Energy Landscape Analysis for Ecological Communities

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Documentation for package ‘ELAplus’ version 1.0.2

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

Help Pages

ELAplus-package	Energy Landscape Analysis for Ecological Communities
baseabtable	Abundance table for 16 taxa across 256 samples
basemetadata	Environmental metadata for 256 samples
Bi	Bi
bin2id	bin2id: map a binary vector to a 64base characters
bootstrap_ELA	Energy landscape analysis with bootstrap resampled SA results
bootstrap_SA	Parameter fitting with bootstrap sampling of datasets
deltaE_histogram	Plot histograms of bootstrap deltaE values
DisconnectivityGraph	DisconnectivityGraph: Generate a disconnectivity graph
ELA	Energy landscape analysis in parallel mode
ELAplus	Energy Landscape Analysis for Ecological Communities
ELPruning	ELPruning
Energy	Energy
Findbp	Search best hyperparameters for SA fitting (lambda and weight decay) by cross-validation
Formatting	Formatting
GELAObj	GELAObj
GradELA	GradELA
GradientDescent	Gradient descent estimation of model parameters
gStability	gstability
hb.paramgen	Randomly generate model parameters for heat-bath sampling
HeatBath	Heat-bath sampling of binary states
id2bin	id2bin: map a 64base characters to a binary vector
MinTippingPath	MinTippingPath
OnestepHBS	Perform one heat-bath update step
PCplot	PCplot:Scatter plot of community compositions colored by basin label
plotSAtest	plotSAtest: plot the results of SA fitting (Findbp output)
runSA	Stochastic approximation for parameter fitting
sa2params	Convert SA output to model parameter objects
saEndpoint	Extract endpoint parameters from runSA output
showDG	showDG: draw DisconnectivityGraph
showGELA3D	GELA3D: draw 3D plot of energy landscape
showIntrGraph	showIntrGraph: draw interaction matrix on a PCoA plot
showSSD	showSSD: draw stable state diagram
showSSD_ggplot	showSSD_ggplot: draw stable state diagram using ggplot
SSentropy	SSentropy
sstable	sstable
Stability	stability
SteepestDescent	SteepestDescent
tptable	tptable