[Vegan-commits] r964 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-08-27 15:30:53 +0200 (Thu, 27 Aug 2009)
New Revision: 964

Modified:
   branches/1.15/R/anosim.R
   branches/1.15/inst/ChangeLog
   branches/1.15/inst/NEWS
   branches/1.15/man/anosim.Rd
Log:
merge anosim to branches/1.15

Modified: branches/1.15/R/anosim.R
===================================================================
--- branches/1.15/R/anosim.R	2009-08-27 13:28:52 UTC (rev 963)
+++ branches/1.15/R/anosim.R	2009-08-27 13:30:53 UTC (rev 964)
@@ -1,7 +1,15 @@
 "anosim" <-
-    function (dis, grouping, permutations = 999, strata) 
+    function (dat, grouping, permutations = 999,
+              distance = "bray", strata) 
 {
-    x <- as.dist(dis)
+    if (inherits(dat, "dist")) 
+        x <- dat
+    else if (is.matrix(dat) && nrow(dat) == ncol(dat) && all(dat[lower.tri(dat)] == 
+        t(dat)[lower.tri(dat)])) {
+        x <- dat
+        attr(x, "method") <- "user supplied square matrix"
+    }
+    else x <- vegdist(dat, method = distance)
     sol <- c(call = match.call())
     grouping <- as.factor(grouping)
     matched <- function(irow, icol, grouping) {
@@ -36,7 +44,7 @@
     sol$statistic <- as.numeric(statistic)
     sol$class.vec <- cl.vec
     sol$dis.rank <- x.rank
-    sol$dissimilarity <- attr(dis, "method") 
+    sol$dissimilarity <- attr(x, "method") 
     if (!missing(strata)) {
         sol$strata <- deparse(substitute(strata))
         sol$stratum.values <- strata

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-08-27 13:28:52 UTC (rev 963)
+++ branches/1.15/inst/ChangeLog	2009-08-27 13:30:53 UTC (rev 964)
@@ -59,6 +59,8 @@
 	column labels. 
 
 	* merged r779: formatting fixes in mrpp.Rd.
+
+	* merged changes to anosim (rev 523, 839, 963).
 	
 Version 1.15-3 (released June 17, 2009)
 

Modified: branches/1.15/inst/NEWS
===================================================================
--- branches/1.15/inst/NEWS	2009-08-27 13:28:52 UTC (rev 963)
+++ branches/1.15/inst/NEWS	2009-08-27 13:30:53 UTC (rev 964)
@@ -5,8 +5,12 @@
 
 			  CHANGES IN 1.15-4
 
-    - Changed package dependency: vegan does not depend on 'ellipse'.  
+    - Changed package dependence: vegan does not depend on 'ellipse'.
 
+    - anosim: user interface identical to 'mrpp'. Most importantly,
+      accepts now data matrix and finds dissimilarities within the
+      function instead of accepting only dissimilarities.
+
     - betadisper: fix removing zero eigenvalues with non-Euclidean
       distances. This may change the results slightly, but in most
       cases the effects are minor or none.

Modified: branches/1.15/man/anosim.Rd
===================================================================
--- branches/1.15/man/anosim.Rd	2009-08-27 13:28:52 UTC (rev 963)
+++ branches/1.15/man/anosim.Rd	2009-08-27 13:30:53 UTC (rev 964)
@@ -11,14 +11,20 @@
   of sampling units.
 }
 \usage{
-anosim(dis, grouping, permutations=999, strata)
+anosim(dat, grouping, permutations = 999, distance = "bray", strata)
 }
 
 \arguments{
-  \item{dis}{Dissimilarity matrix.}
+  \item{dat}{Data matrix or data frame in which rows are samples and
+    columns are response variable(s), or a dissimilarity object or a
+    symmetric square matrix of dissimilarities.}
   \item{grouping}{Factor for grouping observations.}
   \item{permutations}{Number of permutation to assess the significance
     of the ANOSIM statistic. }
+  \item{distance}{Choice of distance metric that measures the
+    dissimilarity between two observations . See \code{\link{vegdist}} for
+    options.  This will be used if \code{dat} was not a dissimilarity
+    structure or a symmetric square matrix.}  
   \item{strata}{An integer vector or factor specifying the strata for
     permutation. If supplied, observations are permuted only within the
     specified strata.}