[Vegan-commits] r2018 - in pkg/vegan: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Dec 11 19:30:07 CET 2011
Author: jarioksa
Date: 2011-12-11 19:30:06 +0100 (Sun, 11 Dec 2011)
New Revision: 2018
Added:
pkg/vegan/R/nestedbetasor.R
Modified:
pkg/vegan/NAMESPACE
pkg/vegan/inst/ChangeLog
pkg/vegan/man/betadiver.Rd
pkg/vegan/man/nestedtemp.Rd
Log:
implement decomposition of multiple Jaccard & Sorensen into turnover and
nestedness components following Baselga (Global Ecol Biogeog 19, 134-143; 2010)
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2011-12-06 17:51:55 UTC (rev 2017)
+++ pkg/vegan/NAMESPACE 2011-12-11 18:30:06 UTC (rev 2018)
@@ -13,7 +13,7 @@
goodness, hiersimu, humpfit, indpower, inertcomp, initMDS,
intersetcor, isomapdist, isomap, linestack, mantel, meandist,
metaMDSdist, metaMDSiter, metaMDSredist, MDSrotate, metaMDS, monoMDS,
-mrpp, msoplot, mso, multipart, make.commsim, nestedchecker,
+mrpp, msoplot, mso, multipart, make.commsim, nestedbetajac, nestedbetasor, nestedchecker,
nesteddisc, nestedn0, nestednodf, nestedtemp, nullmodel, oecosimu,
ordiR2step, ordiarrows, ordicloud, ordicluster, ordiellipse, ordigrid,
ordihull, ordilabel, ordiplot3d, ordiplot, ordipointlabel, ordiresids,
Added: pkg/vegan/R/nestedbetasor.R
===================================================================
--- pkg/vegan/R/nestedbetasor.R (rev 0)
+++ pkg/vegan/R/nestedbetasor.R 2011-12-11 18:30:06 UTC (rev 2018)
@@ -0,0 +1,31 @@
+`nestedbetasor` <-
+ function(comm)
+{
+ beta <- betadiver(comm, method = NA)
+ b <- beta$b
+ c <- beta$c
+ diffbc <- sum(abs(b-c))
+ sumbc <- sum(b+c)
+ bmin <- sum(pmin(b, c))
+ a <- sum(comm) - sum(colSums(comm) > 0)
+ simpson <- bmin/(bmin + a)
+ nest <- a/(bmin + a) * diffbc/(2*a + sumbc)
+ sorensen <- sumbc/(2*a + sumbc)
+ c(turnover = simpson, nestedness = nest, sorensen = sorensen)
+}
+
+`nestedbetajac` <-
+ function(comm)
+{
+ beta <- betadiver(comm, method = NA)
+ b <- beta$b
+ c <- beta$c
+ diffbc <- sum(abs(b-c))
+ sumbc <- sum(b+c)
+ bmin <- sum(pmin(b, c))
+ a <- sum(comm) - sum(colSums(comm) > 0)
+ simpson <- 2*bmin/(2*bmin + a)
+ nest <- a/(2*bmin + a) * diffbc/(a + sumbc)
+ jaccard <- sumbc/(a + sumbc)
+ c(turnover = simpson, nestedness = nest, jaccard = jaccard)
+}
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-12-06 17:51:55 UTC (rev 2017)
+++ pkg/vegan/inst/ChangeLog 2011-12-11 18:30:06 UTC (rev 2018)
@@ -10,6 +10,12 @@
https://stat.ethz.ch/pipermail/r-sig-ecology/2011-November/002525.html
The behaviour is now corrected in ordimedian() which will return NA
for empty factor levels.
+
+ * nestedbetasor, nestedbetajac: New functions that implement
+ decomposition of Sorensen and Jaccard beta diversities into
+ components of turnover and nestedness following Baselga (Global
+ Ecology and Biogeography 19, 134-143; 2010). These are documented
+ with nestedness indices and are ready to be used with oecosimu().
* rarecurve: new function to draw rarefaction curves for each
plot, optionally with sample size vertical and corresponding
Modified: pkg/vegan/man/betadiver.Rd
===================================================================
--- pkg/vegan/man/betadiver.Rd 2011-12-06 17:51:55 UTC (rev 2017)
+++ pkg/vegan/man/betadiver.Rd 2011-12-11 18:30:06 UTC (rev 2018)
@@ -98,20 +98,34 @@
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}
-72, 367--382.
