unstratified Analysis                                                                
#>     p-value (log-rank)                                    0.8668            0.1419     
#>     Hazard Ratio                                           0.93              1.95      
#>     95% CI                                             (0.39, 2.22)      (0.79, 4.80)  
#>   6 MONTHS                                                                             
#>     Patients remaining at risk            10                11                10       
#>     Event Free Rate (%)                  78.32             78.57             80.00     
#>     95% CI                          (56.47, 100.00)   (57.08, 100.00)   (59.76, 100.00)
#>     Difference in Event Free Rate                          0.25              1.68      
#>       95% CI                                          (-30.40, 30.90)   (-28.11, 31.47)
#>       p-value (Z-test)                                    0.9873            0.9121     
#>   12 MONTHS                                                                            
#>     Patients remaining at risk             8                 6                 7       
#>     Event Free Rate (%)                  69.62             55.10             62.22     
#>     95% CI                          (44.40, 94.84)    (27.89, 82.31)    (35.39, 89.06) 
#>     Difference in Event Free Rate                         -14.52             -7.40     
#>       95% CI                                          (-51.62, 22.58)   (-44.22, 29.43)
#>       p-value (Z-test)                                    0.4431            0.6938     
#>   —————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   —————————————————————————————————————————————————————————————————————————————————————

2. Time-to-event Summary (selecting sections to display)

To suspend the section of earliest contributing events, use summarize_event = FALSE.

proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, summarize_event = FALSE)
#>                                        A: Drug X        B: Placebo      C: Combination 
#>                                         (N=15)            (N=15)            (N=15)     
#>   —————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>   Patients without event (%)           5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                               
#>     Median                               17.2              18.1              12.6      
#>       95% CI                         (11.9, 24.4)       (6.5, 34.1)       (7.1, 15.6)  
#>     25% and 75%-ile                   11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                           1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Unstratified Analysis                                                                
#>     p-value (log-rank)                                    0.8668            0.1419     
#>     Hazard Ratio                                           0.93              1.95      
#>     95% CI                                             (0.39, 2.22)      (0.79, 4.80)  
#>   6 MONTHS                                                                             
#>     Patients remaining at risk            10                11                10       
#>     Event Free Rate (%)                  78.32             78.57             80.00     
#>     95% CI                          (56.47, 100.00)   (57.08, 100.00)   (59.76, 100.00)
#>     Difference in Event Free Rate                          0.25              1.68      
#>       95% CI                                          (-30.40, 30.90)   (-28.11, 31.47)
#>       p-value (Z-test)                                    0.9873            0.9121     
#>   12 MONTHS                                                                            
#>     Patients remaining at risk             8                 6                 7       
#>     Event Free Rate (%)                  69.62             55.10             62.22     
#>     95% CI                          (44.40, 94.84)    (27.89, 82.31)    (35.39, 89.06) 
#>     Difference in Event Free Rate                         -14.52             -7.40     
#>       95% CI                                          (-51.62, 22.58)   (-44.22, 29.43)
#>       p-value (Z-test)                                    0.4431            0.6938     
#>   —————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   —————————————————————————————————————————————————————————————————————————————————————

To select either survival estimations or difference in survival or both, please specify in the argument method. - surv calls out the analysis of patients remaining at risk, event free rate and corresponding 95% confidence interval of the rates. - surv_diff calls out the analysis of difference in event free rate, the 95% confidence interval of the difference and its corresponding p-value. - both calls out both.

proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, method = "surv")
#>                                      A: Drug X        B: Placebo      C: Combination 
#>                                       (N=15)            (N=15)            (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)           10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>     Earliest contributing event                                                      
#>       Death                              5                 6                 4       
#>       Disease Progression                5                 5                 7       
#>   Patients without event (%)         5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                             
#>     Median                             17.2              18.1              12.6      
#>       95% CI                       (11.9, 24.4)       (6.5, 34.1)       (7.1, 15.6)  
#>     25% and 75%-ile                 11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                         1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Unstratified Analysis                                                              
#>     p-value (log-rank)                                  0.8668            0.1419     
#>     Hazard Ratio                                         0.93              1.95      
#>     95% CI                                           (0.39, 2.22)      (0.79, 4.80)  
#>   6 MONTHS                                                                           
#>     Patients remaining at risk          10                11                10       
#>     Event Free Rate (%)                78.32             78.57             80.00     
#>     95% CI                        (56.47, 100.00)   (57.08, 100.00)   (59.76, 100.00)
#>   12 MONTHS                                                                          
#>     Patients remaining at risk           8                 6                 7       
#>     Event Free Rate (%)                69.62             55.10             62.22     
#>     95% CI                        (44.40, 94.84)    (27.89, 82.31)    (35.39, 89.06) 
#>   ———————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   ———————————————————————————————————————————————————————————————————————————————————

3. Time-to-event Summary (modifying analysis details like confidence interval type, ties, and alpha level)

  1. The level of the confidence intervals is defined by the argument conf_level.
  2. The type of confidence interval is defined in the argument conf_type. Options are "plain" (default), "log" and "log-log".
  3. Handling of ties is specified in the argument ties. Options are "efron" (default),"breslow" or "exact".
proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, conf_level = 0.90, conf_type = "log-log", ties = "efron")
#>                                        A: Drug X        B: Placebo      C: Combination 
#>                                         (N=15)            (N=15)            (N=15)     
#>   —————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>     Earliest contributing event                                                        
#>       Death                                5                 6                 4       
#>       Disease Progression                  5                 5                 7       
#>   Patients without event (%)           5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                               
#>     Median                               17.2              18.1              12.6      
#>       90% CI                         (11.9, 20.6)       (6.5, 29.5)       (7.1, 15.5)  
#>     25% and 75%-ile                   11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                           1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Unstratified Analysis                                                                
#>     p-value (log-rank)                                    0.8668            0.1419     
#>     Hazard Ratio                                           0.93              1.95      
#>     90% CI                                             (0.45, 1.93)      (0.91, 4.15)  
#>   6 MONTHS                                                                             
#>     Patients remaining at risk            10                11                10       
#>     Event Free Rate (%)                  78.32             78.57             80.00     
#>     90% CI                          (52.89, 91.05)    (53.54, 91.11)    (56.11, 91.74) 
#>     Difference in Event Free Rate                          0.25              1.68      
#>       90% CI                                          (-25.47, 25.97)   (-23.32, 26.68)
#>       p-value (Z-test)                                    0.9873            0.9121     
#>   12 MONTHS                                                                            
#>     Patients remaining at risk             8                 6                 7       
#>     Event Free Rate (%)                  69.62             55.10             62.22     
#>     90% CI                          (43.24, 85.52)    (30.28, 74.28)    (36.15, 80.15) 
#>     Difference in Event Free Rate                         -14.52             -7.40     
#>       90% CI                                          (-45.65, 16.62)   (-38.30, 23.51)
#>       p-value (Z-test)                                    0.4431            0.6938     
#>   —————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   —————————————————————————————————————————————————————————————————————————————————————

