[Vegan-commits] r1002 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-09-11 09:16:53 +0200 (Fri, 11 Sep 2009)
New Revision: 1002

Modified:
   pkg/vegan/R/capscale.R
   pkg/vegan/R/ordiNAexclude.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/capscale.Rd
Log:
capscale got na.action

Modified: pkg/vegan/R/capscale.R
===================================================================
--- pkg/vegan/R/capscale.R	2009-09-10 18:46:20 UTC (rev 1001)
+++ pkg/vegan/R/capscale.R	2009-09-11 07:16:53 UTC (rev 1002)
@@ -1,7 +1,7 @@
 `capscale` <-
     function (formula, data, distance = "euclidean", sqrt.dist = FALSE,
               comm = NULL, add = FALSE, dfun = vegdist,
-              metaMDSdist = FALSE, ...) 
+              metaMDSdist = FALSE, na.action = na.fail, ...) 
 {
     EPS <- sqrt(.Machine$double.eps)
     if (!inherits(formula, "formula")) 
@@ -28,8 +28,6 @@
             X <- dfun(X, distance)
         }
     }
-    if (sqrt.dist)
-        X <- sqrt(X)
     inertia <- attr(X, "method")
     if (is.null(inertia))
         inertia <- "unknown"
@@ -40,7 +38,23 @@
         inertia <- paste("squared", inertia)
     if (add) 
         inertia <- paste(inertia, "(euclidified)")
-    k <- attr(X, "Size") - 1 
+
+    ## evaluate formula: ordiParseFormula will return dissimilarities
+    ## as a symmetric square matrix (except that some rows may be
+    ## deleted due to missing values)
+    fla <- update(formula, X ~ .)
+    environment(fla) <- environment()
+    d <- ordiParseFormula(fla, data, envdepth = 1, na.action = na.action)
+    ## Delete columns if rows were deleted due to missing values
+    if (!is.null(d$na.action)) {
+        d$X <- d$X[, -d$na.action, drop = FALSE]
+        if (!is.null(comm))
+            comm <- comm[-d$na.action,,drop=FALSE]
+    }
+    X <- as.dist(d$X)
+    k <- attr(X, "Size") - 1
+    if (sqrt.dist)
+        X <- sqrt(X)
     if (max(X) >= 4 + .Machine$double.eps) {
         inertia <- paste("mean", inertia)
         adjust <- 1
@@ -48,12 +62,7 @@
     else {
         adjust <- sqrt(k)
     }
-    nm <- attr(X, "Labels")
-    ## evaluate formula
-    fla <- update(formula, X ~ .)
-    environment(fla) <- environment()
-    d <- ordiParseFormula(fla, data, envdepth = 1)
-    X <- as.dist(d$X)
+    nm <- attr(X, "Labels")    
     ## cmdscale is only used if 'add = TRUE': it cannot properly
     ## handle negative eigenvalues and therefore we normally use
     ## wcmdscale. If we have 'add = TRUE' there will be no negative
@@ -125,6 +134,9 @@
     sol$inertia <- inertia
     if (metaMDSdist)
         sol$metaMDSdist <- commname
+    sol$na.action <- d$na.action
     class(sol) <- c("capscale", class(sol))
+    if (!is.null(sol$na.action))
+        sol <- ordiNAexclude(sol, d$excluded)
     sol
 }

Modified: pkg/vegan/R/ordiNAexclude.R
===================================================================
--- pkg/vegan/R/ordiNAexclude.R	2009-09-10 18:46:20 UTC (rev 1001)
+++ pkg/vegan/R/ordiNAexclude.R	2009-09-11 07:16:53 UTC (rev 1002)
@@ -20,7 +20,8 @@
         x$rowsum.excluded <- rowSums(excluded)/x$grand.total
     ## Estimate WA scores for NA cases with newdata of excluded
     ## observations
-    if (is.null(x$pCCA) && inherits(nas, "exclude")) {
+    if (is.null(x$pCCA) && inherits(nas, "exclude") &&
+        !inherits(x, "capscale")) {
         if (!is.null(x$CCA))
             x$CCA$wa.excluded <- predict(x, newdata = excluded,
                                          type = "wa", model = "CCA")

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-09-10 18:46:20 UTC (rev 1001)
+++ pkg/vegan/inst/ChangeLog	2009-09-11 07:16:53 UTC (rev 1002)
@@ -4,9 +4,8 @@
 
 Version 1.16-28 (opened September 10, 200)
 
-	* capscale: internal changes in the function to make it possible
-	to have na.action. The results should be identical to the previous
-	version, and the user should see no change (hope so).
+	* capscale: implemented na.action. The WA scores are always NA for
+	missing observations in capscale.
 	
 Version 1.16-27 (closed September 10, 2009)
 

Modified: pkg/vegan/man/capscale.Rd
===================================================================
--- pkg/vegan/man/capscale.Rd	2009-09-10 18:46:20 UTC (rev 1001)
+++ pkg/vegan/man/capscale.Rd	2009-09-11 07:16:53 UTC (rev 1002)
@@ -21,7 +21,7 @@
 \usage{
 capscale(formula, data, distance = "euclidean", sqrt.dist = FALSE,
     comm = NULL, add = FALSE,  dfun = vegdist, metaMDSdist = FALSE,
-    ...)
+    na.action = na.fail, ...)
 }
 
 \arguments{
@@ -70,6 +70,15 @@
      using extended flexible shortest path dissimilarities (function
      \code{\link{stepacross}}) when there are many dissimilarities based on
      no shared species.}
+   \item{na.action}{Handling of missing values in constraints or
+     conditions. The default (\code{\link{na.fail}}) is to stop
+     with missing values. Choices \code{\link{na.omit}} and
+     \code{\link{na.exclude}} delete rows with missing values, but
+     differ in representation of results. With \code{na.omit} only
+     non-missing site scores are shown, but \code{na.exclude} gives
+     \code{NA} for scores of missing observations. Unlike in
+     \code{\link{rda}}, no WA scores are available for missing
+     constraints or conditions.}
    \item{\dots}{Other parameters passed to \code{\link{rda}} or to
      \code{\link{metaMDSdist}}.  }
 }