cocorresp: Co-correspondence analysis methods

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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 communitities.

Author
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 (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Date of publication
2013-12-12 23:11:44
Maintainer
Gavin L. Simpson <ucfagls@gmail.com>
License
GPL-2
Version
0.2-1
URLs

View on R-Forge

Man pages

beetles
Carabid beetles and vascular plants in Dutch roadside verges
bryophyte
Bryophytes and vascular plants in Carpathian spring meadows
coca
Fit Co-Correspondence Analysis Ordination Models
cocorresp-internal
Internal cocorresp Functions
cocorresp-package
Co-correspondence analysis ordination methods for community...
coinertia
Co-inertia analysis
coinertiaI
Coinertia analysis with identity matrices
corAxis
Correlation between ordination axes
crossval
Cross-validation for predictive Co-Correspondence Analysis...
envfit.coca
Fit an environmental vector or factor to a Co-CA ordination
fitCoinertia
Co-inertia analysis
fitted.symcoca
Fitted values of a Symmetric Co-Correpsondence analysis...
mcChi
Standardised chi-square residuals
permutest.coca
Permutation test for predictive co-correspondence analysis...
plot.predcoca
Biplots for predictive co-correspondence analysis
plot.symcoca
Biplots for symmetric co-correspondence analysis
points.coca
Add points to a Co-CA plot
rescale
Rescales CoCA species scores
resid.symcoca
Extract Model Residuals
scaleChi
Standardised chi-square residuals
scores.predcoca
Get Species or Site Scores from an Ordination
simpls
Modified version of Sijmen de Jong's SIMPLS
summary.predcoca
Summarizing Co-CA Model Fits
weights
Exctract CoCA model weights

Files in this package

cocorresp/DESCRIPTION
cocorresp/NAMESPACE
cocorresp/R
cocorresp/R/coca.R
cocorresp/R/coca.default.R
cocorresp/R/coca.formula.R
cocorresp/R/coinertia.R
cocorresp/R/coinertiaI.R
cocorresp/R/corAxis.R
cocorresp/R/crossval.R
cocorresp/R/eigenvals.coca.R
cocorresp/R/envfit.coca.R
cocorresp/R/fitCoinertia.R
cocorresp/R/fitted.symcoca.R
cocorresp/R/mcChi.R
cocorresp/R/permutest.coca.R
cocorresp/R/plot.predcoca.R
cocorresp/R/plot.symcoca.R
cocorresp/R/points.coca.R
cocorresp/R/predcoca.eigen.R
cocorresp/R/predcoca.simpls.R
cocorresp/R/print.coinertia.R
cocorresp/R/print.crossval.R
cocorresp/R/print.fitted.symcoca.R
cocorresp/R/print.permutest.coca.R
cocorresp/R/print.predcoca.R
cocorresp/R/print.summary.coinertia.R
cocorresp/R/print.summary.crossval.R
cocorresp/R/print.summary.permutest.coca.R
cocorresp/R/print.summary.predcoca.R
cocorresp/R/print.summary.symcoca.R
cocorresp/R/print.symcoca.R
cocorresp/R/rescale.R
cocorresp/R/rescale.default.R
cocorresp/R/rescale.symcoca.R
cocorresp/R/resid.symcoca.R
cocorresp/R/scaleChi.R
cocorresp/R/scores.predcoca.R
cocorresp/R/scores.symcoca.R
cocorresp/R/simpls.R
cocorresp/R/summary.coinertia.R
cocorresp/R/summary.crossval.R
cocorresp/R/summary.permutest.coca.R
cocorresp/R/summary.predcoca.R
cocorresp/R/summary.symcoca.R
cocorresp/R/symcoca.R
cocorresp/R/weights.R
cocorresp/data
cocorresp/data/beetles.rda
cocorresp/data/bryophyte.rda
cocorresp/data/plants.rda
cocorresp/data/vascular.rda
cocorresp/data/verges.rda
cocorresp/inst
cocorresp/inst/CITATION
cocorresp/inst/ChangeLog
cocorresp/inst/INDEX
cocorresp/man
cocorresp/man/beetles.Rd
cocorresp/man/bryophyte.Rd
cocorresp/man/coca.Rd
cocorresp/man/cocorresp-internal.Rd
cocorresp/man/cocorresp-package.Rd
cocorresp/man/coinertia.Rd
cocorresp/man/coinertiaI.Rd
cocorresp/man/corAxis.Rd
cocorresp/man/crossval.Rd
cocorresp/man/envfit.coca.Rd
cocorresp/man/fitCoinertia.Rd
cocorresp/man/fitted.symcoca.Rd
cocorresp/man/mcChi.Rd
cocorresp/man/permutest.coca.Rd
cocorresp/man/plot.predcoca.Rd
cocorresp/man/plot.symcoca.Rd
cocorresp/man/points.coca.Rd
cocorresp/man/rescale.Rd
cocorresp/man/resid.symcoca.Rd
cocorresp/man/scaleChi.Rd
cocorresp/man/scores.predcoca.Rd
cocorresp/man/simpls.Rd
cocorresp/man/summary.predcoca.Rd
cocorresp/man/weights.Rd
cocorresp/tests
cocorresp/tests/Examples
cocorresp/tests/Examples/cocorresp-Ex.Rout.save