[Vegan-commits] r2901 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 16 10:50:18 CEST 2014
Author: jarioksa
Date: 2014-10-16 10:50:18 +0200 (Thu, 16 Oct 2014)
New Revision: 2901
Modified:
pkg/vegan/man/tsallis.Rd
Log:
uh
Modified: pkg/vegan/man/tsallis.Rd
===================================================================
--- pkg/vegan/man/tsallis.Rd 2014-10-14 09:06:39 UTC (rev 2900)
+++ pkg/vegan/man/tsallis.Rd 2014-10-16 08:50:18 UTC (rev 2901)
@@ -1,134 +1,134 @@
-\encoding{UTF-8}
-\name{tsallis}
-\alias{tsallis}
-\alias{tsallisaccum}
-\alias{persp.tsallisaccum}
-\title{Tsallis Diversity and Corresponding Accumulation Curves}
-\description{
-Function \code{tsallis} find Tsallis diversities with any scale or the corresponding evenness measures. Function \code{tsallisaccum} finds these statistics with accumulating sites.
-}
-\usage{
-tsallis(x, scales = seq(0, 2, 0.2), norm = FALSE, hill = FALSE)
-tsallisaccum(x, scales = seq(0, 2, 0.2), permutations = 100,
- raw = FALSE, subset, ...)
-\method{persp}{tsallisaccum}(x, theta = 220, phi = 15, col = heat.colors(100), zlim, ...)
-}
-
-\arguments{
- \item{x}{Community data matrix or plotting object. }
- \item{scales}{Scales of Tsallis diversity.}
-
- \item{norm}{Logical, if \code{TRUE} diversity values are normalized
- by their maximum (diversity value at equiprobability conditions).}
-
- \item{hill}{Calculate Hill numbers.}
-
- \item{permutations}{Number of random permutations in accumulating
- sites.}
-
- \item{raw}{If \code{FALSE} then return summary statistics of
- permutations, and if TRUE then returns the individual
- permutations.}
-
- \item{subset}{logical expression indicating sites (rows) to keep:
- missing values are taken as \code{FALSE}.}
-
- \item{theta, phi}{angles defining the viewing
- direction. \code{theta} gives the azimuthal direction and
- \code{phi} the colatitude.}
-
- \item{col}{Colours used for surface.} \item{zlim}{Limits of
- vertical axis.}
-
- \item{\dots}{Other arguments which are passed to \code{tsallis} and
- to graphical functions.}
-
-}
-
-\details{ The Tsallis diversity (also equivalent to Patil and Taillie
-diversity) is a one-parametric generalised entropy function, defined
-as:
-
-\deqn{H_q = \frac{1}{q-1} (1-\sum_{i=1}^S p_i^q)}{H.q = 1/(q-1)(1-sum(p^q))}
-
-where \eqn{q} is a scale parameter, \eqn{S} the number of species in
-the sample (Tsallis 1988, Tothmeresz 1995). This diversity is concave
-for all \eqn{q>0}, but non-additive (Keylock 2005). For \eqn{q=0} it
-gives the number of species minus one, as \eqn{q} tends to 1 this
-gives Shannon diversity, for \eqn{q=2} this gives the Simpson index
-(see function \code{\link{diversity}}).
-
-If \code{norm = TRUE}, \code{tsallis} gives values normalized by the
-maximum:
-
-\deqn{H_q(max) = \frac{S^{1-q}-1}{1-q}}{H.q(max) = (S^(1-q)-1)/(1-q)}
-
-where \eqn{S} is the number of species. As \eqn{q} tends to 1, maximum
-is defined as \eqn{ln(S)}.
-
-If \code{hill = TRUE}, \code{tsallis} gives Hill numbers (numbers
-equivalents, see Jost 2007):
-
-\deqn{D_q = (1-(q-1) H)^{1/(1-q)}}{D.q = (1-(q-1)*H)^(1/(1-q))}
-
-Details on plotting methods and accumulating values can be found on
-the help pages of the functions \code{\link{renyi}} and
-\code{\link{renyiaccum}}.
