[Vegan-commits] r2268 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2012-09-04 06:25:12 +0200 (Tue, 04 Sep 2012)
New Revision: 2268

Modified:
   pkg/vegan/R/mantel.R
   pkg/vegan/R/mantel.partial.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/mantel.Rd
Log:
mantel & mantel.partial gained arg na.rm = FALSE

Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R	2012-09-03 18:42:46 UTC (rev 2267)
+++ pkg/vegan/R/mantel.R	2012-09-04 04:25:12 UTC (rev 2268)
@@ -1,10 +1,15 @@
 `mantel` <-
   function (xdis, ydis, method = "pearson", permutations = 999, 
-            strata, parallel = getOption("mc.cores")) 
+            strata, na.rm = FALSE, parallel = getOption("mc.cores")) 
 {
     xdis <- as.dist(xdis)
     ydis <- as.vector(as.dist(ydis))
-    statistic <- cor(as.vector(xdis), ydis, method = method)
+    ## Handle missing values
+    if (na.rm)
+        use <- "complete.obs"
+    else
+        use = "all.obs"
+    statistic <- cor(as.vector(xdis), ydis, method = method, use = use)
     variant <- match.arg(method, eval(formals(cor)$method))
     variant <- switch(variant,
                       pearson = "Pearson's product-moment correlation",
@@ -33,7 +38,7 @@
         asdist <- row(xmat) > col(xmat)
         ptest <- function(take, ...) {
             permvec <- (xmat[take, take])[asdist]
-            drop(cor(permvec, ydis, method = method))
+            drop(cor(permvec, ydis, method = method, use = use))
         }
         ## Parallel processing
         if (is.null(parallel) && getRversion() >= "2.15.0")

Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R	2012-09-03 18:42:46 UTC (rev 2267)
+++ pkg/vegan/R/mantel.partial.R	2012-09-04 04:25:12 UTC (rev 2268)
@@ -1,6 +1,6 @@
 `mantel.partial` <-
   function (xdis, ydis, zdis, method = "pearson", permutations = 999, 
-            strata, parallel = getOption("mc.cores")) 
+            strata, na.rm = FALSE, parallel = getOption("mc.cores")) 
 {
     part.cor <- function(rxy, rxz, ryz) {
         (rxy - rxz * ryz)/sqrt(1-rxz*rxz)/sqrt(1-ryz*ryz)
@@ -8,9 +8,14 @@
     xdis <- as.dist(xdis)
     ydis <- as.vector(as.dist(ydis))
     zdis <- as.vector(as.dist(zdis))
-    rxy <- cor(as.vector(xdis), ydis, method = method)
-    rxz <- cor(as.vector(xdis), zdis, method = method)
-    ryz <- cor(ydis, zdis, method = method)
+    ## Handle missing values
+    if (na.rm)
+        use <- "complete.obs"
+    else
+        use = "all.obs"
+    rxy <- cor(as.vector(xdis), ydis, method = method, use = use)
+    rxz <- cor(as.vector(xdis), zdis, method = method, use = use)
+    ryz <- cor(ydis, zdis, method = method, use = use)
     variant <- match.arg(method, eval(formals(cor)$method))
     variant <- switch(variant,
                       pearson = "Pearson's product-moment correlation",
@@ -39,8 +44,8 @@
         asdist <- row(xmat) > col(xmat)
         ptest <- function(take, ...) {
             permvec <- (xmat[take, take])[asdist]
-            rxy <- cor(permvec, ydis, method = method)
-            rxz <- cor(permvec, zdis, method = method)
+            rxy <- cor(permvec, ydis, method = method, use = use)
+            rxz <- cor(permvec, zdis, method = method, use = use)
             part.cor(rxy, rxz, ryz)
         }
         ## parallel processing

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-09-03 18:42:46 UTC (rev 2267)
+++ pkg/vegan/inst/ChangeLog	2012-09-04 04:25:12 UTC (rev 2268)
@@ -48,10 +48,13 @@
 	oecosimu-compliant earlier and simultaneously they also gained the
 	density and densityplot methods.
 
-	* mantel, mantel.partial: mixed cor.test() and cor(), but now only
-	use cor(). The use of cor.test() was only used to get the textual
-	presentation of the correlation 'method'. Internal changes that
-	should have no effect in results, but consistency is a good thing.
+	* mantel, mantel.partial: Gained argument na.rm (defaults FALSE)
+	to remove missing values from dissimilarities. To implement this,
+	there were some internal changes in functions (that should not
+	influence the results): The functions mixed cor.test() and cor(),
+	but now only use cor(). Function cor.test() was only used to get the
+	textual presentation of the correlation 'method', but this is now
+	found internally.
 
 	* protest: do not return the observed statistic as one of the
 	permuted values but separately.

Modified: pkg/vegan/man/mantel.Rd
===================================================================
--- pkg/vegan/man/mantel.Rd	2012-09-03 18:42:46 UTC (rev 2267)
+++ pkg/vegan/man/mantel.Rd	2012-09-04 04:25:12 UTC (rev 2268)
@@ -14,9 +14,9 @@
 }
 \usage{
 mantel(xdis, ydis, method="pearson", permutations=999, strata,
-    parallel = getOption("mc.cores"))
+    na.rm = FALSE, parallel = getOption("mc.cores"))
 mantel.partial(xdis, ydis, zdis, method = "pearson", permutations = 999, 
-    strata, parallel = getOption("mc.cores"))
+    strata, na.rm = FALSE, parallel = getOption("mc.cores"))
 }
 
 \arguments{
@@ -28,6 +28,10 @@
   \item{strata}{An integer vector or factor specifying the strata for
     permutation. If supplied, observations are permuted only within the
     specified strata.}
+  \item{na.rm}{Remove missing values in calculation of Mantel
+    correlation. Use this option with care. When two dissimilarities
+    have both missing values in matching positions, these matches will
+    be broken in permutation tests can be biased.}
   \item{parallel}{Number of parallel processes or a predefined socket
     cluster.  With \code{parallel = 1} uses ordinary, non-parallel
     processing. The parallel processing is done with \pkg{parallel}