[Vegan-commits] r899 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jul 16 14:30:03 CEST 2009
Author: jarioksa
Date: 2009-07-16 14:30:01 +0200 (Thu, 16 Jul 2009)
New Revision: 899
Added:
pkg/vegan/man/indpower.Rd
Modified:
pkg/vegan/man/beals.Rd
Log:
split indpower.Rd from beals.Rd: too different in goal and usage
Modified: pkg/vegan/man/beals.Rd
===================================================================
--- pkg/vegan/man/beals.Rd 2009-07-16 12:11:14 UTC (rev 898)
+++ pkg/vegan/man/beals.Rd 2009-07-16 12:30:01 UTC (rev 899)
@@ -2,22 +2,19 @@
\name{beals}
\alias{beals}
\alias{swan}
-\alias{indpower}
-\title{Beals Smoothing, Degree of Absence and Indicator Power}
+\title{Beals Smoothing and Degree of Absence}
\description{
Beals smoothing replaces each entry in the community data with a
probability of target species occurring in that particular site, based
on the joint occurrences of target species with the species that
actually occur in the site. Swan's (1970) degree of absence applies
Beals smoothing to zero items so long that all zeros are replaced
- with smoothed values. Indicator power calculation of Halme et al.
- (2009) scales up the conguence between indicator and target species.
+ with smoothed values.
}
\usage{
beals(x, species = NA, reference = x, type = 0, include = TRUE)
swan(x)
-indpower(x, type = 0)
}
\arguments{
\item{x}{Community data frame or matrix. }
@@ -27,8 +24,7 @@
joint occurrences. By default, \code{x} is used as reference to
compute the joint occurrences.}
\item{type}{Numeric. For function \code{beals} it specifies if and how abundance
- values have to be used. For function \code{indpower} it specifies the type of
- statistic to be returned. See details for more explanation.}
+ values have to be used. See details for more explanation.}
\item{include}{This logical flag indicates whether the target species has to be
included when computing the mean of the conditioned probabilities. The
original Beals (1984) definition is equivalent to \code{include=TRUE},
@@ -82,28 +78,10 @@
there are no zeros left in the data. This is actually very similar to
extended dissimilarities (implemented in function
\code{\link{stepacross}}), but very rarely used.
-
- Halme et al. (2009) described an index of indicator power defined as
- \code{IP_I = sqrt(a * b)}, where \code{a = S / O_I} and
- \code{a = 1 - (O_T - S) / (N - O_I)}. \code{N} is the number of sites,
- \code{S} is the number of shared occurrences of the indicator (\code{I})
- and the target (\code{T}) species. \code{O_I} and \code{O_T} are number
- of occurrences of the indicator and target species. The \code{type}
- argument in the function call enables to choose which statistic to
- return. \code{type = 0} returns \code{IP_I}, \code{type = 1} returns
- \code{a}, \code{type = 2} returns \code{b}.
- Total indicator power (TIP) of an indicator species is the column mean
- (without its own value, see examples).
- In the paper, one can find how to calculate confidence
- intervals for these statistics.
}
\value{
The function returns a transformed data matrix or a vector in case of
asking Beals smoothing for a single species.
-
- \code{indpower} returns a matrix with indicator species as rows and
- target species as columns (this is indicated by the first letters of the
- row/column names).
}
\references{
@@ -117,10 +95,6 @@
Ewald, J. 2002. A probabilistic approach to estimating species pools
from large compositional matrices. \emph{J. Veg. Sci.} 13: 191--198.
-Halme, P., \enc{Mönkkönen}{Monkkonen}, M., Kotiaho, J. S,
-\enc{Ylisirniö}{Ylisirnio}, A-L. 2009. Quantifying the indicator power
-of an indicator species. \emph{Conservation Biology} 23: 1008--1016.
-
McCune, B. 1994. Improving community ordination with the Beals smoothing
function. \emph{Ecoscience} 1: 82--86.
@@ -133,7 +107,7 @@
simulated vegetational data. \emph{Ecology} 51, 89--102.
}
-\author{Miquel De \enc{Cáceres}{Caceres}, Jari Oksanen and Peter Solymos}
+\author{Miquel De \enc{Cáceres}{Caceres} and Jari Oksanen}
\seealso{\code{\link{decostand}} for proper standardization methods,
\code{\link{specpool}} for an attempt to assess the size of species
@@ -153,11 +127,6 @@
## Vector with beals smoothing values corresponding to the first species
## in dune.
beals(dune, species=1, include=TRUE)
-## calculating IP values
-ip <- indpower(dune)
-## and TIP values
-diag(ip) <- NA
-rowMeans(ip, na.rm=TRUE)
}
\keyword{ manip }
\keyword{ smooth }
Added: pkg/vegan/man/indpower.Rd
===================================================================
--- pkg/vegan/man/indpower.Rd (rev 0)
+++ pkg/vegan/man/indpower.Rd 2009-07-16 12:30:01 UTC (rev 899)
@@ -0,0 +1,60 @@
+\encoding{UTF-8}
+\name{indpower}
+\alias{indpower}
+
+\title{Indicator Power of Species}
+
+\description{ Indicator power calculation of Halme et al. (2009)
+ scales up the congruence between indicator and target species.
+
+
+\usage{
+indpower(x, type = 0)
+}
+\arguments{
+ \item{x}{Community data frame or matrix. }
+ \item{type}{Thehe type of
+ statistic to be returned. See details for more explanation.}
+}
+\details{
+
+ Halme et al. (2009) described an index of indicator power defined as
+ \code{IP_I = sqrt(a * b)}, where \code{a = S / O_I} and
+ \code{a = 1 - (O_T - S) / (N - O_I)}. \code{N} is the number of sites,
+ \code{S} is the number of shared occurrences of the indicator (\code{I})
+ and the target (\code{T}) species. \code{O_I} and \code{O_T} are number
+ of occurrences of the indicator and target species. The \code{type}
+ argument in the function call enables to choose which statistic to
+ return. \code{type = 0} returns \code{IP_I}, \code{type = 1} returns
+ \code{a}, \code{type = 2} returns \code{b}.
+ Total indicator power (TIP) of an indicator species is the column mean
+ (without its own value, see examples).
+ In the paper, one can find how to calculate confidence
+ intervals for these statistics.
+
+}
+\value{
+ A matrix with indicator species as rows and
+ target species as columns (this is indicated by the first letters of the
+ row/column names).
+}
+\references{
+Halme, P., \enc{Mönkkönen}{Monkkonen}, M., Kotiaho, J. S,
+\enc{Ylisirniö}{Ylisirnio}, A-L. 2009. Quantifying the indicator power
+of an indicator species. \emph{Conservation Biology} 23: 1008--1016.
+}
+\author{Peter Solymos}
+
+\seealso{ \code{\link[labdsv]{duleg}} (package \pkg{labdsv}) for the
+indicator species analysis of \enc{Dufrêne}{Dufrene} & Legendre. }
+
+\examples{
+data(dune)
+## IP values
+ip <- indpower(dune)
+## and TIP values
+diag(ip) <- NA
+rowMeans(ip, na.rm=TRUE)
+}
+\keyword{ multivariate }
+
More information about the Vegan-commits
mailing list