[Vegan-commits] r1288 - in pkg/vegan: R man

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

Author: psolymos
Date: 2010-08-27 18:46:12 +0200 (Fri, 27 Aug 2010)
New Revision: 1288

Modified:
   pkg/vegan/R/rankindex.R
   pkg/vegan/man/rankindex.Rd
Log:
rankindex accepts list of functions as indices arg

Modified: pkg/vegan/R/rankindex.R
===================================================================
--- pkg/vegan/R/rankindex.R	2010-08-26 09:34:01 UTC (rev 1287)
+++ pkg/vegan/R/rankindex.R	2010-08-27 16:46:12 UTC (rev 1288)
@@ -12,15 +12,39 @@
     }
     veg <- as.matrix(veg)
     res <- numeric(length(indices))
-    names(res) <- indices
-    for (i in indices) {
-        y <- vegdist(veg, i)
-        if (stepacross) {
-            is.na(y) <- no.shared(veg)
-            y <- stepacross(y, trace = FALSE, toolong = -1, ...)
+    ## create names if indices is a list of functions without names
+    if (is.list(indices)) {
+        nam <- names(indices)
+        if (is.null(nam))
+            nam <- paste("dis", 1:length(idices), sep="")
+    } else nam <- indices
+    names(res) <- nam
+    ## indices is a list of functions which return dist objects
+    if (is.list(indices)) {
+        for (i in 1:length(indices)) {
+            ## don't accept similarities
+            if (indices[[i]](matrix(1, 2, 2)) != 0)
+                stop("define dissimilarity and not similarity")
+            y <- indices[[i]](veg)
+            ## check class of output
+            if (!inherits(y, "dist"))
+                stop("function in 'indices' must return a 'dist' object")
+            if (stepacross) {
+                is.na(y) <- no.shared(veg)
+                y <- stepacross(y, trace = FALSE, toolong = -1, ...)
+            }
+            res[i] <- cor(span, y, method = method)
         }
-        res[i] <- cor(span, y, method = method)
+    ## indices is a character vector naming methods in vegdist
+    } else {
+        for (i in indices) {
+            y <- vegdist(veg, i)
+            if (stepacross) {
+                is.na(y) <- no.shared(veg)
+                y <- stepacross(y, trace = FALSE, toolong = -1, ...)
+            }
+            res[i] <- cor(span, y, method = method)
+        }
     }
     res
 }
-

Modified: pkg/vegan/man/rankindex.Rd
===================================================================
--- pkg/vegan/man/rankindex.Rd	2010-08-26 09:34:01 UTC (rev 1287)
+++ pkg/vegan/man/rankindex.Rd	2010-08-27 16:46:12 UTC (rev 1288)
@@ -15,7 +15,9 @@
   \item{grad}{The gradient variable or matrix. }
   \item{veg}{The community data matrix. }
   \item{indices}{Dissimilarity indices compared, partial matches to
-    alternatives in \code{\link{vegdist}}.}
+    alternatives in \code{\link{vegdist}}.
+    Alternatively, it can be a (named) list of functions returning
+    objects of class 'dist'.}
   \item{stepacross}{Use \code{\link{stepacross}} to find
     a shorter path dissimilarity. The dissimilarities for site pairs
     with no shared species are set \code{NA} using
@@ -33,6 +35,14 @@
   point is assessed as Euclidean distance for continuous variables, and
   as Gower metric for mixed data using function
   \code{\link[cluster]{daisy}} when \code{grad} has factors.
+
+  The \code{indices} argument can accept any dissimilarity 
+  indices besides the ones calculated by the 
+  \code{\link{vegdist}} function. For this, the argument value
+  should be a (possibly named) list of functions.
+  Each function must return a valid 'dist' object with dissimilarities,
+  similarities are not accepted and should be converted into dissimilarities
+  beforehand.
 }
 \value{
   Returns a named vector of rank correlations.
@@ -40,7 +50,7 @@
 \references{ Faith, F.P., Minchin, P.R. and Belbin,
   L. (1987).  Compositional dissimilarity as a robust measure of
     ecological distance. \emph{Vegetatio} 69, 57-68. }
-\author{Jari Oksanen }
+\author{Jari Oksanen, with additions from Peter Solymos}
 \note{
   There are several problems in using rank correlation coefficients.
   Typically there are very many ties when \eqn{n(n-1)/2} gradient
@@ -59,6 +69,11 @@
 
   Earlier version of this function used \code{method = "kendall"}, but
   that is far too slow in large data sets.
+
+  The functions returning dissimilarity objects ahould be self contained,
+  because the \code{...} argument passes additional parameters
+  to \code{\link{stepacross}} and not to the functions supplied
+  via the \code{indices} argument.
 }
 
 \seealso{\code{\link{vegdist}}, \code{\link{stepacross}},
@@ -74,5 +89,10 @@
 ## Some would use PCA transformation.
 rankindex(scale(varechem), varespec)
 rankindex(scale(varechem), wisconsin(varespec))
+## Using non vegdist indices as functions
+funs <- list(Manhattan=function(x) dist(x, "manhattan"),
+    Gower=function(x) daisy(x, "gower"),
+    Ochiai=function(x) designdist(x, "1-J/sqrt(A*B)"))
+rankindex(scale(varechem), varespec, funs)
 }
 \keyword{ multivariate }