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EcotoneFinder (version 0.2.3)

Characterising and Locating Ecotones and Communities

Description

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) ), fuzzy clustering (De Cceres et al. (2010) ), biodiversity indices (Jost (2006) ), and network analyses (Epskamp et al. (2012) ) - as well as tools to explore the number of clusters in the data. Functions to produce synthetic ecological datasets are also provided.

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Version

Install

install.packages('EcotoneFinder')

Monthly Downloads

270

Version

0.2.3

License

MIT + file LICENSE

Maintainer

Antoine Bagnaro

Last Published

February 16th, 2021

Functions in EcotoneFinder (0.2.3)

EcotoneFinder

Wraper function to perform ecological gradient analysis
DistEco

Tools for internal data structure exploration
CommunityColor

Tool to assign color to species distribution plots given fuzzy clustering results.
ExtractCentroid

Visualisation of fuzzy centroids:
NetworkEcoSeries

Networkeco for data series
NetworkCommunity

Perform Spinglass algorythm and find networks communities
Slope

Method to calculate the derivative of irregular functions:
FuzzyIndice.plot.matlines

Plot function for fuzzy indices with clustergram.
EcotoneFinderSeries

Extension of EcotoneFinder for space/time series
clustergram.cmeans

cmeans function for clustergram
plotEco

Plotting component for EcotoneFinder
plotEcotone

Plot method for EcotoneFinder
SyntheticDataSeries

Synthetic data for Space/Time series
SyntheticData

Create synthetic gaussian-shaped species abundance data
curveNoPlot

Adaptation of the curve function (without plot).
ggEcotone

GGplot method for EcotoneFinder
clustergram.plot.matlines

Plot function for clustergram
arrange.vars

Re-ordering columns in dataframes:
cbindna

qpcR cbind.na method.
NetworkEco

Networks for ecotones and communities
clustergram.cmeans.Ind

cmeans clustering with fuzzy indices computation for clustergram
clustergram

Clustergram base function
rbindna

qpcR rbind.na method.
clustergram.kmeans

Type function that clustergram takes for clustering.
clustergram.vegclust

Vegclust function for clustergram
clustergramInd

Clustergram with fuzzy indices plot
plotEnv

Plotting component for EcotoneFinder when run on environmental data
clustergram.vegclust.Ind

Vegclust clustering with fuzzy indices computation for clustergram
plotSlope

Plotting component for Slope