[Vegan-commits] r1755 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-08-24 13:50:11 +0200 (Wed, 24 Aug 2011)
New Revision: 1755

Modified:
   pkg/vegan/R/specpool.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/NEWS.Rd
Log:
specpool works with NA values in 'pool', empty factor levels and checks input

Modified: pkg/vegan/R/specpool.R
===================================================================
--- pkg/vegan/R/specpool.R	2011-08-24 10:30:54 UTC (rev 1754)
+++ pkg/vegan/R/specpool.R	2011-08-24 11:50:11 UTC (rev 1755)
@@ -4,6 +4,14 @@
     x <- as.matrix(x)
     if (missing(pool)) 
         pool <- rep("All", nrow(x))
+    ## check dims
+    if (length(pool) != NROW(x))
+        stop("length of 'pool' and number rows in 'x' do not match")
+    ## remove missing values
+    if (any(nas <- is.na(pool))) {
+        pool <- pool[!nas]
+        x <- x[!nas, , drop = FALSE]
+    }
     out <- seq(1:nrow(x))
     groups <- table(pool)
     inds <- names(groups)
@@ -15,6 +23,8 @@
         a1 <- a2 <- NA
         gr <- out[pool == is]
         n <- length(gr)
+        if (n <= 0)
+            next
         X <- x[gr, , drop = FALSE]
         freq <- colSums(X > 0)
         p <- freq[freq > 0]/n

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-08-24 10:30:54 UTC (rev 1754)
+++ pkg/vegan/inst/ChangeLog	2011-08-24 11:50:11 UTC (rev 1755)
@@ -12,6 +12,9 @@
 	each fitted model. Function fitspecaccum() is written so that
 	default fitted(), residuals() and coef() work.
 
+	* specpool: failed if 'pool' had NA values or empty factor
+	levels. Checks that 'pool' length matches nrow of data.
+
 	* NAMESPACE: imports nobs from permute_0.5-3 in R 2.12.2 and older
 	which do not yet have nobs() generic.
 

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2011-08-24 10:30:54 UTC (rev 1754)
+++ pkg/vegan/inst/NEWS.Rd	2011-08-24 11:50:11 UTC (rev 1755)
@@ -86,7 +86,12 @@
   
   \subsection{BUG FIXES}{
     \itemize{
-      \item None yet.
+
+      \item \code{specpool} failed if the grouping factor \code{pool}
+      had missing values or empty factor levels.  Now also checks that
+      the length of the \code{pool} matches the number of
+      observations.
+
     }
   } % end BUG FIXES