From 07f1857f9d7807b43daecaa17a6b0d640524c675 Mon Sep 17 00:00:00 2001
From: Jari Oksanen <jari.oksanen@oulu.fi>
Date: Tue, 16 Aug 2016 21:45:06 +0300
Subject: [PATCH] goodness.cca failed for rank=1 component

reported as issue #189 in github
---
 R/goodness.cca.R | 8 ++++++--
 R/inertcomp.R    | 6 ++++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/goodness.cca.R b/R/goodness.cca.R
index cf968471c..c21eb2fc3 100644
--- a/R/goodness.cca.R
+++ b/R/goodness.cca.R
@@ -33,8 +33,12 @@
         else
             pCCA <- diag(crossprod(pCCA))/nr
     }
-    CA <- t(apply(diag(w) %*% CA^2 %*% diag(eig), 1,
-                  cumsum))
+    CA <- t(apply(
+        diag(w, length(w)) %*% CA^2 %*% diag(eig, length(eig)),
+        1, cumsum))
+    ## rank=1 solutions comes out transposed: back transpose
+    if (length(eig) == 1)
+        CA <- t(CA)
     totals <- inertcomp(object, display = display)
     comps <- colnames(totals)
     if (statistic == "explained") {
diff --git a/R/inertcomp.R b/R/inertcomp.R
index e6591d3ae..c3acc1d99 100644
--- a/R/inertcomp.R
+++ b/R/inertcomp.R
@@ -40,9 +40,11 @@
             pCCA <- diag(crossprod(pCCA))/nr
     }
     if (!is.null(CCA))
-        CCA <- rowSums(diag(w) %*% CCA^2 %*% diag(object$CCA$eig))
+        CCA <- rowSums(diag(w, length(w)) %*% CCA^2 %*%
+                           diag(object$CCA$eig, length(object$CCA$eig)))
     if (!is.null(CA))
-        CA <- rowSums(diag(w) %*% CA^2 %*% diag(object$CA$eig))
+        CA <- rowSums(diag(w, length(w)) %*% CA^2 %*%
+                          diag(object$CA$eig, length(object$CA$eig)))
     out <- cbind(pCCA, CCA, CA)
     if (statistic == "distance" && !proportional) {
         w <- weights(object, display = display)