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sjSDM - Fast and accurate Joint Species Distribution Modeling

sjSDM - an R package to estimates joint Species Distribution Models (jSDMs) in a scalable way. For more info on the package, go to https://theoreticalecology.github.io/s-jSDM/

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Version

Install

install.packages('sjSDM')

Monthly Downloads

279

Version

1.0.7

License

GPL-3

Issues

49

Pull Requests

0

Stars

71

Forks

15

Maintainer

Maximilian Pichler

Last Published

September 17th, 2025

Functions in sjSDM (1.0.7)

checkModel

check model check model and rebuild if necessary
installation_help

Installation help
install_diagnostic

install diagnostic
internalStructure

Plot internal metacommunity structure
new_image

new_image function
plot.sjSDM.DNN

Training history
install_sjSDM

Install sjSDM and its dependencies
plotAssemblyEffects

Plot predictors of assembly processes
plot.sjSDMinternalStructure

Plot internal structure
print.linear

Print a linear object
print.sjSDM

Print a fitted sjSDM model
plotsjSDMcoef

Internal coefficients plot
predict.sjSDM

Predict from a fitted sjSDM model
logLik.sjSDM

Extract negative-log-Likelihood from a fitted sjSDM model
print.sjSDMinternalStructure

Print internal structure object
print.sjSDMimportance

Print importance
plot.sjSDManova

Plot anova results
is_torch_available

is_torch_available
linear

Linear model of environmental response
getWeights

Get weights
importance

Importance of environmental, spatial and association components
plot.sjSDM_cv

Plot elastic net tuning
plot.sjSDM

Coefficients plot
residuals.sjSDM

Residuals for a sjSDM model
plot.sjSDMimportance

Plot importance
summary.sjSDM_cv

Return summary of a fitted sjSDM_cv model
sjSDM_cv

Cross validation of elastic net tuning
setWeights

Set weights
summary.sjSDM

Return summary of a fitted sjSDM model
print.sjSDM_cv

Print a fitted sjSDM_cv model
print.sjSDManova

Print sjSDM anova object
madgrad

madgrad
summary.sjSDManova

Summary table of sjSDM anova
update.sjSDM

Update and re-fit a model call
simulate_SDM

Simulate joint Species Distribution Models
simulate.sjSDM

Generates simulations from sjSDM model
print.bioticStruct

Print a bioticStruct object
print.DNN

Print a DNN object
sjSDM

Fitting scalable joint Species Distribution Models (sjSDM)
sjSDMControl

sjSDM control object
Rsquared

R-squared
bioticStruct

biotic structure
AccSGD

AccSGD
anova.sjSDM

Anova / Variation partitioning
Adamax

Adamax
SGD

SGD
eucalypts

eucalypts
DiffGrad

DiffGrad
DNN

Non-linear model (deep neural network) of environmental responses
getSe

Post hoc calculation of standard errors
AdaBound

AdaBound
RMSprop

RMSprop
getCor

getCor
generateSpatialEV

Generate spatial eigenvectors
getCov

getCov
getImportance

getImportance
butterflies

butterflies
coef.sjSDM

Return coefficients from a fitted sjSDM model
check_module

check module