4. Time-to-event Summary (with stratified analysis)

  1. A stratified analysis can be added by specifying the argument perform_analysis = "strat" and providing the stratification variable to the argument strata . The argument strata is expected if perform_analysis is set to include stratified analysis.
  2. The stratification variables are expected to be available in adrs.
  3. If unstratified and stratified analysis are both required, users can use perform_analysis = c("unstrat", "strat").
proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, perform_analysis = "strat", strata = "STRATA1")
#>                                        A: Drug X        B: Placebo      C: Combination 
#>                                         (N=15)            (N=15)            (N=15)     
#>   —————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>     Earliest contributing event                                                        
#>       Death                                5                 6                 4       
#>       Disease Progression                  5                 5                 7       
#>   Patients without event (%)           5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                               
#>     Median                               17.2              18.1              12.6      
#>       95% CI                         (11.9, 24.4)       (6.5, 34.1)       (7.1, 15.6)  
#>     25% and 75%-ile                   11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                           1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Stratified Analysis                                                                  
#>     p-value (log-rank)                                    0.6624            0.2020     
#>     Hazard Ratio                                           0.82              1.90      
#>     95% CI                                             (0.33, 2.02)      (0.70, 5.15)  
#>   6 MONTHS                                                                             
#>     Patients remaining at risk            10                11                10       
#>     Event Free Rate (%)                  78.32             78.57             80.00     
#>     95% CI                          (56.47, 100.00)   (57.08, 100.00)   (59.76, 100.00)
#>     Difference in Event Free Rate                          0.25              1.68      
#>       95% CI                                          (-30.40, 30.90)   (-28.11, 31.47)
#>       p-value (Z-test)                                    0.9873            0.9121     
#>   12 MONTHS                                                                            
#>     Patients remaining at risk             8                 6                 7       
#>     Event Free Rate (%)                  69.62             55.10             62.22     
#>     95% CI                          (44.40, 94.84)    (27.89, 82.31)    (35.39, 89.06) 
#>     Difference in Event Free Rate                         -14.52             -7.40     
#>       95% CI                                          (-51.62, 22.58)   (-44.22, 29.43)
#>       p-value (Z-test)                                    0.4431            0.6938     
#>   —————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   —————————————————————————————————————————————————————————————————————————————————————

5. Time-to-event Summary (modifying time point for the “survival at xx months” analysis)

The time point for the “survival at xx months” analysis can be modified by specifying the argument time_point. By default, the function takes AVAL from adtte in days and converts it to months. The survival estimates are then summarized in month, and the numeric values should be provided in months to time_point.

proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, perform_analysis = "unstrat", time_point = c(3, 6))
#>                                        A: Drug X        B: Placebo      C: Combination 
#>                                         (N=15)            (N=15)            (N=15)     
#>   —————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)        11 (73.3%)        11 (73.3%)   
#>     Earliest contributing event                                                        
#>       Death                                5                 6                 4       
#>       Disease Progression                  5                 5                 7       
#>   Patients without event (%)           5 (33.3%)         4 (26.7%)         4 (26.7%)   
#>   Time to Event (MONTHS)                                                               
#>     Median                               17.2              18.1              12.6      
#>       95% CI                         (11.9, 24.4)       (6.5, 34.1)       (7.1, 15.6)  
#>     25% and 75%-ile                   11.9, 24.4         6.5, 34.1         7.1, 15.5   
#>     Range                           1.2 to 46.9 {1}   1.0 to 50.5 {2}     1.9 to 28.9  
#>   Unstratified Analysis                                                                
#>     p-value (log-rank)                                    0.8668            0.1419     
#>     Hazard Ratio                                           0.93              1.95      
#>     95% CI                                             (0.39, 2.22)      (0.79, 4.80)  
#>   3 MONTHS                                                                             
#>     Patients remaining at risk            12                12                12       
#>     Event Free Rate (%)                  86.15             85.71             80.00     
#>     95% CI                          (68.31, 100.00)   (67.38, 100.00)   (59.76, 100.00)
#>     Difference in Event Free Rate                          -0.44             -6.15     
#>       95% CI                                          (-26.02, 25.14)   (-33.14, 20.83)
#>       p-value (Z-test)                                    0.9731            0.6549     
#>   6 MONTHS                                                                             
#>     Patients remaining at risk            10                11                10       
#>     Event Free Rate (%)                  78.32             78.57             80.00     
#>     95% CI                          (56.47, 100.00)   (57.08, 100.00)   (59.76, 100.00)
#>     Difference in Event Free Rate                          0.25              1.68      
#>       95% CI                                          (-30.40, 30.90)   (-28.11, 31.47)
#>       p-value (Z-test)                                    0.9873            0.9121     
#>   —————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   —————————————————————————————————————————————————————————————————————————————————————

