Revert "use natural way of calculationg RsquareAdj for cca: conflicts…

… varpart"

This reverts commit 6ac3365.

see github issue #295

R/RsquareAdj.R

@@ -33,20 +33,30 @@
     list(r.squared = R2, adj.r.squared = radj)
 }
 
-## cca result: R2_adj calculation for partial models differs from
-## varpart(), where it is assessed as difference of R2_adj values for
-## conditions and constraints. Here we use difference of unadjusted R2
-## values, and adjust that difference.
+## cca result: RsquareAdj is calculated similarly as in
+## varpart(). This is similar "semipartial" model as for rda() and
+## found as a difference of R2-adj values of combined model with
+## constraints + conditions and only conditions.
 `RsquareAdj.cca` <-
     function (x, permutations = 1000, ...)
 {
     r2 <- x$CCA$tot.chi / x$tot.chi
-    ## model='direct' makes a difference in pCCA: it guarantees that
-    ## dependent data are permuted in the same way in the partial and
-    ## constrained components so that we can take their difference for
-    ## the correction term.
-    p <- permutest(x, permutations, model = "direct")
-    radj <- 1 - ((1 - r2) / (1 - mean(p$num) / x$tot.chi))
+    if (is.null(x$pCCA)) {
+        p <- permutest(x, permutations, ...)
+        radj <- 1 - ((1 - r2) / (1 - mean(p$num / x$tot.chi)))
+    } else {
+        p <- getPermuteMatrix(permutations, nobs(x))
+        Y <- ordiYbar(x, "initial")
+        r2tot <- (x$pCCA$tot.chi + x$CCA$tot.chi) / x$tot.chi
+        r2null <- mean(sapply(seq_len(nrow(p)), function(i)
+            sum(qr.fitted(x$CCA$QR, Y[p[i,],])^2)))
+        r2tot <- 1 - ((1-r2tot)/(1-r2null/x$tot.chi))
+        r2p <- x$pCCA$tot.chi / x$tot.chi
+        r2null <- mean(sapply(seq_len(nrow(p)), function(i)
+            sum(qr.fitted(x$pCCA$QR, Y[p[i,],])^2)))
+        r2p <- 1 - ((1-r2p)/(1-r2null/x$tot.chi))
+        radj <- r2tot - r2p
+    }
     list(r.squared = r2, adj.r.squared = radj)
 }
 

man/RsquareAdj.Rd

@@ -32,9 +32,8 @@ Adjusted R-square
   R-squared for a cca. The permutations can be calculated in parallel by
   specifying the number of cores which is passed to \code{\link{permutest}}}
 
-  \item{\dots}{ Other arguments (ignored) except in the \code{cca}
-    method, where these are passed to \code{\link{permutest.cca}}.
-  }
+  \item{\dots}{ Other arguments (ignored) except in the case of cca in 
+  which these arguments are passed to \code{\link{permutest}}.} 
 }
 
 \details{ The default method finds the adjusted \eqn{R^2}{R-squared}
@@ -50,7 +49,9 @@ Adjusted R-square
   \code{\link{glm}}.
 
   The adjusted, \eqn{R^2}{R-squared} of \code{cca} is computed using a
-  permutation approach developed by Peres-Neto et al. (2006).
+  permutation approach developed by Peres-Neto et al. (2006). By
+  default 1000 permutations are used. Adjusted \eqn{R^2}{R-squared} is
+  not calculated for partial CCA.
 
 }