-}
-
-\value{
-Function \code{tsallis} returns a data frame of selected
-indices. Function \code{tsallisaccum} with argument \code{raw = FALSE}
-returns a three-dimensional array, where the first dimension are the
-accumulated sites, second dimension are the diversity scales, and
-third dimension are the summary statistics \code{mean}, \code{stdev},
-\code{min}, \code{max}, \code{Qnt 0.025} and \code{Qnt 0.975}. With
-argument \code{raw = TRUE} the statistics on the third dimension are
-replaced with individual permutation results. }
-
-\references{
-
-Tsallis, C. (1988) Possible generalization of Boltzmann-Gibbs
- statistics. \emph{J. Stat. Phis.} 52, 479--487.
-
-Tothmeresz, B. (1995) Comparison of different methods for diversity
- ordering. \emph{Journal of Vegetation Science} \bold{6}, 283--290.
-
-Patil, G. P. and Taillie, C. (1982) Diversity as a concept and its
- measurement. \emph{J. Am. Stat. Ass.} \bold{77}, 548--567.
-
-Keylock, C. J. (2005) Simpson diversity and the Shannon-Wiener index
- as special cases of a generalized entropy. \emph{Oikos} \bold{109},
- 203--207.
-
-Jost, L (2007) Partitioning diversity into independent alpha and beta
- components. \emph{Ecology} \bold{88}, 2427--2439.
-}
-
-\author{\enc{Péter Sólymos}{Peter Solymos},
-\email{solymos at ualberta.ca}, based on the code of Roeland Kindt and
-Jari Oksanen written for \code{renyi}}
-
-\seealso{ Plotting methods and accumulation routines are based on
-functions \code{\link{renyi}} and \code{\link{renyiaccum}}. An object
-of class 'tsallisaccum' can be used with function
-\code{\link[vegan3d]{rgl.renyiaccum}} as well. See also settings for
-\code{\link{persp}}. }
-
-\examples{
-data(BCI)
-i <- sample(nrow(BCI), 12)
-x1 <- tsallis(BCI[i,])
-x1
-diversity(BCI[i,],"simpson") == x1[["2"]]
-plot(x1)
-x2 <- tsallis(BCI[i,],norm=TRUE)
-x2
-plot(x2)
-mod1 <- tsallisaccum(BCI[i,])
-plot(mod1, as.table=TRUE, col = c(1, 2, 2))
-persp(mod1)
-mod2 <- tsallisaccum(BCI[i,], norm=TRUE)
-persp(mod2,theta=100,phi=30)
-}
-\keyword{multivariate}
+\encoding{UTF-8}
+\name{tsallis}
+\alias{tsallis}
+\alias{tsallisaccum}
+\alias{persp.tsallisaccum}
+\title{Tsallis Diversity and Corresponding Accumulation Curves}
+\description{
+Function \code{tsallis} find Tsallis diversities with any scale or the corresponding evenness measures. Function \code{tsallisaccum} finds these statistics with accumulating sites.
+}
+\usage{
+tsallis(x, scales = seq(0, 2, 0.2), norm = FALSE, hill = FALSE)
+tsallisaccum(x, scales = seq(0, 2, 0.2), permutations = 100,
+ raw = FALSE, subset, ...)
+\method{persp}{tsallisaccum}(x, theta = 220, phi = 15, col = heat.colors(100), zlim, ...)
+}
+
+\arguments{
+ \item{x}{Community data matrix or plotting object. }
+ \item{scales}{Scales of Tsallis diversity.}
+
+ \item{norm}{Logical, if \code{TRUE} diversity values are normalized
+ by their maximum (diversity value at equiprobability conditions).}
+
+ \item{hill}{Calculate Hill numbers.}
+
+ \item{permutations}{Number of random permutations in accumulating
+ sites.}
+
+ \item{raw}{If \code{FALSE} then return summary statistics of
+ permutations, and if TRUE then returns the individual
+ permutations.}
+
+ \item{subset}{logical expression indicating sites (rows) to keep:
+ missing values are taken as \code{FALSE}.}
+
+ \item{theta, phi}{angles defining the viewing
+ direction. \code{theta} gives the azimuthal direction and
+ \code{phi} the colatitude.}
+
+ \item{col}{Colours used for surface.} \item{zlim}{Limits of
+ vertical axis.}
+
+ \item{\dots}{Other arguments which are passed to \code{tsallis} and
+ to graphical functions.}
+
+}
+
+\details{ The Tsallis diversity (also equivalent to Patil and Taillie
+diversity) is a one-parametric generalised entropy function, defined
+as:
+
+\deqn{H_q = \frac{1}{q-1} (1-\sum_{i=1}^S p_i^q)}{H.q = 1/(q-1)(1-sum(p^q))}
+
+where \eqn{q} is a scale parameter, \eqn{S} the number of species in
+the sample (Tsallis 1988, Tothmeresz 1995). This diversity is concave
+for all \eqn{q>0}, but non-additive (Keylock 2005). For \eqn{q=0} it
+gives the number of species minus one, as \eqn{q} tends to 1 this
+gives Shannon diversity, for \eqn{q=2} this gives the Simpson index
+(see function \code{\link{diversity}}).