The following example shows how to specify the time point in user-defined unit.

proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

preprocess(ttet01) <- function(adam_db, dataset = "adtte",
                               ...) {
  adam_db[[dataset]] <- adam_db[[dataset]] %>%
    mutate(
      AVALU = "DAYS",
      IS_EVENT = .data$CNSR == 0,
      IS_NOT_EVENT = .data$CNSR == 1,
      EVNT1 = factor(
        case_when(
          IS_EVENT == TRUE ~ render_safe("{Patient_label} with event (%)"),
          IS_EVENT == FALSE ~ render_safe("{Patient_label} without event (%)")
        ),
        levels = render_safe(c("{Patient_label} with event (%)", "{Patient_label} without event (%)"))
      ),
      EVNTDESC = factor(.data$EVNTDESC)
    )

  adam_db
}

run(ttet01, proc_data, perform_analysis = "unstrat", time_point = c(91, 183))
#>                                         A: Drug X            B: Placebo       C: Combination 
#>                                           (N=15)               (N=15)             (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)               10 (66.7%)           11 (73.3%)         11 (73.3%)   
#>     Earliest contributing event                                                              
#>       Death                                 5                    6                   4       
#>       Disease Progression                   5                    5                   7       
#>   Patients without event (%)            5 (33.3%)            4 (26.7%)           4 (26.7%)   
#>   Time to Event (DAYS)                                                                       
#>     Median                                523.9                549.7               382.9     
#>       95% CI                          (363.0, 743.3)      (196.5, 1037.2)     (215.4, 474.4) 
#>     25% and 75%-ile                    363.0, 743.3        196.5, 1037.2       215.4, 470.5  
#>     Range                           38.0 to 1426.9 {1}   30.0 to 1537.5 {2}    57.3 to 880.2 
#>   Unstratified Analysis                                                                      
#>     p-value (log-rank)                                         0.8668             0.1419     
#>     Hazard Ratio                                                0.93               1.95      
#>     95% CI                                                  (0.39, 2.22)       (0.79, 4.80)  
#>   91 DAYS                                                                                    
#>     Patients remaining at risk              12                   12                 12       
#>     Event Free Rate (%)                   86.15                85.71               80.00     
#>     95% CI                           (68.31, 100.00)      (67.38, 100.00)     (59.76, 100.00)
#>     Difference in Event Free Rate                              -0.44               -6.15     
#>       95% CI                                              (-26.02, 25.14)     (-33.14, 20.83)
#>       p-value (Z-test)                                         0.9731             0.6549     
#>   183 DAYS                                                                                   
#>     Patients remaining at risk              10                   11                 10       
#>     Event Free Rate (%)                   78.32                78.57               80.00     
#>     95% CI                           (56.47, 100.00)      (57.08, 100.00)     (59.76, 100.00)
#>     Difference in Event Free Rate                               0.25               1.68      
#>       95% CI                                              (-30.40, 30.90)     (-28.11, 31.47)
#>       p-value (Z-test)                                         0.9873             0.9121     
#>   ———————————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   ———————————————————————————————————————————————————————————————————————————————————————————

6. Time-to-event Summary (modifying the p-value method for testing hazard ratio)

The default p-value method for testing hazard ratio is “log-rank”. Alternative methods can be requested by specifying the argument pval_method and options include, log-rank (default), wald or likelihood. The syntax currently does not allow requesting more than one p-value.

