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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

211

Version

1.0.6

License

GPL-3

Issues

45

Pull Requests

0

Stars

70

Forks

15

Maintainer

Maximilian Pichler

Last Published

August 19th, 2024

Functions in sjSDM (1.0.6)

getCor

getCor
bioticStruct

biotic structure
madgrad

madgrad
plot.sjSDM.DNN

Training history
Adamax

Adamax
print.sjSDMinternalStructure

Print internal structure object
Rsquared

R-squared
new_image

new_image function
getWeights

Get weights
coef.sjSDM

Return coefficients from a fitted sjSDM model
print.sjSDManova

Print sjSDM anova object
print.sjSDM_cv

Print a fitted sjSDM_cv model
check_module

check module
importance

Importance of environmental, spatial and association components
logLik.sjSDM

Extract negative-log-Likelihood from a fitted sjSDM model
DNN

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

getCov
SGD

SGD
is_torch_available

is_torch_available
getSe

Post hoc calculation of standard errors
print.sjSDMimportance

Print importance
getImportance

getImportance
linear

Linear model of environmental response
installation_help

Installation help
sjSDM_cv

Cross validation of elastic net tuning
internalStructure

Plot internal metacommunity structure
RMSprop

RMSprop
simulate.sjSDM

Generates simulations from sjSDM model
residuals.sjSDM

Residuals for a sjSDM model
setWeights

Set weights
plotsjSDMcoef

Internal coefficients plot
AccSGD

AccSGD
plot.sjSDMinternalStructure

Plot internal structure
anova.sjSDM

Anova / Variation partitioning
print.DNN

Print a DNN object
plotAssemblyEffects

Plot predictors of assembly processes
sjSDM

Fitting scalable joint Species Distribution Models (sjSDM)
AdaBound

AdaBound
eucalypts

eucalypts
sjSDMControl

sjSDM control object
summary.sjSDM

Return summary of a fitted sjSDM model
generateSpatialEV

Generate spatial eigenvectors
plot.sjSDM

Coefficients plot
plot.sjSDM_cv

Plot elastic net tuning
plot.sjSDMimportance

Plot importance
predict.sjSDM

Predict from a fitted sjSDM model
install_diagnostic

install diagnostic
DiffGrad

DiffGrad
install_sjSDM

Install sjSDM and its dependencies
simulate_SDM

Simulate joint Species Distribution Models
butterflies

butterflies
checkModel

check model check model and rebuild if necessary
plot.sjSDManova

Plot anova results
print.bioticStruct

Print a bioticStruct object
update.sjSDM

Update and re-fit a model call
print.sjSDM

Print a fitted sjSDM model
summary.sjSDM_cv

Return summary of a fitted sjSDM_cv model
print.linear

Print a linear object
summary.sjSDManova

Summary table of sjSDM anova