Scalable Joint Species Distribution Modeling

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Documentation for package ‘sjSDM’ version 1.0.5

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

Help Pages

AccSGD	AccSGD
AdaBound	AdaBound
Adamax	Adamax
anova.sjSDM	Anova
bioticStruct	biotic structure
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
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
installation_help	Installation help
install_diagnostic	install diagnostic
install_sjSDM	Install sjSDM and its dependencies
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.sjSDM_cv	Plot elastic net tuning
plotInternalStructure	Plot internal metacommunity structure
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
print.sjSDMimportance	Print importance
print.sjSDM_cv	Print a fitted sjSDM_cv 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.sjSDM_cv	Return summary of a fitted sjSDM_cv model
update.sjSDM	Update and re-fit a model call