Package: ELAplus 1.0.2

Kenta Suzuki

ELAplus: Energy Landscape Analysis for Ecological Communities

Energy landscape analysis (ELA) is a systematic method for analyzing an energy landscape represented as a weighted network. This R package is especially designed to analyze ecological dynamics, i.e., transitions in community compositions. For details of the analysis framework, please visit Suzuki K et al. (2021) <doi:10.1002/ecm.1469>.

Authors:Kenta Suzuki [aut, cre, cph], Sotaro Takano [aut], Hiroaki Fujita [aut], Zeus Sato [ctb], Fumihiko Ayabe [ctb]

ELAplus_1.0.2.tar.gz
ELAplus_1.0.2.tar.gz(r-4.7-arm64)ELAplus_1.0.2.tar.gz(r-4.7-x86_64)ELAplus_1.0.2.tar.gz(r-4.6-arm64)ELAplus_1.0.2.tar.gz(r-4.6-x86_64)
ELAplus_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ELAplus/json (API)

# Install 'ELAplus' in R:
install.packages('ELAplus', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppopenmp

2.00 score 35 exports 41 dependencies

Last updated from:f75446e862. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK202
linux-devel-x86_64OK203
source / vignettesOK278
linux-release-arm64OK198
linux-release-x86_64OK212
wasm-releaseOK175

Exports:Bibin2idbootstrap_ELAbootstrap_SAdeltaE_histogramDisconnectivityGraphELAELPruningEnergyFindbpFormattingGELAObjGradELAGradientDescentgStabilityhb.paramgenHeatBathid2binMinTippingPathOnestepHBSPCplotplotSAtestrunSAsa2paramssaEndpointshowDGshowGELA3DshowIntrGraphshowSSDshowSSD_ggplotSSentropysstableStabilitySteepestDescenttptable

Dependencies:clicodetoolscpp11data.tabledoParalleldplyrfarverforeachgenericsggplot2gluegtablegtoolsigraphisobanditeratorslabelinglatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringdiststringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

An introduction to ELAplus: Energy Landscape Analysis

Sotaro Takano, Kenta Suzuki, Hiroaki Fujita

Rendered fromELAplus-intro.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-05-28
Started: 2026-05-28

Readme and manuals

Help Manual

Help pageTopics
Energy Landscape Analysis for Ecological CommunitiesELAplus-package ELAplus
Abundance table for 16 taxa across 256 samplesbaseabtable
Environmental metadata for 256 samplesbasemetadata
BiBi
bin2id: map a binary vector to a 64base charactersbin2id
Energy landscape analysis with bootstrap resampled SA resultsbootstrap_ELA
Parameter fitting with bootstrap sampling of datasetsbootstrap_SA
Plot histograms of bootstrap deltaE valuesdeltaE_histogram
DisconnectivityGraph: Generate a disconnectivity graphDisconnectivityGraph
Energy landscape analysis in parallel modeELA
ELPruningELPruning
EnergyEnergy
Search best hyperparameters for SA fitting (lambda and weight decay) by cross-validationFindbp
FormattingFormatting
GELAObjGELAObj
GradELAGradELA
Gradient descent estimation of model parametersGradientDescent
gstabilitygStability
Randomly generate model parameters for heat-bath samplinghb.paramgen
Heat-bath sampling of binary statesHeatBath
id2bin: map a 64base characters to a binary vectorid2bin
MinTippingPathMinTippingPath
Perform one heat-bath update stepOnestepHBS
PCplot:Scatter plot of community compositions colored by basin labelPCplot
plotSAtest: plot the results of SA fitting (Findbp output)plotSAtest
Stochastic approximation for parameter fittingrunSA
Convert SA output to model parameter objectssa2params
Extract endpoint parameters from runSA outputsaEndpoint
showDG: draw DisconnectivityGraphshowDG
GELA3D: draw 3D plot of energy landscapeshowGELA3D
showIntrGraph: draw interaction matrix on a PCoA plotshowIntrGraph
showSSD: draw stable state diagramshowSSD
showSSD_ggplot: draw stable state diagram using ggplotshowSSD_ggplot
SSentropySSentropy
sstablesstable
stabilityStability
SteepestDescentSteepestDescent
tptabletptable