[Vegan-commits] r1080 - in pkg/vegan: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 14 18:42:13 CET 2009
Author: jarioksa
Date: 2009-12-14 18:42:13 +0100 (Mon, 14 Dec 2009)
New Revision: 1080
Modified:
pkg/vegan/R/vegdist.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/decostand.Rd
pkg/vegan/man/vegdist.Rd
Log:
interface to alternative Gower skipping double zeros: closes FR#473
Modified: pkg/vegan/R/vegdist.R
===================================================================
--- pkg/vegan/R/vegdist.R 2009-12-14 11:22:34 UTC (rev 1079)
+++ pkg/vegan/R/vegdist.R 2009-12-14 17:42:13 UTC (rev 1080)
@@ -7,7 +7,7 @@
method <- "euclidean"
METHODS <- c("manhattan", "euclidean", "canberra", "bray",
"kulczynski", "gower", "morisita", "horn", "mountford",
- "jaccard", "raup", "binomial", "chao")
+ "jaccard", "raup", "binomial", "chao", "altGower")
method <- pmatch(method, METHODS)
inm <- METHODS[method]
if (is.na(method))
@@ -20,7 +20,7 @@
warning("results may be meaningless because data have negative entries in method ", inm,"\n")
if (method == 11 && any(colSums(x) == 0))
warning("data have empty species which influence the results im method ", inm, "\n")
- if (method == 6)
+ if (method %in% c(6, 14))
x <- decostand(x, "range", 2, na.rm = TRUE, ...)
if (binary)
x <- decostand(x, "pa")
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2009-12-14 11:22:34 UTC (rev 1079)
+++ pkg/vegan/inst/ChangeLog 2009-12-14 17:42:13 UTC (rev 1080)
@@ -6,6 +6,12 @@
* goodness.cca: was not using correct weights. Broken in r992 (Sep
6, 2009).
+
+ * vegdist: added UI for the alternative Gower index ("altGower")
+ that skips double zeros. The C code has been in vegan since Oct 24
+ (r1051), but no R interface. Together with decostand(..., "log")
+ of r1052 this closes Feature Request #473 submitted by Etienne
+ Laliberte in R-Forge.
Version 1.16-33 (closed December 13, 2009)
Modified: pkg/vegan/man/decostand.Rd
===================================================================
--- pkg/vegan/man/decostand.Rd 2009-12-14 11:22:34 UTC (rev 1079)
+++ pkg/vegan/man/decostand.Rd 2009-12-14 17:42:13 UTC (rev 1080)
@@ -95,7 +95,7 @@
Anderson, M.J., Ellingsen, K.E. & McArdle, B.H. (2006) Multivariate
dispersion as a measure of beta diversity. \emph{Ecology Letters}
- \strong{9}, 683-693.
+ \strong{9}, 683--693.
Legendre, P. & Gallagher, E.D. (2001) Ecologically meaningful
transformations for ordination of species data. \emph{Oecologia}
Modified: pkg/vegan/man/vegdist.Rd
===================================================================
--- pkg/vegan/man/vegdist.Rd 2009-12-14 11:22:34 UTC (rev 1079)
+++ pkg/vegan/man/vegdist.Rd 2009-12-14 17:42:13 UTC (rev 1080)
@@ -26,8 +26,9 @@
\item{x}{Community data matrix.}
\item{method}{Dissimilarity index, partial match to \code{"manhattan"},
\code{"euclidean"}, \code{"canberra"}, \code{"bray"}, \code{"kulczynski"},
- \code{"jaccard"}, \code{"gower"}, \code{"morisita"}, \code{"horn"},
- \code{"mountford"}, \code{"raup"} , \code{"binomial"} or \code{"chao"}.}
+ \code{"jaccard"}, \code{"gower"}, \code{"altGower"}, \code{"morisita"},
+ \code{"horn"}, \code{"mountford"}, \code{"raup"} , \code{"binomial"} or
+ \code{"chao"}.}
\item{binary}{Perform presence/absence standardization before analysis
using \code{\link{decostand}}.}
\item{diag}{Compute diagonals. }
@@ -57,6 +58,10 @@
\tab where \eqn{M} is the number of columns (excluding missing
values)
\cr
+ \code{altGower}
+ \tab like \code{gower}, but \eqn{M} is the number of pairs with at least
+ one non-zero value (excluding double zeros)
+ \cr
\code{canberra}
\tab \eqn{d_{jk}=\frac{1}{NZ} \sum_i
\frac{|x_{ij}-x_{ik}|}{x_{ij}+x_{ik}}}{d[jk] = (1/NZ) sum
@@ -193,20 +198,25 @@
Zealand. \emph{Journal of Experimental Marine Biology and Ecology}
305, 191--221.
+ Anderson, M.J., Ellingsen, K.E. & McArdle, B.H. (2006) Multivariate
+ dispersion as a measure of beta diversity. \emph{Ecology Letters}
+ 9, 683--693.
+
Chao, A., Chazdon, R. L., Colwell, R. K. and Shen, T. (2005). A new
statistical approach for assessing similarity of species composition
with incidence and abundance data. \emph{Ecology Letters} 8, 148--159.
-
-
+
Faith, D. P, Minchin, P. R. and Belbin, L. (1987).
Compositional dissimilarity as a robust measure of ecological
distance. \emph{Vegetatio} 69, 57--68.
+ Gower, J. C. (1971). A general coefficient of similarity and some
+ of its properties. \emph{Biometrics} 27, 623--637.
+
Krebs, C. J. (1999). \emph{Ecological Methodology.} Addison Wesley Longman.
Legendre, P, & Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
Edition. Elsevier.
-
Mountford, M. D. (1962). An index of similarity and its application to
classification problems. In: P.W.Murphy (ed.),
@@ -228,7 +238,15 @@
So these differ by a constant multiplier, and the alternative in
\code{vegdist} is in range (0,1). Function \code{\link[cluster]{daisy}}
(package \pkg{cluster}) provides alternative implementation of Gower
- index that also can handle mixed data of numeric and class variables.
+ index that also can handle mixed data of numeric and class variables.
+ There are two versions of Gower distance (\code{"gower"},
+ \code{"altGower"}) which differ in scaling: \code{"gower"} divides
+ all distances by the number of observations (rows), but
+ \code{"altGower"} omits double-zeros and divides by the number of
+ pairs with at least one above-zero value. Gower (1971) suggested this for
+ presences, but it is often taken as the general feature of the Gower
+ distances. See Examples for implementing the Anderson et al. (2006)
+ variant of the Gower index.
Most dissimilarity indices in \code{vegdist} are designed for
community data, and they will give misleading values if there are
@@ -252,5 +270,7 @@
vare.dist <- vegdist(varespec)
# Orlóci's Chord distance: range 0 .. sqrt(2)
vare.dist <- vegdist(decostand(varespec, "norm"), "euclidean")
+# Anderson et al. version of Gower
+vare.dist <- vegdist(decostand(varespec, "log"), "altGower")
}
\keyword{ multivariate }
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