# Energy Landscape Analysis for Ecological Communities

## 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