+
+If \code{norm = TRUE}, \code{tsallis} gives values normalized by the
+maximum:
+
+\deqn{H_q(max) = \frac{S^{1-q}-1}{1-q}}{H.q(max) = (S^(1-q)-1)/(1-q)}
+
+where \eqn{S} is the number of species. As \eqn{q} tends to 1, maximum
+is defined as \eqn{ln(S)}.
+
+If \code{hill = TRUE}, \code{tsallis} gives Hill numbers (numbers
+equivalents, see Jost 2007):
+
+\deqn{D_q = (1-(q-1) H)^{1/(1-q)}}{D.q = (1-(q-1)*H)^(1/(1-q))}
+
+Details on plotting methods and accumulating values can be found on
+the help pages of the functions \code{\link{renyi}} and
+\code{\link{renyiaccum}}.
+}
+
+\value{
+Function \code{tsallis} returns a data frame of selected
+indices. Function \code{tsallisaccum} with argument \code{raw = FALSE}
+returns a three-dimensional array, where the first dimension are the
+accumulated sites, second dimension are the diversity scales, and
+third dimension are the summary statistics \code{mean}, \code{stdev},
+\code{min}, \code{max}, \code{Qnt 0.025} and \code{Qnt 0.975}. With
+argument \code{raw = TRUE} the statistics on the third dimension are
+replaced with individual permutation results. }
+
+\references{
+
+Tsallis, C. (1988) Possible generalization of Boltzmann-Gibbs
+ statistics. \emph{J. Stat. Phis.} 52, 479--487.
+
+Tothmeresz, B. (1995) Comparison of different methods for diversity
+ ordering. \emph{Journal of Vegetation Science} \bold{6}, 283--290.
+
+Patil, G. P. and Taillie, C. (1982) Diversity as a concept and its
+ measurement. \emph{J. Am. Stat. Ass.} \bold{77}, 548--567.
+
+Keylock, C. J. (2005) Simpson diversity and the Shannon-Wiener index
+ as special cases of a generalized entropy. \emph{Oikos} \bold{109},
+ 203--207.
+
+Jost, L (2007) Partitioning diversity into independent alpha and beta
+ components. \emph{Ecology} \bold{88}, 2427--2439.
+}
+
+\author{\enc{Péter Sólymos}{Peter Solymos},
+\email{solymos at ualberta.ca}, based on the code of Roeland Kindt and
+Jari Oksanen written for \code{renyi}}
+
+\seealso{ Plotting methods and accumulation routines are based on
+functions \code{\link{renyi}} and \code{\link{renyiaccum}}. An object
+of class 'tsallisaccum' can be used with function
+\code{\link[vegan3d]{rgl.renyiaccum}} as well. See also settings for
+\code{\link{persp}}. }
+
+\examples{
+data(BCI)
+i <- sample(nrow(BCI), 12)
+x1 <- tsallis(BCI[i,])
+x1
+diversity(BCI[i,],"simpson") == x1[["2"]]
+plot(x1)
+x2 <- tsallis(BCI[i,],norm=TRUE)
+x2
+plot(x2)
+mod1 <- tsallisaccum(BCI[i,])
+plot(mod1, as.table=TRUE, col = c(1, 2, 2))
+persp(mod1)
+mod2 <- tsallisaccum(BCI[i,], norm=TRUE)
+persp(mod2,theta=100,phi=30)
+}
+\keyword{multivariate}
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