[Vegan-commits] r2503 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2013-05-24 09:02:13 +0200 (Fri, 24 May 2013)
New Revision: 2503

Modified:
   pkg/vegan/R/bioenv.default.R
   pkg/vegan/inst/ChangeLog
Log:
bioenv passes ... to cor() like documented

Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R	2013-05-13 07:44:33 UTC (rev 2502)
+++ pkg/vegan/R/bioenv.default.R	2013-05-24 07:02:13 UTC (rev 2503)
@@ -10,14 +10,14 @@
     if (any(sapply(env, is.factor)) && metric != "gower")
         stop("you have factors in 'env': only 'metric = \"gower\"' is allowed")
     if (is.null(partial)) {
-        corfun <- function(dx, dy, dz, method) {
-            cor(dx, dy, method=method)
+        corfun <- function(dx, dy, dz, method, ...) {
+            cor(dx, dy, method=method, ...)
         }
     } else {
-        corfun <- function(dx, dy, dz, method) {
-            rxy <- cor(dx, dy, method=method)
-            rxz <- cor(dx, dz, method=method)
-            ryz <- cor(dy, dz, method=method)
+        corfun <- function(dx, dy, dz, method, ...) {
+            rxy <- cor(dx, dy, method=method, ...)
+            rxz <- cor(dx, dz, method=method, ...)
+            ryz <- cor(dy, dz, method=method, ...)
             (rxy - rxz*ryz)/sqrt(1-rxz*rxz)/sqrt(1-ryz*ryz)
         }
     }
@@ -103,17 +103,17 @@
                 est <- unlist(mclapply(1:nrow(sets), function(j)
                                        corfun(comdis,
                                               distfun(x[,sets[j,],drop = FALSE]),
-                                              partial, method = method),
+                                              partial, method = method, ...),
                                        mc.cores = parallel))
             } else {
                 est <- parSapply(parallel, 1:nrow(sets), function(j)
                                   corfun(comdis, distfun(x[,sets[j,],drop = FALSE]),
-                                         partial, method = method))
+                                         partial, method = method, ...))
             }
         } else {
             est <- sapply(1:nrow(sets), function(j) 
                           corfun(comdis, distfun(x[,sets[j,], drop=FALSE ]),
-                                 partial, method = method))
+                                 partial, method = method, ...))
         }
         best[[i]] <- list(best = sets[which.max(est), ], est = max(est))
         if (trace) {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-05-13 07:44:33 UTC (rev 2502)
+++ pkg/vegan/inst/ChangeLog	2013-05-24 07:02:13 UTC (rev 2503)
@@ -11,11 +11,12 @@
 	also handle factor variables. This involves adding internal
 	function veganMahatrans() for Mahalanobis transformation.  The
 	change was triggered by a recent email by Lydia Beaudrot (UC
-	Davis) to implement Mahalanobis distances, and in the same I
-	also implemented Robby Marotte's suggestion of using Gower
-	distances (vegan Forum item in R-Forge in July 2012). The output
-	is changed to show the 'metric' and the name of the 'method' is
-	fully expanded. No more fails if 'upto' is too large.
+	Davis) to implement Mahalanobis distances, and in the same I also
+	implemented Robby Marotte's suggestion of using Gower distances
+	(vegan Forum item in R-Forge in July 2012). The output is changed
+	to show the 'metric' and the name of the 'method' is fully
+	expanded. No more fails if 'upto' is too large. Passes "..." to
+	cor() like documented, but never done.
 
 	* rankindex: can now use Mahalanobis or Manhattan
 	distances. Scales automatically gradient variables to unit