Note that ttet01 has been modified in the previous example (i.e., preprocess(ttet01) has been overridden); to access the default template, try chevron::ttet01.

proc_data <- log_filter(syn_data, PARAMCD == "PFS", "adtte")

run(ttet01, proc_data, pval_method = "wald")
#>                                       A: Drug X            B: Placebo        C: Combination 
#>                                         (N=15)               (N=15)              (N=15)     
#>   ——————————————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             10 (66.7%)           11 (73.3%)          11 (73.3%)   
#>     Earliest contributing event                                                             
#>       Death                               5                    6                   4        
#>       Disease Progression                 5                    5                   7        
#>   Patients without event (%)          5 (33.3%)            4 (26.7%)           4 (26.7%)    
#>   Time to Event (DAYS)                                                                      
#>     Median                              523.9                549.7               382.9      
#>       95% CI                        (363.0, 743.3)      (196.5, 1037.2)      (215.4, 474.4) 
#>     25% and 75%-ile                  363.0, 743.3        196.5, 1037.2        215.4, 470.5  
#>     Range                         38.0 to 1426.9 {1}   30.0 to 1537.5 {2}    57.3 to 880.2  
#>   Unstratified Analysis                                                                     
#>     p-value (wald)                                           0.8669              0.1476     
#>     Hazard Ratio                                              0.93                1.95      
#>     95% CI                                                (0.39, 2.22)        (0.79, 4.80)  
#>   6 DAYS                                                                                    
#>     Patients remaining at risk            15                   15                  15       
#>     Event Free Rate (%)                 100.00               100.00              100.00     
#>     95% CI                         (100.00, 100.00)     (100.00, 100.00)    (100.00, 100.00)
#>   12 DAYS                                                                                   
#>     Patients remaining at risk            15                   15                  15       
#>     Event Free Rate (%)                 100.00               100.00              100.00     
#>     95% CI                         (100.00, 100.00)     (100.00, 100.00)    (100.00, 100.00)
#>   ——————————————————————————————————————————————————————————————————————————————————————————
#> 
#>   {1} - Censored observation: range maximum
#>   {2} - Censored observations: range minimum & maximum
#>   ——————————————————————————————————————————————————————————————————————————————————————————

Vital Signs (VST01)

1. Vital Sign Results and Change from Baseline by Visit

t_vs_chg <- run(vst01, syn_data)
head(t_vs_chg, 20)
#>                                         A: Drug X                        B: Placebo                       C: Combination         
#>                                                Change from                       Change from                        Change from  
#>                              Value at Visit      Baseline      Value at Visit      Baseline      Value at Visit      Baseline    
#>                                  (N=15)           (N=15)           (N=15)           (N=15)           (N=15)           (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Diastolic Blood Pressure                                                                                                       
#>     SCREENING                                                                                                                    
#>       n                            15               0                15               0                15                0       
#>       Mean (SD)              47.754 (6.827)      NE (NE)       52.552 (8.234)      NE (NE)       52.587 (5.051)       NE (NE)    
#>       Median                     47.973             NE             54.453             NE             53.344             NE       
#>       Min - Max              32.28 - 58.80       NE - NE       34.09 - 62.76       NE - NE       43.31 - 60.87        NE - NE    
#>     BASELINE                                                                                                                     
#>       n                            15                                15                                15                        
#>       Mean (SD)              48.453 (8.983)                    53.244 (6.030)                    51.260 (7.901)                  
#>       Median                     47.331                            53.581                            51.140                      
#>       Min - Max              34.23 - 64.64                     43.38 - 62.65                     36.42 - 64.62                   
#>     WEEK 1 DAY 8                                                                                                                 
#>       n                            15               15               15               15               15               15       
#>       Mean (SD)              49.591 (8.543)   1.138 (11.242)   51.644 (6.469)   -1.601 (8.747)   50.330 (7.611)   -0.929 (10.007)
#>       Median                     46.979           -1.626           53.081           1.291            51.223           -0.990     
#>       Min - Max              37.02 - 62.15    -13.13 - 19.07   38.36 - 63.15    -21.18 - 11.45   38.02 - 61.47    -22.06 - 16.72 
#>     WEEK 2 DAY 15                                                                                                                
#>       n                            15               15               15               15               15               15       
#>       Mean (SD)              49.903 (5.791)   1.450 (8.476)    48.989 (6.919)   -4.255 (8.332)   47.709 (6.784)   -3.551 (10.892)
#>       Median                     50.599           0.692            49.800           -3.891           48.715           -4.062

