DESCRIPTION

Package: dcCA
Type: Package
Title: Double Constrained Correspondence Analysis (dc-CA) For Trait-Environment Analysis in Ecology
Version: 1.0.9
Authors@R: person(given ="Cajo J.F", family = "ter Braak", email="cajo.terbraak@wur.nl", 
   role=c("aut","cre"), comment=c(ORCID="0000-0002-0414-8745"))
Maintainer: Cajo J.F. ter Braak <cajo.terbraak@wur.nl>
Description:  
   This repository has been closed and continues under a new repository with
   the name douconca (double constrained correspondence analysis). 
   The names dcca,DCCA and dcCA refer to different methods and packages. The new name douconca is hopefully unique.
   dcCA analyzes multi-trait multi-environment ecological data by
   double constrained correspondence analysis (ter Braak et al. 2018) using \code{vegan}, \code{ade4} and native R code.
   Throughout the two step algorithm of ter Braak et al. (2018) is used. This algorithm
   combines and extends community- (sample-) and species-level analyses, i.e.
   the usual community weigthed means (CWM)-based regression analysis and the
   species-level analysis of species-niche centroids (SNC)-based regression analysis.
   The two steps use \code{\link[vegan]{cca}} to regress the abundance data on to the traits
   and \code{\link[vegan]{rda}} to regress the CWM of the orthonormalized traits on to the environemtal predictors.
   The abundance data are divided by the sample total
   (i.e. 'closed') in the vegan-based version. This
   has the advantage that this multivariate analysis corresponds with an unweighted (multi-trait)
   community-level analysis, instead of being weighted.
   The current vegan-based analysis is efficient for sample-based permutation tests but slow or
   -not yet available- for species-based permutation tests.
   The technical reason for the closure, is that \code{vegan} \code{\link[vegan]{rda}} cannot do a weighted analysis.
   The main user function is \code{\link{dcCA}} .
   The easiest example is the code demo \code{dune}.
URL: https://doi.org/10.1007/s10651-017-0395-x
BugReports: https://github.com/CajoterBraak/dcCA/issues
Depends: R (>= 3.5.0), stats
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: vegan, permute, ggplot2, gridExtra, ggrepel
RoxygenNote: 7.3.0
NeedsCompilation: no
Packaged: 2024-01-17 15:15:02 UTC; braak008