[Vegan-commits] r2008 - in pkg/vegan: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Nov 19 07:54:09 CET 2011
Author: jarioksa
Date: 2011-11-19 07:54:08 +0100 (Sat, 19 Nov 2011)
New Revision: 2008
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/NAMESPACE
pkg/vegan/inst/ChangeLog
pkg/vegan/man/diversity.Rd
Log:
add rarecurve: draw rarefaction curves for each data row
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2011-11-17 17:50:15 UTC (rev 2007)
+++ pkg/vegan/DESCRIPTION 2011-11-19 06:54:08 UTC (rev 2008)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-7
-Date: November 12, 2011
+Version: 2.1-8
+Date: November 19, 2011
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2011-11-17 17:50:15 UTC (rev 2007)
+++ pkg/vegan/NAMESPACE 2011-11-19 06:54:08 UTC (rev 2008)
@@ -6,29 +6,28 @@
export(CCorA, MOStest, RsquareAdj, SSarrhenius, SSgitay, SSgleason,
SSlomolino, adipart, adonis, anosim, beals, betadisper, betadiver,
bgdispersal, bioenv, bstick, cIndexKM, calibrate, capscale, cascadeKM,
-cca, commsimulator, contribdiv, clamtest, commsim,
-decorana, decostand, designdist,
-coverscale, dispindmorisita, distconnected, diversity, downweight,
-drarefy, eigengrad, eigenvals, envfit, estaccumR, estimateR, eventstar,
-factorfit, fisherfit, fitspecaccum, 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, nesteddisc, nestedn0, nestednodf, nestedtemp, nullmodel,
-oecosimu, ordiR2step, ordiarrows, ordicloud, ordicluster,
-ordiellipse, ordigrid, ordihull, ordilabel, ordiplot3d,
-ordiplot, ordipointlabel, ordiresids, ordirgl, ordisegments,
-ordispider, ordisplom, ordistep, ordisurf, orditkplot, orditorp,
-ordixyplot, orglpoints, orglsegments, orglspider, orgltext,
-pcnm, permatfull, permatswap,
-permutest, poolaccum, postMDS, prc,
-prestondistr, prestonfit, procrustes, protest, radfit, radlattice,
-rankindex, rarefy,raupcrick, rda, renyiaccum, renyi, rrarefy, scores,
-showvarparts, spandepth, spantree, specaccum, specnumber,
-specpool2vect, specpool, spenvcor, stepacross, stressplot, swan,
-taxa2dist, taxondive, tolerance, treedist, treedive, treeheight,
-tsallisaccum, tsallis, varpart, vectorfit, vegandocs, vegdist,
-vegemite, veiledspec, wascores, wcmdscale, wisconsin)
+cca, commsimulator, contribdiv, clamtest, commsim, decorana,
+decostand, designdist, coverscale, dispindmorisita, distconnected,
+diversity, downweight, drarefy, eigengrad, eigenvals, envfit,
+estaccumR, estimateR, eventstar, factorfit, fisherfit, fitspecaccum,
+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,
+nesteddisc, nestedn0, nestednodf, nestedtemp, nullmodel, oecosimu,
+ordiR2step, ordiarrows, ordicloud, ordicluster, ordiellipse, ordigrid,
+ordihull, ordilabel, ordiplot3d, ordiplot, ordipointlabel, ordiresids,
+ordirgl, ordisegments, ordispider, ordisplom, ordistep, ordisurf,
+orditkplot, orditorp, ordixyplot, orglpoints, orglsegments,
+orglspider, orgltext, pcnm, permatfull, permatswap, permutest,
+poolaccum, postMDS, prc, prestondistr, prestonfit, procrustes,
+protest, radfit, radlattice, rankindex, rarefy, rarecurve, raupcrick,
+rda, renyiaccum, renyi, rrarefy, scores, showvarparts, spandepth,
+spantree, specaccum, specnumber, specpool2vect, specpool, spenvcor,
+stepacross, stressplot, swan, taxa2dist, taxondive, tolerance,
+treedist, treedive, treeheight, tsallisaccum, tsallis, varpart,
+vectorfit, vegandocs, vegdist, vegemite, veiledspec, wascores,
+wcmdscale, wisconsin)
## export pasteCall for 'permute'
export(pasteCall)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-11-17 17:50:15 UTC (rev 2007)
+++ pkg/vegan/inst/ChangeLog 2011-11-19 06:54:08 UTC (rev 2008)
@@ -2,8 +2,16 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-7 (opened November 12, 2011)
+Version 2.1-8 (opened November 19, 2011)
+ * rarecurve: new function to draw rarefaction curves for each
+ plot, optionally with sample size vertical and corresponding
+ horizontal richness lines. Soil microbiologists with sequencing
+ data seem to want these, and I have seen them used elsewhere as
+ well.
