Package: cocorresp 0.4-4

cocorresp: Co-Correspondence Analysis Methods

Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.

Authors:Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson. Function simpls based on simpls.fit by Ron Wehrens and Bjorn-Helge Mevik.

cocorresp_0.4-4.tar.gz
cocorresp_0.4-4.zip(r-4.5)cocorresp_0.4-4.zip(r-4.4)cocorresp_0.4-4.zip(r-4.3)
cocorresp_0.4-4.tgz(r-4.4-any)cocorresp_0.4-4.tgz(r-4.3-any)
cocorresp_0.4-4.tar.gz(r-4.5-noble)cocorresp_0.4-4.tar.gz(r-4.4-noble)
cocorresp_0.4-4.tgz(r-4.4-emscripten)cocorresp_0.4-4.tgz(r-4.3-emscripten)
cocorresp.pdf |cocorresp.html✨
cocorresp/json (API)

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

Peer review:

Bug tracker:https://github.com/gavinsimpson/cocorresp/issues

Datasets:
  • beetles - Carabid beetles and vascular plants in Dutch roadside verges
  • bryophyte - Bryophytes and vascular plants in Carpathian spring meadows
  • plants - Carabid beetles and vascular plants in Dutch roadside verges
  • vascular - Bryophytes and vascular plants in Carpathian spring meadows
  • verges - Carabid beetles and vascular plants in Dutch roadside verges

On CRAN:

5 exports 4 stars 1.77 score 8 dependencies 3 mentions 22 scripts 476 downloads

Last updated 7 months agofrom:f5b468970a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winNOTESep 17 2024
R-4.5-linuxNOTESep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:cocacoinertiacorAxiscrossvalrescale

Dependencies:clusterlatticeMASSMatrixmgcvnlmepermutevegan

Introduction to Co-correspondence Analysis

Gavin L. Simpson

Rendered fromcocorresp-intro.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2020-03-24
Started: 2016-02-28

Readme and manuals

Help Manual

Help pageTopics
Co-correspondence analysis ordination methods for community ecologycocorresp-package cocorresp
Carabid beetles and vascular plants in Dutch roadside vergesbeetles plants verges
Biplots of co-correspondence analysis modelsbiplot.predcoca biplot.symcoca
Bryophytes and vascular plants in Carpathian spring meadowsbryophyte vascular
Fit Co-Correspondence Analysis Ordination Modelscoca coca.default coca.formula print.predcoca print.symcoca
Co-inertia analysiscoinertia coinertia.default
Coinertia analysis with identity matricescoinertiaI
Correlation between ordination axescorAxis corAxis.default corAxis.symcoca
Cross-validation for predictive Co-Correspondence Analysis modelscrossval print.crossval print.summary.crossval summary.crossval
Fit an environmental vector or factor to a Co-CA ordinationenvfit.coca
Co-inertia analysisfitCoinertia print.fitCoinertia print.summary.fitCoinertia summary.fitCoinertia
Fitted values of a Symmetric Co-Correpsondence analysis model.fitted.symcoca print.fitted.symcoca
CoCA species loadingsloadings loadings.predcoca loadings.symcoca lodaings.default
Standardised chi-square residualsmcChi
Permutation test for predictive co-correspondence analysis modelspermutest.coca print.permutest.coca print.summary.permutest.coca summary.permutest.coca
Biplots for predictive co-correspondence analysisplot.predcoca
Plots for symmetric co-correspondence analysisplot.symcoca
Add points to a Co-CA plotpoints.coca
Rescales CoCA species scoresrescale rescale.default rescale.symcoca
Extract Model Residualsresid.symcoca
Standardised chi-square residualsscaleChi
Get Species or Site Scores from an Ordinationscores.predcoca scores.symcoca
Screeplot for symmetric co-correspondence analysisscreeplot.symcoca
Modified version of Sijmen de Jong's SIMPLSsimpls
Summarizing Co-CA Model Fitsprint.summary.predcoca print.summary.symcoca summary.predcoca summary.symcoca
Exctract CoCA model weightsweights.predcoca weights.symcoca