[Vegan-commits] r2796 - pkg/vegan/R

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2013-12-03 17:02:58 +0100 (Tue, 03 Dec 2013)
New Revision: 2796

Modified:
   pkg/vegan/R/anova.ccalist.R
   pkg/vegan/R/anovacca.R
   pkg/vegan/R/anovacca.byterm.R
Log:
adopt column header Variance/ChiSquare to ordination method

Modified: pkg/vegan/R/anova.ccalist.R
===================================================================
--- pkg/vegan/R/anova.ccalist.R	2013-12-03 15:39:14 UTC (rev 2795)
+++ pkg/vegan/R/anova.ccalist.R	2013-12-03 16:02:58 UTC (rev 2796)
@@ -72,13 +72,18 @@
     ## collect table
     table <- data.frame(resdf, resdev, c(NA, df),
                         c(NA,changedev), c(NA,fval), c(NA,pval))
-    dimnames(table) <- list(1L:nmodels, c("Resid. Df", "Res. Chisq", 
-                                          "Df", "Chisq", "F", "Pr(>F)"))
+    isRDA <- method != "cca"
+    dimnames(table) <- list(1L:nmodels,
+                            c("Res.Df",
+                              ifelse(isRDA,"Res.Variance", "Res.ChiSquare"), 
+                              "Df",
+                              ifelse(isRDA,"Variance","ChiSquare"),
+                                     "F", "Pr(>F)"))
     ## Collect header information
     formulae <- sapply(object, function(z) deparse(formula(z)))
     head <- paste0("Permutation tests for ", method, " under ",
-                  mods[[big]]$model, " model\nwith ", nperm,
-                   " permutations\n")
+                  mods[[big]]$model, " model\n",
+                   howHead(attr(permutations, "control")))
     topnote <- paste("Model ", format(1L:nmodels), ": ", formulae,
                      sep = "", collapse = "\n")
     structure(table, heading=c(head,topnote), class = c("anova", "data.frame"))

Modified: pkg/vegan/R/anovacca.R
===================================================================
--- pkg/vegan/R/anovacca.R	2013-12-03 15:39:14 UTC (rev 2795)
+++ pkg/vegan/R/anovacca.R	2013-12-03 16:02:58 UTC (rev 2796)
@@ -79,7 +79,7 @@
     Pval <- c(Pval, NA)
     table <- data.frame(tst$df, tst$chi, Fval, Pval)
     is.rda <- inherits(object, "rda")
-    colnames(table) <- c("Df", ifelse(is.rda, "Var", "Chisq"), 
+    colnames(table) <- c("Df", ifelse(is.rda, "Variance", "ChiSquare"), 
                          "F", "Pr(>F)")
     head <- paste0("Permutation test for ", tst$method, " under ", 
                   tst$model, " model\n", howHead(control))

Modified: pkg/vegan/R/anovacca.byterm.R
===================================================================
--- pkg/vegan/R/anovacca.byterm.R	2013-12-03 15:39:14 UTC (rev 2795)
+++ pkg/vegan/R/anovacca.byterm.R	2013-12-03 16:02:58 UTC (rev 2796)
@@ -31,7 +31,9 @@
                       c(sol[-1,4], sol[ntrm+1,2]),
                       c(sol[-1,5], NA),
                       c(sol[-1,6], NA))
-    colnames(out) <- c("Df", "Chisq", "F", "Pr(>F)")
+    isRDA <- inherits(object, "rda")
+    colnames(out) <- c("Df", ifelse(isRDA, "Variance", "ChiSquare"),
+                       "F", "Pr(>F)")
     rownames(out) <- c(trmlab, "Residual")
     head <- paste0("Permutation test for ", object$method, " under ",
                    model, " model\n",
@@ -92,7 +94,9 @@
     ## Collect results to anova data.frame
     out <- data.frame(c(Df, dfbig), c(Chisq, chibig),
                       c(Fstat, NA), c(Pval, NA))
-    colnames(out) <- c("Df", "Chisq", "F", "Pr(>F)")
+    isRDA <- inherits(object, "rda")
+    colnames(out) <- c("Df", ifelse(isRDA, "Variance", "ChiSquare"),
+                       "F", "Pr(>F)")
     rownames(out) <- c(trmlab, "Residual")
     head <- paste0("Permutation test for ", object$method, " under ",
                    mods[[1]]$model, " model\n",
@@ -153,7 +157,9 @@
     out <- data.frame(c(Df, resdf), c(eig, object$CA$tot.chi),
                       c(Fstat, NA), c(Pvals,NA))
     rownames(out) <- c(names(eig), "Residual")
-    colnames(out) <- c("Df", "Chisq", "F", "Pr(>F)")
+    isRDA <- inherits(object, "rda")
+    colnames(out) <- c("Df", ifelse(isRDA, "Variance", "ChiSquare"),
+                       "F", "Pr(>F)")
     head <- paste0("Permutation test for ", object$method, " under ",
                    model, " model\n",
                    "Marginal tests for axes\n",