From f226518a7a61e742b51848722ef225bb667af224 Mon Sep 17 00:00:00 2001
From: Jari Oksanen <jhoksane@gmail.com>
Date: Tue, 26 Nov 2024 11:45:10 +0200
Subject: [PATCH] vegan 2.7.0 splits scores and summary into separate functions

This fix works both with the old vegan code and new vegan code
scheduled for the next major CRAN release.
---
 NAMESPACE          | 2 ++
 R/tbRDA_analysis.R | 9 +++++++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 37f7b8e..1ed2d9c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -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)
@@ -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)
diff --git a/R/tbRDA_analysis.R b/R/tbRDA_analysis.R
index bf75606..2ae8593 100644
--- a/R/tbRDA_analysis.R
+++ b/R/tbRDA_analysis.R
@@ -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 ###
@@ -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))