[Vegan-commits] r1678 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-07-05 13:28:23 +0200 (Tue, 05 Jul 2011)
New Revision: 1678

Modified:
   pkg/vegan/R/betadiver.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/betadiver.Rd
Log:
'index' was renamed to 'method' for dist() compatibility of betadiver()

Modified: pkg/vegan/R/betadiver.R
===================================================================
--- pkg/vegan/R/betadiver.R	2011-07-05 08:22:30 UTC (rev 1677)
+++ pkg/vegan/R/betadiver.R	2011-07-05 11:28:23 UTC (rev 1678)
@@ -1,6 +1,14 @@
 `betadiver` <-
-    function(x, index = NA, order = FALSE, help = FALSE,  ...)
+    function(x, method = NA, order = FALSE, help = FALSE,  ...)
 {
+    ## 'index' was renamed to 'method' in vegan 1.90-1 for dist()
+    ## compatibility. Below we implement backward compatibility (with
+    ## warning) for 'index'.
+    dots <- match.call(expand.dots = FALSE)$...
+    if (any(k <- pmatch(names(dots), "index", nomatch = FALSE))) {
+        warning("argument 'index' deprecated: use 'method'")
+        method <- dots[[which(k==1)]]
+    }
     beta <- list("w"="(b+c)/(2*a+b+c)", "-1"="(b+c)/(2*a+b+c)", "c"="(b+c)/2",
                  "wb"="b+c", "r"="2*b*c/((a+b+c)^2-2*b*c)",
                  "I"="log(2*a+b+c)-2*a*log(2)/(2*a+b+c)-((a+b)*log(a+b)+(a+c)*log(a+c))/(2*a+b+c)",
@@ -33,14 +41,14 @@
     N <- length(S)
     b <- as.dist(matrix(rep(S, N), nrow=N)) - a
     c <- as.dist(matrix(rep(S, each=N), nrow=N)) - a
-    if (is.na(index) || is.null(index) || is.logical(index) && !index) {
+    if (is.na(method) || is.null(method) || is.logical(method) && !method) {
         out <- list(a = a, b = b, c = c)
         class(out) <- "betadiver"
         return(out)
     }
-    out <- eval(parse(text=beta[[index]]))
+    out <- eval(parse(text=beta[[method]]))
     out <- as.dist(out)
-    attr(out, "method") <- paste("beta", names(beta[index]), sep=".")
+    attr(out, "method") <- paste("beta", names(beta[method]), sep=".")
     attr(out, "call") <- match.call()
     out
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-07-05 08:22:30 UTC (rev 1677)
+++ pkg/vegan/inst/ChangeLog	2011-07-05 11:28:23 UTC (rev 1678)
@@ -4,6 +4,10 @@
 
 Version 1.90-1 (opened July 3, 2011)
 
+	* betadiver: argument 'index' was renamed to 'method' for
+	compatibility with dist() objects. Argument 'index' is
+	still recognized with a warning.
+
 	* metaMDS: Documentation and interface adapted to monoMDS().
 	Argument 'noshare' defaults to FALSE with monoMDS(), since tie
 	breaking seem to handle tied maximum dissimilarities even better

Modified: pkg/vegan/man/betadiver.Rd
===================================================================
--- pkg/vegan/man/betadiver.Rd	2011-07-05 08:22:30 UTC (rev 1677)
+++ pkg/vegan/man/betadiver.Rd	2011-07-05 11:28:23 UTC (rev 1678)
@@ -13,7 +13,7 @@
 }
 
 \usage{
-betadiver(x, index = NA, order = FALSE, help = FALSE, ...)
+betadiver(x, method = NA, order = FALSE, help = FALSE, ...)
 \method{plot}{betadiver}(x, ...)
 \method{scores}{betadiver}(x, triangular = TRUE, ...)
 }
@@ -21,7 +21,7 @@
 \arguments{
   \item{x}{Community data matrix, or the \code{betadiver} result for
   \code{plot} and \code{scores} functions. }
-  \item{index}{The index of beta diversity as defined in Koleff et al.
+  \item{method}{The index of beta diversity as defined in Koleff et al.
   (2003), Table 1. You can use either the subscript of \eqn{\beta} or
   the number of the index. See argument \code{help} below. }
   \item{order}{Order sites by increasing number of species. This will
@@ -67,7 +67,7 @@
   alternatives is much lower than 24 formally provided. The formulations
   used in functions differ occasionally from those in Koleff et
   al. (2003), but they are still mathematically equivalent. With
-  \code{index = NA}, no index is calculated, but instead an object of
+  \code{method = NA}, no index is calculated, but instead an object of
   class \code{betadiver} is returned. This is a list of elements
   \code{a}, \code{b} and \code{c}. Function \code{plot} can be used to
   display the proportions of these elements in triangular plot as
@@ -77,9 +77,9 @@
   object. 
 }
 
-\value{ With \code{index = NA}, the function returns an object of
+\value{ With \code{method = NA}, the function returns an object of
   class \code{"betadisper"} with elements \code{a}, \code{b}, and
-  \code{c}. If \code{index} is specified, the function returns a
+  \code{c}. If \code{method} is specified, the function returns a
   \code{"dist"} object which can be used in any function analysing
   dissimilarities. For beta diversity, particularly useful functions
   are \code{\link{betadisper}} to study the betadiversity in groups,
@@ -92,6 +92,11 @@
   are two such similarity indices.
 }
 
+\note{The argument \code{method} was called \code{index} in older
+  versions of the function (upto \pkg{vegan} version
+  1.17-11). Argument \code{index} is deprecated, but still recognized
+  with a warning. }
+
 \references{
 Koleff, P., Gaston, K.J. and Lennon, J.J. (2003) Measuring beta
 diversity for presence-absence data. \emph{Journal of Animal Ecology}