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NEWS
sjSDM 1.0.6 New features
- Datasets: butterflies and eucalypt species
- Conditional predictions
- Assembly regression plots
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(â¦,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(â¦) #113 (thanks to @AndrewCSlater)
- fixed whitespaces in species names #115 @dansmi-hub
sjSDM 1.0.3 Minor changes
- changed weight_decay in âRMSpropâ from 0.01 to 0.0001
Important bug fix
- fixed sjSDM_cv(â¦) #104 (thanks to @Cdevenish)
sjSDM 1.0.2 Minor changes
- changed to as requested by the CRAN team
Bug fixes
- fixed plot.sjSDM(â¦) #97
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
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