Changes in version 1.0.7 (2025-09-17)                  

  - importance function was removed (deprecated)

Bug fixes

  - cv function, use correct indices in parallel block modus #155,
    thanks to @jannebor
  - remove ggtern dependency

                 Changes in version 1.0.6 (2024-08-19)                  

New features

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

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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)

                 Changes in version 1.0.2 (2022-06-23)                  

Minor changes

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

Bug fixes

  - fixed plot.sjSDM(...) #97

                 Changes in version 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

                 Changes in version 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