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vegan 2.7.0 splits scores and summary into separate functions #2

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vegan 2.7.0 splits scores and summary into separate functions #2

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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@ importFrom(tidyr,gather)
importFrom(tidyr,separate)
importFrom(tidyr,spread)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
Expand All @@ -147,6 +148,7 @@ importFrom(vegan,decostand)
importFrom(vegan,estimateR)
importFrom(vegan,metaMDS)
importFrom(vegan,rda)
importFrom(vegan,scores)
importFrom(vegan,specnumber)
importFrom(vegan,vegdist)
importFrom(vegan,vif.cca)
9 changes: 7 additions & 2 deletions R/tbRDA_analysis.R
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Expand Up @@ -14,7 +14,8 @@
#' @export
#'
#' @importFrom stats na.omit
#' @importFrom vegan decostand decorana rda vif.cca anova.cca RsquareAdj
#' @importFrom utils packageVersion
#' @importFrom vegan decostand decorana rda vif.cca anova.cca RsquareAdj scores
#'
#' @examples
#' ### Data preparation ###
Expand Down Expand Up @@ -115,7 +116,11 @@ tbRDA_analysis<-function(otudata,envdata,collinearity,perm.test=TRUE){
Diagnostic<-vif.cca(otu.tab.1)
Diagnostic=Diagnostic[!is.na(Diagnostic)]
i=i-1}}}else if (collinearity==FALSE){} else{stop("Please choose TRUE/FALSE on collinearity");return()}
summaryrda<-summary(otu.tab.1)
if (packageVersion("vegan") < "2.7.0") {
summaryrda<-summary(otu.tab.1)
} else { # summary and scores are separated in modern vegan
summaryrda<-c(summary(otu.tab.1), scores(otu.tab.1))
}
if(perm.test==TRUE){
message("###Global permutation test###","\n")
print(anova.cca(otu.tab.1))
Expand Down