Bi                      Bi
DisconnectivityGraph    DisconnectivityGraph: Generate a
                        disconnectivity graph
ELA                     Energy landscape analysis in parallel mode
ELAplus-package         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
HeatBath                Heat-bath sampling of binary states
MinTippingPath          MinTippingPath
OnestepHBS              Perform one heat-bath update step
PCplot                  PCplot:Scatter plot of community compositions
                        colored by basin label
SSentropy               SSentropy
Stability               stability
SteepestDescent         SteepestDescent
baseabtable             Abundance table for 16 taxa across 256 samples
basemetadata            Environmental metadata for 256 samples
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
gStability              gstability
hb.paramgen             Randomly generate model parameters for
                        heat-bath sampling
id2bin                  id2bin: map a 64base characters to a binary
                        vector
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
sstable                 sstable
tptable                 tptable
