Merge branch 'issue-#610'

R/RsquareAdj.R

@@ -41,7 +41,9 @@
     function (x, permutations = 1000, ...)
 {
     r2 <- x$CCA$tot.chi / x$tot.chi
-    if (is.null(x$pCCA)) {
+    if (df.residual(x) == 0) {
+        radj <- NA
+    } else if (is.null(x$pCCA)) {
         p <- permutest(x, permutations, ...)
         radj <- 1 - ((1 - r2) / (1 - mean(p$num / x$tot.chi)))
     } else {

R/ordConstrained.R

@@ -416,6 +416,9 @@
     }
     ## Residuals
     resid <- ordResid(Y)
+    if (resid$rank < 1)
+        warning("overfitted model with no unconstrained component",
+                call. = FALSE)
     ## return a CCA object
     out <- c(head,
              call = match.call(),

R/ordiR2step.R

@@ -34,7 +34,7 @@
         R2.all <- list(adj.r.squared = NA)
     ## Check that the full model can be evaluated
     if (is.na(R2.all$adj.r.squared) && R2scope)
-        stop("the upper scope cannot be fitted (too many terms?)")
+        stop("R2 cannot be adjusted in upper scope (too many terms?)")
     R2.all <- R2.all$adj.r.squared
     ## Collect data to anotab returned as the 'anova' object
     anotab <-  list()
@@ -58,7 +58,7 @@
             fla <- paste(". ~ .", names(R2.adds[trm]))
             R2.tmp <- RsquareAdj(update(object, fla),
                                  permutations = R2permutations, ...)$adj.r.squared
-            if (!length(R2.tmp))
+            if (!length(R2.tmp) || is.na(R2.tmp))
                 R2.tmp <- 0
             R2.adds[trm] <- R2.tmp
         }

man/ordistep.Rd

@@ -107,16 +107,17 @@ ordiR2step(object, scope, Pin = 0.05, R2scope = TRUE,
   step, and stopping when the adjusted \eqn{R^2}{R2} starts to decrease,
   or the adjusted \eqn{R^2}{R2} of the \code{scope} is exceeded, or the
   selected permutation \eqn{P}-value is exceeded (Blanchet et
-  al. 2008). The second criterion is ignored with option
-  \code{R2scope = FALSE}, and the third criterion can be ignored setting
-  \code{Pin = 1} (or higher).
-  The function cannot be used if adjusted \eqn{R^2}{R2}
-  cannot be calculated, including partial models.  If the number of
-  predictors is higher than the number of observations, adjusted
-  \eqn{R^2}{R2} is also unavailable, but such models can be analysed
-  with \code{R2scope = FALSE}.  The \eqn{R^2}{R2} of \code{\link{cca}}
-  is based on simulations (see \code{\link{RsquareAdj}}) and different
-  runs of \code{ordiR2step} can give different results.
+  al. 2008). The second criterion is ignored with option \code{R2scope =
+  FALSE}, and the third criterion can be ignored setting \code{Pin = 1}
+  (or higher).  The function cannot be used if adjusted \eqn{R^2}{R2}
+  cannot be calculated. If the number of predictors is higher than the
+  number of observations, adjusted \eqn{R^2}{R2} is also unavailable.
+  Such models can be analysed with \code{R2scope = FALSE}, but the
+  variable selection will stop if models become overfitted and adjusted
+  \eqn{R^2}{R2} cannot be calculated, and the adjusted \eqn{R^2}{R2}
+  will be reported as zero. The \eqn{R^2}{R2} of \code{\link{cca}} is
+  based on simulations (see \code{\link{RsquareAdj}}) and different runs
+  of \code{ordiR2step} can give different results.
 
   Functions \code{ordistep} (based on \eqn{P} values) and \code{ordiR2step}
   (based on adjusted \eqn{R^2}{R2} and hence on eigenvalues) can select