Vital Signs Abnormalities (Regardless of Abnormality at Baseline) (VST02_1)

1. Vital Sign Abnormalities (Regardless of Abnormality at Baseline)

run(vst02_1, syn_data)
#>   Assessment                  A: Drug X      B: Placebo     C: Combination
#>    Abnormality                  (N=15)         (N=15)           (N=15)    
#>   ————————————————————————————————————————————————————————————————————————
#>   Diastolic Blood Pressure                                                
#>     Low                       6/15 (40%)    10/15 (66.7%)     9/15 (60%)  
#>     High                      6/15 (40%)    8/15 (53.3%)     12/15 (80%)  
#>   Pulse Rate                                                              
#>     Low                      8/15 (53.3%)   5/15 (33.3%)     7/15 (46.7%) 
#>     High                     7/15 (46.7%)   8/15 (53.3%)     7/15 (46.7%) 
#>   Respiratory Rate                                                        
#>     Low                      7/15 (46.7%)   7/15 (46.7%)     5/15 (33.3%) 
#>     High                     7/15 (46.7%)   4/15 (26.7%)     8/15 (53.3%) 
#>   Systolic Blood Pressure                                                 
#>     Low                      7/15 (46.7%)   10/15 (66.7%)    4/15 (26.7%) 
#>     High                     8/15 (53.3%)   8/15 (53.3%)      6/15 (40%)  
#>   Temperature                                                             
#>     Low                       6/15 (40%)    8/15 (53.3%)      9/15 (60%)  
#>     High                      9/15 (60%)     9/15 (60%)       9/15 (60%)  
#>   Weight                                                                  
#>     Low                      12/15 (80%)    7/15 (46.7%)      9/15 (60%)  
#>     High                     7/15 (46.7%)   10/15 (66.7%)     9/15 (60%)

Vital Signs Abnormalities (Among Subject Without Abnormality at Baseline) (VST02_2)

1. Vital Sign Abnormalities (Among Subject Without Abnormality at Baseline)

run(vst02_2, syn_data)
#>   Assessment                  A: Drug X      B: Placebo    C: Combination
#>    Abnormality                  (N=15)         (N=15)          (N=15)    
#>   ———————————————————————————————————————————————————————————————————————
#>   Diastolic Blood Pressure                                               
#>     Low                      4/13 (30.8%)    5/10 (50%)     7/13 (53.8%) 
#>     High                     5/14 (35.7%)    7/14 (50%)      9/12 (75%)  
#>   Pulse Rate                                                             
#>     Low                      5/12 (41.7%)   3/13 (23.1%)    6/14 (42.9%) 
#>     High                     7/15 (46.7%)   5/12 (41.7%)    6/14 (42.9%) 
#>   Respiratory Rate                                                       
#>     Low                      5/13 (38.5%)   6/14 (42.9%)    5/15 (33.3%) 
#>     High                     6/14 (42.9%)   4/15 (26.7%)    8/15 (53.3%) 
#>   Systolic Blood Pressure                                                
#>     Low                      5/13 (38.5%)   9/14 (64.3%)    4/15 (26.7%) 
#>     High                      7/14 (50%)    8/15 (53.3%)    4/13 (30.8%) 
#>   Temperature                                                            
#>     Low                      4/13 (30.8%)   6/13 (46.2%)     9/15 (60%)  
#>     High                      9/15 (60%)    8/14 (57.1%)    7/13 (53.8%) 
#>   Weight                                                                 
#>     Low                       9/12 (75%)     2/10 (20%)     7/13 (53.8%) 
#>     High                     4/12 (33.3%)   9/14 (64.3%)    7/13 (53.8%)

LISTINGS

Glossary of Adverse Event Preferred Terms and Investigator-Specified Terms (AEL01_NOLLT)

