[Vegan-commits] r2808 - in branches/2.0: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 5 13:34:47 CET 2013
Author: jarioksa
Date: 2013-12-05 13:34:46 +0100 (Thu, 05 Dec 2013)
New Revision: 2808
Modified:
branches/2.0/R/plot.renyiaccum.R
branches/2.0/R/print.oecosimu.R
branches/2.0/R/renyiaccum.R
branches/2.0/inst/ChangeLog
branches/2.0/man/nobs.adonis.Rd
branches/2.0/man/renyi.Rd
branches/2.0/man/screeplot.cca.Rd
Log:
merge revs in range 2678 to 2713 to 2.0-10
Modified: branches/2.0/R/plot.renyiaccum.R
===================================================================
--- branches/2.0/R/plot.renyiaccum.R 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/R/plot.renyiaccum.R 2013-12-05 12:34:46 UTC (rev 2808)
@@ -1,12 +1,15 @@
`plot.renyiaccum` <-
-function (x, what=c("mean", "Qnt 0.025", "Qnt 0.975"), type = "l", ...)
+function (x, what=c("Collector", "mean", "Qnt 0.025", "Qnt 0.975"),
+ type = "l", ...)
{
- if (any(what %in% colnames(x[,1,])))
- x <- x[,,what]
+ what <- what[what %in% dimnames(x)[[3]]]
+ if (any(what %in% dimnames(x)[[3]]))
+ x <- x[,,what, drop = FALSE]
dm <- dim(x)
- lin <- rep(colnames(x[,1,]), each=dm[1]*dm[2])
+ dnam <- dimnames(x)
+ lin <- rep(dnam[[3]], each=dm[1]*dm[2])
Sites <- rep(1:dm[1], len=prod(dm))
- alp <- factor(rownames(x[1,,]), levels=rownames(x[1,,]))
+ alp <- factor(dnam[[2]], levels=dnam[[2]])
alpha <- rep(rep(alp, each=dm[1]), len=prod(dm))
Diversity <- as.vector(x)
xyplot(Diversity ~ Sites | alpha, groups=lin, type=type, ...)
Modified: branches/2.0/R/print.oecosimu.R
===================================================================
--- branches/2.0/R/print.oecosimu.R 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/R/print.oecosimu.R 2013-12-05 12:34:46 UTC (rev 2808)
@@ -28,8 +28,8 @@
}
probs <- switch(x$oecosimu$alternative,
two.sided = c(0.025, 0.5, 0.975),
- less = c(0, 0.5, 0.95),
- greater = c(0.05, 0.5, 1))
+ greater = c(0, 0.5, 0.95),
+ less = c(0.05, 0.5, 1))
qu <- apply(x$oecosimu$simulated, 1, quantile, probs=probs, na.rm = TRUE)
m <- cbind("statistic" = x$oecosimu$statistic,
"z" = x$oecosimu$z, "mean" = x$oecosimu$means, t(qu),
Modified: branches/2.0/R/renyiaccum.R
===================================================================
--- branches/2.0/R/renyiaccum.R 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/R/renyiaccum.R 2013-12-05 12:34:46 UTC (rev 2808)
@@ -1,6 +1,6 @@
`renyiaccum` <-
function(x, scales=c(0, 0.5, 1, 2, 4, Inf), permutations = 100,
- raw = FALSE, subset, ...)
+ raw = FALSE, collector = FALSE, subset, ...)
{
if (!missing(subset))
x <- subset(x, subset)
@@ -20,12 +20,16 @@
result[,,k] <- as.matrix(renyi((apply(x[sample(n),],2,cumsum)),
scales=scales, ...))
}
+ if (raw)
+ collector <- FALSE
+ if (collector)
+ ref <- as.matrix(renyi(apply(x, 2, cumsum), scales = scales, ...))
