NEWS

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sjSDM 1.0.6 (2024-08-19)

New features

• Datasets: butterflies and eucalypt species
• Conditional predictions
• Assembly regression plots

sjSDM 1.0.5 (2023-06-17)

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 (2023-03-30)

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 (2022-09-14)

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 (2022-06-23)

Minor changes

• changed \mjeqn{}{} to \mjeqn{} as requested by the CRAN team

Bug fixes

• fixed plot.sjSDM(...) #97

sjSDM 1.0.1 (2022-03-11)

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 (2022-01-10)

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