+
+Version 2.1-7 (closed November 19, 2011)
+
* adonis: speed up implemented in r1636 was not passing the
transposed matrices to internal f.test function. Reported by
Nicholas Lewin-Koh.
@@ -13,6 +21,8 @@
triggers stepacross(), whereas FALSE is logical and never triggers
stepacross.
+ * vegan 2.0-2 was released on November 15, based on this version.
+
Version 2.1-6 (closed November 12, 2011)
* FAQ: correct mark-up of hyper links (@uref{} instead of @url{}),
Modified: pkg/vegan/man/diversity.Rd
===================================================================
--- pkg/vegan/man/diversity.Rd 2011-11-17 17:50:15 UTC (rev 2007)
+++ pkg/vegan/man/diversity.Rd 2011-11-19 06:54:08 UTC (rev 2008)
@@ -4,6 +4,7 @@
\alias{rarefy}
\alias{rrarefy}
\alias{drarefy}
+\alias{rarecurve}
\alias{fisher.alpha}
\alias{specnumber}
@@ -17,6 +18,8 @@
rarefy(x, sample, se = FALSE, MARGIN = 1)
rrarefy(x, sample)
drarefy(x, sample)
+rarecurve(x, step = 1, sample, xlab = "Sample Size", ylab = "Species",
+ label = TRUE, ...)
fisher.alpha(x, MARGIN = 1, se = FALSE, ...)
specnumber(x, groups, MARGIN = 1)
}
@@ -30,9 +33,13 @@
\item{sample}{Subsample size for rarefying community, either a single
value or a vector.}
\item{se}{Estimate standard errors.}
+ \item{step}{Step size for sample sizes in rarefaction curves.}
+ \item{xlab, ylab}{Axis labels in plots of rarefaction curves.}
+ \item{label}{Label rarefaction curves by rownames of \code{x} (logical).}
\item{groups}{A grouping factor: if given, finds the total number of
species in each group.}
- \item{...}{Parameters passed to \code{\link{nlm}}}
+ \item{...}{Parameters passed to \code{\link{nlm}}, or to \code{\link{plot}}
+ and \code{link{link{lines}} in \code{rarecurve}.}
}
\details{
Shannon or Shannon--Weaver (or Shannon--Wiener) index is defined as
@@ -69,6 +76,14 @@
rarefied community of size \code{sample}. The \code{sample} can be a
vector giving the sample sizes for each row.
+ Function \code{rarecurve} draws a rarefaction curve for each row of
+ the input data. The rarefaction curves are evaluated using the
+ interval of \code{step} sample sizes, always including 1 and total
+ sample size. If \code{sample} is specified, a vertical line is
+ drawn at \code{sample} with horizontal lines for the sections of
+ rarefaction curves and the vertical \code{sample} size to show the
+ rarefied sample sizes.
+
\code{fisher.alpha} estimates the \eqn{\alpha} parameter of
Fisher's logarithmic series (see \code{\link{fisherfit}}).
The estimation is possible only for genuine
@@ -105,6 +120,10 @@
function returns a matrix with a column for each \code{sample} size,
and if \code{se = TRUE}, rarefied richness and its standard error are
on consecutive lines.
+
+ Function \code{rarecurve} retunrs \code{\link{invisible}} list of
+ \code{rarefy} results corresponding each drawn curve.
+
With option \code{se = TRUE}, function \code{fisher.alpha} returns a
data frame with items for \eqn{\alpha} (\code{alpha}), its approximate
standard errors (\code{se}), residual degrees of freedom
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