if (raw) {
if (m==1) {
result <- result[,1,]
}
}else{
- tmp <- array(dim=c(n,m,6))
+ tmp <- array(dim=c(n,m,6 + as.numeric(collector)))
for (i in 1:n) {
for (j in 1:m) {
tmp[i,j,1] <- mean(result[i,j,1:permutations])
@@ -34,12 +38,14 @@
tmp[i,j,4] <- max(result[i,j,1:permutations])
tmp[i,j,5] <- quantile(result[i,j,1:permutations],0.025)
tmp[i,j,6] <- quantile(result[i,j,1:permutations],0.975)
+ if (collector)
+ tmp[i,j,7] <- ref[i,j]
}
}
result <- tmp
dimnames(result) <- list(pooled.sites=c(1:n),
scale=scales,
- c("mean", "stdev", "min", "max", "Qnt 0.025", "Qnt 0.975"))
+ c("mean", "stdev", "min", "max", "Qnt 0.025", "Qnt 0.975", if (collector) "Collector"))
}
class(result) <- c("renyiaccum", class(result))
result
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/inst/ChangeLog 2013-12-05 12:34:46 UTC (rev 2808)
@@ -4,6 +4,11 @@
Version 2.0-10 (opened December 5, 2013)
+ * merge 2713 man/: remove references to very old R versions in man
+ files (R/ part of this rev not applied)
+ * merge 2708: adapt quantilesto test direction.
+ * merge 2679: add collector curve to renyiaccum.
+ * merge 2678: renyiaccum can plot one scale.
* merge 2641: subset in renyi/spec/tsallisaccum.
* merge 2630,1,2: fisherfit new algo and delete profile & confint.
* merge 2628,9: plot vectorfit *should* work with constant
Modified: branches/2.0/man/nobs.adonis.Rd
===================================================================
--- branches/2.0/man/nobs.adonis.Rd 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/man/nobs.adonis.Rd 2013-12-05 12:34:46 UTC (rev 2808)
@@ -31,14 +31,15 @@
}
}
-\details{ Function \code{nobs} is generic in \R version 2.13.0, and
+\details{ Function \code{nobs} is generic in \R, and
\pkg{vegan} provides methods for objects from \code{\link{adonis}},
\code{\link{betadisper}}, \code{\link{cca}} and other related
methods, \code{\link{CCorA}}, \code{\link{decorana}},
\code{\link{isomap}}, \code{\link{metaMDS}}, \code{\link{pcnm}},
\code{\link{procrustes}}, \code{\link{radfit}},
- \code{\link{varpart}} and \code{\link{wcmdscale}}. } \value{ A
- single number, normally an integer, giving the number of
+ \code{\link{varpart}} and \code{\link{wcmdscale}}. }
+
+\value{ A single number, normally an integer, giving the number of
observations. }
\author{
Modified: branches/2.0/man/renyi.Rd
===================================================================
--- branches/2.0/man/renyi.Rd 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/man/renyi.Rd 2013-12-05 12:34:46 UTC (rev 2808)
@@ -18,8 +18,9 @@
hill = FALSE)
\method{plot}{renyi}(x, ...)
renyiaccum(x, scales = c(0, 0.5, 1, 2, 4, Inf), permutations = 100,
- raw = FALSE, subset, ...)
-\method{plot}{renyiaccum}(x, what = c("mean", "Qnt 0.025", "Qnt 0.975"), type = "l",
+ raw = FALSE, collector = FALSE, subset, ...)
+\method{plot}{renyiaccum}(x, what = c("Collector", "mean", "Qnt 0.025", "Qnt 0.975"),
+ type = "l",
...)
\method{persp}{renyiaccum}(x, theta = 220, col = heat.colors(100), zlim, ...)
rgl.renyiaccum(x, rgl.height = 0.2, ...)
@@ -34,6 +35,10 @@
\item{raw}{if \code{FALSE} then return summary statistics of
permutations, and if \code{TRUE} then returns the individual
permutations.}
+ \item{collector}{Accumulate the diversities in the order the sites are
+ in the data set, and the collector curve can be plotted against
+ summary of permutations. The argument is ignored if \code{raw = TRUE}.
+ }
\item{subset}{logical expression indicating sites (rows) to keep: missing
values are taken as \code{FALSE}.}
\item{what}{Items to be plotted.}
Modified: branches/2.0/man/screeplot.cca.Rd
===================================================================
--- branches/2.0/man/screeplot.cca.Rd 2013-12-05 11:50:52 UTC (rev 2807)
+++ branches/2.0/man/screeplot.cca.Rd 2013-12-05 12:34:46 UTC (rev 2808)
@@ -116,10 +116,7 @@
Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
ed. Elsevier.
}
-\note{Function \code{screeplot} is generic from \code{R} version
- 2.5.0. In these versions you can use plain \code{screeplot} command
- without suffices \code{cca}, \code{prcomp} etc.
- }
+
\author{Gavin L. Simpson}
\seealso{
\code{\link{cca}}, \code{\link{decorana}}, \code{\link{princomp}} and
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