Scalable Joint Species Distribution Modeling


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Documentation for package ‘sjSDM’ version 1.0.6

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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