-Whittaker, R.H. (1960) Vegetation of Siskiyou mountains, Oregon and
- California. \emph{Ecological Monographs} 30, 279--338.
+ Baselga, A. (2010) Partitioning the turnover and nestedness
+ components of beta diversity. \emph{Global Ecology and Biogeography}
+ 19, 134--143.
+
+ Koleff, P., Gaston, K.J. and Lennon, J.J. (2003) Measuring beta
+ diversity for presence-absence data. \emph{Journal of Animal
+ Ecology} 72, 367--382.
+
+ Whittaker, R.H. (1960) Vegetation of Siskiyou mountains, Oregon and
+ California. \emph{Ecological Monographs} 30, 279--338.
+
}
+
\author{Jari Oksanen }
\section{Warning }{Some indices return similarities instead of dissimilarities.}
\seealso{ \code{\link{designdist}} for an alternative to implement all
-these functions, \code{\link{vegdist}} for some canned alternatives,
-and \code{\link{betadisper}}, \code{\link{adonis}},
-\code{\link{mantel}} for analysing beta diversity objects.}
+ these functions, \code{\link{vegdist}} for some canned alternatives,
+ and \code{\link{betadisper}}, \code{\link{adonis}},
+ \code{\link{mantel}} for analysing beta diversity objects.
+ Functions \code{\link{nestedbetasor}} and
+ \code{\link{nestedbetajac}} implement decomposition beta diversity
+ measures (\enc{Sørensen}{Sorensen} and Jaccard) into turnover and
+ nestedness components following Baselga (2010).
+}
+
+
\examples{
## Raw data and plotting
data(sipoo)
Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd 2011-12-06 17:51:55 UTC (rev 2017)
+++ pkg/vegan/man/nestedtemp.Rd 2011-12-11 18:30:06 UTC (rev 2018)
@@ -5,6 +5,8 @@
\alias{nestedn0}
\alias{nesteddisc}
\alias{nestednodf}
+\alias{nestedbetasor}
+\alias{nestedbetajac}
\alias{plot.nestedtemp}
\title{ Nestedness Indices for Communities of Islands or Patches }
@@ -22,6 +24,8 @@
nesteddisc(comm)
nestedtemp(comm, ...)
nestednodf(comm, order = TRUE, weighted = FALSE)
+nestedbetasor(comm)
+nestedbetajac(comm)
\method{plot}{nestedtemp}(x, kind = c("temperature", "incidence"),
col=rev(heat.colors(100)), names = FALSE, ...)
}
@@ -106,8 +110,22 @@
al. 2008). With \code{weighted = TRUE}, the function finds the
weighted version of the index (Almeida-Neto & Ulrich,
2011). However, this requires quantitative null models for adequate
- testing.}
+ testing.
+ Functions \code{nestedbetasor} and \code{nestedbetajac} find
+ multiple-site dissimilarities and decompose these into components of
+ turnover and nestedness following Baselga (2010). This can be seen
+ as a decomposition of beta diversity (see \code{\link{betadiver}}).
+ Function \code{nestedbetasor} uses \enc{Sørensen}{Sorensen}
+ dissimilarity and the turnover component is Simpson dissimilarity
+ (Baselga 2010), and \code{nestedbetajac} uses analogous methods with
+ the Jaccard index. The functions return a vector of three items:
+ turnover, nestedness and their sum which is the multiple
+ \enc{Sørensen}{Sorensen} or Jaccard dissimilarity. The last one is
+ the total beta diversity (Baselga 2010).
+
+}
+
\value{
The result returned by a nestedness function contains an item called
\code{statistic}, but the other components differ among functions. The
@@ -130,6 +148,10 @@
disorder in the distribution of species in fragmented
habitat. \emph{Oecologia} 96, 373--382.
+ Baselga, A. (2010). Partitioning the turnover and nestedness
+ components of beta diversity. \emph{Global Ecol. Biogeog.} 19,
+ 134--143.
+
Brualdi, R.A. & Sanderson, J.G. (1999). Nested species subsets, gaps,
and discrepancy. \emph{Oecologia} 119, 256--264.
More information about the Vegan-commits
mailing list