# Scalable Joint Species Distribution Modeling

## Documentation for package ‘sjSDM’ version 1.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

sjSDM-package | Installation help
AccSGD | AccSGD
AdaBound | AdaBound
Adamax | Adamax
anova.sjSDM | Anova / Variation partitioning
bioticStruct | biotic structure
butterflies | butterflies
checkModel | check model check model and rebuild if necessary
check_module | check module
coef.sjSDM | Return coefficients from a fitted sjSDM model
DiffGrad | DiffGrad
DNN | Non-linear model (deep neural network) of environmental responses
eucalypts | eucalypts
generateSpatialEV | Generate spatial eigenvectors
getCor | getCor
getCor.sjSDM | getCor
getCov | getCov
getCov.sjSDM | getCov
getImportance | getImportance
getSe | Post hoc calculation of standard errors
getWeights | Get weights
getWeights.sjSDM | Get weights
importance | Importance of environmental, spatial and association components
installation_help | Installation help
install_diagnostic | install diagnostic
install_sjSDM | Install sjSDM and its dependencies
internalStructure | Plot internal metacommunity structure
is_torch_available | is_torch_available
linear | Linear model of environmental response
logLik.sjSDM | Extract negative-log-Likelihood from a fitted sjSDM model
madgrad | madgrad
new_image | new_image function
plot.sjSDM | Coefficients plot
plot.sjSDM.DNN | Training history
plot.sjSDManova | Plot anova results
plot.sjSDMimportance | Plot importance
plot.sjSDMinternalStructure | Plot internal structure
plot.sjSDM_cv | Plot elastic net tuning
plotAssemblyEffects | Plot predictors of assembly processes
plotsjSDMcoef | Internal coefficients plot
predict.sjSDM | Predict from a fitted sjSDM model
print.bioticStruct | Print a bioticStruct object
print.DNN | Print a DNN object
print.linear | Print a linear object
print.sjSDM | Print a fitted sjSDM model
print.sjSDManova | Print sjSDM anova object
print.sjSDMimportance | Print importance
print.sjSDMinternalStructure | Print internal structure object
print.sjSDM_cv | Print a fitted sjSDM_cv model
residuals.sjSDM | Residuals for a sjSDM model
RMSprop | RMSprop
Rsquared | R-squared
setWeights | Set weights
setWeights.sjSDM | Set weights
SGD | SGD
simulate.sjSDM | Generates simulations from sjSDM model
simulate_SDM | Simulate joint Species Distribution Models
sjSDM | Fitting scalable joint Species Distribution Models (sjSDM)
sjSDM.tune | Fitting scalable joint Species Distribution Models (sjSDM)
sjSDMControl | sjSDM control object
sjSDM_cv | Cross validation of elastic net tuning
summary.sjSDM | Return summary of a fitted sjSDM model
summary.sjSDManova | Summary table of sjSDM anova
summary.sjSDM_cv | Return summary of a fitted sjSDM_cv model
update.sjSDM | Update and re-fit a model call