1. Glossary of Adverse Event Preferred Terms and Investigator-Specified Terms

  1. The ael01_nollt template produces the standard glossary of adverse event preferred terms and investigator-specified terms.
  2. The example below uses head function to print only the first 10 lines of the output.
l_ae_nollt <- run(ael01_nollt, syn_data)
head(l_ae_nollt, 10)
#> MedDRA System Organ Class   MedDRA Preferred Term   Reported Term for the Adverse Event
#> ———————————————————————————————————————————————————————————————————————————————————————
#> cl A.1                      dcd A.1.1.1.1           trm A.1.1.1.1                      
#>                             dcd A.1.1.1.2           trm A.1.1.1.2                      
#> cl B.1                      dcd B.1.1.1.1           trm B.1.1.1.1                      
#> cl B.2                      dcd B.2.1.2.1           trm B.2.1.2.1                      
#>                             dcd B.2.2.3.1           trm B.2.2.3.1                      
#> cl C.1                      dcd C.1.1.1.3           trm C.1.1.1.3                      
#> cl C.2                      dcd C.2.1.2.1           trm C.2.1.2.1                      
#> cl D.1                      dcd D.1.1.1.1           trm D.1.1.1.1                      
#>                             dcd D.1.1.4.2           trm D.1.1.4.2                      
#> cl D.2                      dcd D.2.1.5.3           trm D.2.1.5.3

Graphics

Kaplan-Meier Plot (KMG01)

1. Kaplan-Meier Plot (without comparative statistics)

  1. The kmg01 template produces the standard Kaplan-Meier Plot.
  2. Users are expected to select a particular parameter for analysis.
  3. Users are expected to select the treatment groups to compare, otherwise, all treatment groups available in the input datasets will be plotted.
  4. The comparative statistics are not included by default.
  5. The estimation of median survival time per treatment group by default.
  6. More arguments in the g_km and control_coxph functions can be passed through, please use the Help to find out more information.
proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(kmg01, proc_data, dataset = "adtte")

2. Kaplan-Meier Plot (with comparative statistics)

To enable the comparative statistics (hazard ratio and p-value), the argument annot_coxph needs to be set to TRUE. The compare group is determined by the levels in the factorized variable of treatment group and the first level is used as reference group in the statistics.

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(
  kmg01,
  proc_data,
  dataset = "adtte",
  annot_coxph = TRUE,
  control_annot_coxph = tern::control_coxph_annot(x = 0.33, y = 0.42)
)

3. Kaplan-Meier Plot (without censoring marks)

To suppress the censoring marks, set the argument cencor_show to FALSE.

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(kmg01, proc_data, dataset = "adtte", censor_show = FALSE)

4. Kaplan-Meier Plot (without estimation of median survival time)

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(kmg01, proc_data, dataset = "adtte", annot_surv_med = FALSE)

5. Kaplan-Meier Plot (with statistical annotation of either median or min of survival time)

To add the statistics annotation, use the function annot_stats. Options are min or median.

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(kmg01, proc_data, dataset = "adtte", annot_stats = "median")

run(kmg01, proc_data, dataset = "adtte", annot_stats = c("min", "median"))

6. Kaplan-Meier Plot (without the table of patients at risk)

proc_data <- log_filter(syn_data, PARAMCD == "OS", "adtte")
run(kmg01, proc_data, dataset = "adtte", annot_at_risk = FALSE)

Mean Plot (MNG01)

1. Plot of Mean and Confidence Interval (with Table Section)

  1. The mng01 template produces the standard mean plot.
  2. Note that the template mng01 is quite general. The users are expected to specify the analysis dataset and the visit variable in the run function, and select the parameters prior to the run function.
  3. The table of summary statistics is included by default.
  4. The variable Analysis Value AVAL is used for plotting by default.
  5. If the input dataset contains results of the same analyses in multiple units,(e.g. SI/CV units in ADLB), please make sure that the parameters in appropriate units are selected in advance.
proc_data <- log_filter(syn_data, PARAMCD == "DIABP", "advs")
run(mng01, proc_data, dataset = "advs", x_var = c("AVISIT", "AVISITN"))
#> $`Diastolic Blood Pressure`