Last updated on 2024-09-17 19:49:18 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.2-5-2 | 42.02 | 341.68 | 383.70 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 4.2-5-2 | 27.08 | 252.11 | 279.19 | OK | |
| r-devel-linux-x86_64-fedora-clang | 4.2-5-2 | 700.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.2-5-2 | 714.64 | OK | |||
| r-devel-windows-x86_64 | 4.2-5-2 | 41.00 | 322.00 | 363.00 | OK | |
| r-patched-linux-x86_64 | 4.2-5-2 | 43.28 | 367.10 | 410.38 | OK | |
| r-release-linux-x86_64 | 4.2-5-2 | 43.51 | 364.72 | 408.23 | OK | |
| r-release-macos-arm64 | 4.2-5-2 | 165.00 | OK | |||
| r-release-macos-x86_64 | 4.2-5-2 | 554.00 | OK | |||
| r-release-windows-x86_64 | 4.2-5-2 | 42.00 | 333.00 | 375.00 | OK | |
| r-oldrel-macos-arm64 | 4.2-5-2 | 172.00 | OK | |||
| r-oldrel-macos-x86_64 | 4.2-5-2 | 398.00 | OK | |||
| r-oldrel-windows-x86_64 | 4.2-5-2 | 59.00 | 458.00 | 517.00 | OK |
Version: 4.2-5-2
Check: examples
Result: ERROR
Running examples in ‘biomod2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BIOMOD_EnsembleModeling
> ### Title: Create and evaluate an ensemble set of models and predictions
> ### Aliases: BIOMOD_EnsembleModeling
> ### Keywords: ensemble models weights
>
> ### ** Examples
>
>
> library(terra)
terra 1.7.78
Attaching package: ‘terra’
The following object is masked from ‘package:plotrix’:
rescale
> # Load species occurrences (6 species available)
> data(DataSpecies)
> head(DataSpecies)
X_WGS84 Y_WGS84 ConnochaetesGnou GuloGulo PantheraOnca PteropusGiganteus
1 -94.5 82.00001 0 0 0 0
2 -91.5 82.00001 0 1 0 0
3 -88.5 82.00001 0 1 0 0
4 -85.5 82.00001 0 1 0 0
5 -82.5 82.00001 0 1 0 0
6 -79.5 82.00001 0 1 0 0
TenrecEcaudatus VulpesVulpes
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
>
> # Select the name of the studied species
> myRespName <- 'GuloGulo'
>
> # Get corresponding presence/absence data
> myResp <- as.numeric(DataSpecies[, myRespName])
>
> # Get corresponding XY coordinates
> myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
>
> # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
> data(bioclim_current)
> myExpl <- terra::rast(bioclim_current)
>
> ## Don't show:
> myExtent <- terra::ext(0,30,45,70)
> myExpl <- terra::crop(myExpl, myExtent)
> ## End(Don't show)
>
> ## ----------------------------------------------------------------------- #
> file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
> if (file.exists(file.out)) {
+ myBiomodModelOut <- get(load(file.out))
+ } else {
+
+ # Format Data with true absences
+ myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
+ expl.var = myExpl,
+ resp.xy = myRespXY,
+ resp.name = myRespName)
+
+ # Model single models
+ myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
+ modeling.id = 'AllModels',
+ models = c('RF', 'GLM'),
+ CV.strategy = 'random',
+ CV.nb.rep = 2,
+ CV.perc = 0.8,
+ OPT.strategy = 'bigboss',
+ metric.eval = c('TSS','ROC'),
+ var.import = 3,
+ seed.val = 42)
+ }
>
> ## ----------------------------------------------------------------------- #
> # Model ensemble models
> myBiomodEM <- BIOMOD_EnsembleModeling(bm.mod = myBiomodModelOut,
+ models.chosen = 'all',
+ em.by = 'all',
+ em.algo = c('EMmean', 'EMca'),
+ metric.select = c('TSS'),
+ metric.select.thresh = c(0.7),
+ metric.eval = c('TSS', 'ROC'),
+ var.import = 3,
+ seed.val = 42)
-=-=-=-=-=-=-=-=-=-=-=-=-=-= Build Ensemble Models -=-=-=-=-=-=-=-=-=-=-=-=-=-=
! all models available will be included in ensemble.modeling
! Ensemble Models will be filtered and/or weighted using validation dataset (if possible). Please use `metric.select.dataset` for alternative options.
> Evaluation & Weighting methods summary :
TSS over 0.7
!!! Removed models using the Full dataset as ensemble models cannot merge repetition dataset (RUN1, RUN2, ...) with Full dataset unless em.by = 'PA+run'.
!! Ensemble Model mergedData_mergedRun_mergedAlgo selected by TSS have no model selected and will fail.
!! Please make sure this is intended or review your selection metrics and threshold.
> mergedData_mergedRun_mergedAlgo ensemble modeling
! No models kept due to threshold filtering... Ensemble Modeling will fail!
! Note : GuloGulo_EMmeanByTSS_mergedData_mergedRun_mergedAlgo failed!
! Note : GuloGulo_EMcaByTSS_mergedData_mergedRun_mergedAlgo failed!
! All models failed> myBiomodEM
-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.ensemble.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=
sp.name : GuloGulo
expl.var.names : bio3 bio4 bio7 bio11 bio12
models computed: none
models failed:
GuloGulo_EMmeanByTSS_mergedData_mergedRun_mergedAlgo, GuloGulo_EMcaByTSS_mergedData_mergedRun_mergedAlgo
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
> # Get evaluation scores & variables importance
> get_evaluations(myBiomodEM)
Warning in .local(obj, ...) : No link provided for this object
Error in if (nrow(out) == 0) { : argument is of length zero
Calls: get_evaluations -> get_evaluations -> .local
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BIOMOD.projection.out 5.166 0.035 7.223
BIOMOD.ensemble.models.out 4.571 0.197 6.482
BIOMOD.formated.data.PA 4.222 0.110 5.998
BIOMOD_EnsembleForecasting 3.050 0.008 5.251
Flavor: r-devel-linux-x86_64-debian-clang
Version: 4.2-5-2
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘GuloGulo’
Flavor: r-devel-linux-x86_64-debian-clang