# sjSDM 1.0.5

## New features

- Pass custom test indices to sjSDM function via CV argument
- improve reproducibility (seeding)
- improve stability of ANOVA

## Bug fixes

- fixed small bug in the calculation of the partial Rsquareds

# sjSDM 1.0.4

## New features

- Anova function is now based on conditional probabilities to better
separate the biotic components
- Anova can use shared components (plot(…,internal=TRUE,
add_shared=TRUE))
- Simulation methods for all supported families (binomial, poisson,
and negative binomial)
- Support for negative binomial distribution
- plotInternalStructure for plotting internal metacommunity
structure
- getCor to return species-species association matrix

## Bug fixes

- fixed Rsquared(…) #113 (thanks to @AndrewCSlater)
- fixed whitespaces in species names #115 @dansmi-hub

# sjSDM 1.0.3

## Minor changes

- changed weight_decay in ‘RMSprop’ from 0.01 to 0.0001

## Important bug fix

- fixed sjSDM_cv(…) #104 (thanks to @Cdevenish)

# sjSDM 1.0.2

## Minor changes

- changed to as requested by the CRAN team

## Bug fixes

# sjSDM 1.0.1

## New Features

- anova plots for internal meta-community structure (based on
individual R-squared values)

## Minor changes

- first layer of DNN now always without an explicit bias
(bias/intercept is passed by model/formula, if desired)
- revised prediction function, improved stability
- revised simulation function, samples now from a multivariate probit
model

## Bug fixes

- unlisting of config objects in
`sjSDM::sjSDM_cv`

(thanks
to Máté) (added unit tests) #88
`sjSDM::Rsquared`

bug for spatial models (thanks to Máté)
#90
- revised regularization behavior, l1 and l2 were not correctly
imposed on DNN structure
- revised and improved setWeights function
- bugs in vignettes (thanks to Doug) #92
- bugs in plot function for models with DNN objects

# sjSDM 1.0.0

## Major changes

- revised anova:
`sjSDM::anova(...)`

corresponds now to a
type I anova (removed CV) #76
`sjSDM::Rsquared()`

uses now Nagelkerke or McFadden
R-squared (which is also used in the anova) #76
- deprecated
`sjSDM::sLVM`

because of instability issues
and other reasons
- revised
`sjSDM::install_sjSDM()`

, it works now for all
x64 systems/versions #81 #79 #71

## Minor changes

- removed several unnecessary dependencies (e.g. dplyr)
- improved documentation of all functions, e.g. see
`?sjSDM`

- new
`sjSDM::update.sjSDM`

method to re-fit model with
different formula(s)
- new
`sjSDM::sjSDM.tune`

method to fit quickly a model
with optimized regularization parameters (from
`sjSDM::sjSDM_cv`

)

## Bug fixes

- revised memory problem in
`sjSDM::sjSDM_cv()`

#84