Package: EcotoneFinder 0.2.3

Antoine Bagnaro

EcotoneFinder: Characterising and Locating Ecotones and Communities

Analytical methods to locate and characterise ecotones, ecosystems and environmental patchiness along ecological gradients. Methods are implemented for isolated sampling or for space/time series. It includes Detrended Correspondence Analysis (Hill & Gauch (1980) <doi:10.1007/BF00048870>), fuzzy clustering (De Cáceres et al. (2010) <doi:10.1080/01621459.1963.10500845>), biodiversity indices (Jost (2006) <doi:10.1111/j.2006.0030-1299.14714.x>), and network analyses (Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>) - as well as tools to explore the number of clusters in the data. Functions to produce synthetic ecological datasets are also provided.

Authors:Antoine Bagnaro

EcotoneFinder_0.2.3.tar.gz
EcotoneFinder_0.2.3.tar.gz(r-4.5-noble)EcotoneFinder_0.2.3.tar.gz(r-4.4-noble)
EcotoneFinder_0.2.3.tgz(r-4.4-emscripten)EcotoneFinder_0.2.3.tgz(r-4.3-emscripten)
EcotoneFinder.pdf |EcotoneFinder.html
EcotoneFinder/json (API)

# Install 'EcotoneFinder' in R:
install.packages('EcotoneFinder', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

1.00 score 1 scripts 214 downloads 29 exports 99 dependencies

Last updated 4 years agofrom:d5efe402fb. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 12 2024
R-4.5-linuxNOTEOct 12 2024

Exports:arrange.varscbindnaclustergramclustergram.cmeansclustergram.cmeans.Indclustergram.kmeansclustergram.plot.matlinesclustergram.vegclustclustergram.vegclust.IndclustergramIndCommunityColorcurveNoPlotDistEcoEcotoneFinderEcotoneFinderSeriesExtractCentroidFuzzyIndice.plot.matlinesggEcotoneNetworkCommunityNetworkEcoNetworkEcoSeriesplotEcoplotEcotoneplotEnvplotSloperbindnaSlopeSyntheticDataSyntheticDataSeries

Dependencies:abindbackportsbase64encbslibcachemcheckmateclasscliclustercolorspacecorpcorcorrplotcpp11data.tabledigeste1071evaluatefansifarverfastmapfdrtoolfontawesomeforeignFormulafsggplot2glassoglueGPArotationgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglatticelavaanlifecyclemagrittrMASSMatrixmemoisemgcvmimemnormtmunsellnlmennetnumDerivpbapplypbivnormpermutephilentropypillarpkgconfigplyrpngpoormanproxypsychpurrrqgraphquadprogR6rappdirsRColorBrewerRcppreshapereshape2rlangrmarkdownRmiscrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsveganvegclustviridisviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Re-ordering columns in dataframes:arrange.vars
qpcR cbind.na method.cbindna
Clustergram base functionclustergram
cmeans function for clustergramclustergram.cmeans
cmeans clustering with fuzzy indices computation for clustergramclustergram.cmeans.Ind
Type function that clustergram takes for clustering.clustergram.kmeans
Plot function for clustergramclustergram.plot.matlines
Vegclust function for clustergramclustergram.vegclust
Vegclust clustering with fuzzy indices computation for clustergramclustergram.vegclust.Ind
Clustergram with fuzzy indices plotclustergramInd
Tool to assign color to species distribution plots given fuzzy clustering results.CommunityColor
Adaptation of the curve function (without plot).curveNoPlot
Tools for internal data structure explorationDistEco
Wraper function to perform ecological gradient analysisEcotoneFinder
Extension of EcotoneFinder for space/time seriesEcotoneFinderSeries
Visualisation of fuzzy centroids:ExtractCentroid
Plot function for fuzzy indices with clustergram.FuzzyIndice.plot.matlines
GGplot method for EcotoneFinderggEcotone
Perform Spinglass algorythm and find networks communitiesNetworkCommunity
Networks for ecotones and communitiesNetworkEco
Networkeco for data seriesNetworkEcoSeries
Plotting component for EcotoneFinderplotEco
Plot method for EcotoneFinderplotEcotone
Plotting component for EcotoneFinder when run on environmental dataplotEnv
Plotting component for SlopeplotSlope
qpcR rbind.na method.rbindna
Method to calculate the derivative of irregular functions:Slope
Create synthetic gaussian-shaped species abundance dataSyntheticData
Synthetic data for Space/Time seriesSyntheticDataSeries