[Vegan-commits] r1511 - pkg/vegan/man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2011-02-28 08:59:07 +0100 (Mon, 28 Feb 2011)
New Revision: 1511

Modified:
   pkg/vegan/man/beals.Rd
Log:
edits of beals.Rd

Modified: pkg/vegan/man/beals.Rd
===================================================================
--- pkg/vegan/man/beals.Rd	2011-02-27 07:06:22 UTC (rev 1510)
+++ pkg/vegan/man/beals.Rd	2011-02-28 07:59:07 UTC (rev 1511)
@@ -6,9 +6,9 @@
 \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
+  probability of a target species occurring in that particular site, based
+  on the joint occurrences of the 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. 
 }
@@ -23,8 +23,8 @@
   \item{reference}{ Community data frame or matrix to be used to compute
   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. See details for more explanation.}  
+  \item{type}{Numeric. Specifies if and how abundance values have to be 
+  used in function \code{beals}. 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},
@@ -34,17 +34,17 @@
 \details{
 
   Beals smoothing is the estimated probability \eqn{p_{ij}}{p[ij]} that
-  species \eqn{j} occurs in site \eqn{i}.  It is defined as \eqn{p_{ij}
+  species \eqn{j} occurs at site \eqn{i}. It is defined as \eqn{p_{ij}
   = \frac{1}{S_i} \sum_k \frac{N_{jk} I_{ik}}{N_k}}{p[ij] = 1/S[i]
   Sum(k) N[jk] I[ik] / N[k]}, where \eqn{S_i}{S[i]} is the number of
-  species on site \eqn{i}, \eqn{N_{jk}}{N[jk]} is the number of joint
+  species at site \eqn{i}, \eqn{N_{jk}}{N[jk]} is the number of joint
   occurrences of species \eqn{j} and \eqn{k}, \eqn{N_k}{N[k]} is the
   number of occurrences of species \eqn{k}, and \eqn{I} is the incidence
   (0 or 1) of species (this last term is usually omitted from the
   equation, but it is necessary). As \eqn{N_{jk}}{N[jk]} can be
   interpreted as a mean of conditional probability, the \code{beals}
   function can be interpreted as a mean of conditioned probabilities (De
-  \enc{Cáceres}{Caceres} & Legendre 2008).  The current function is
+  \enc{Cáceres}{Caceres} & Legendre 2008). The present function is
   generalized to abundance values (De \enc{Cáceres}{Caceres} & Legendre
   2008).
   
@@ -52,23 +52,23 @@
   used. \code{type = 0} presence/absence mode. \code{type = 1}
   abundances in \code{reference} (or \code{x}) are used to compute
   conditioned probabilities. \code{type = 2} abundances in \code{x} are
-  used to compute weighted average of conditioned
+  used to compute weighted averages of conditioned
   probabilities. \code{type = 3} abundances are used to compute both
-  conditioned probabilities and the weighted average.
+  conditioned probabilities and weighted averages.
 
   Beals smoothing was originally suggested as a method of data
   transformation to remove excessive zeros (Beals 1984, McCune
   1994).  However, it is not a suitable method for this purpose since it
-  does not maintain the information on species presences:  A species may
-  have a higher probability of occurrence in a site where it does not
-  occur than in sites where it occurs.  Moreover, it regularizes data
-  too strongly.  The method may be useful in identifying species that
+  does not maintain the information on species presences: a species may
+  have a higher probability of occurrence at a site where it does not
+  occur than at sites where it occurs. Moreover, it regularizes data
+  too strongly. The method may be useful in identifying species that
   belong to the species pool (Ewald 2002) or to identify suitable
   unoccupied patches in metapopulation analysis
   (\enc{Münzbergová}{Munzbergova} & Herben 
-  2004).  In this case, the function should be called with \code{include
-  = FALSE} for cross-validatory smoothing for species, and argument
-  \code{species} can be used if only one species was studied.
+  2004). In this case, the function should be called with \code{include
+  = FALSE} for cross-validation smoothing for species; argument
+  \code{species} can be used if only one species is studied.
 
   Swan (1970) suggested replacing zero values with degrees of absence of
   a species in a community data matrix. Swan expressed the method in
@@ -80,14 +80,15 @@
   \code{\link{stepacross}}), but very rarely used. 
 }
 \value{
-  The function returns a transformed data matrix or a vector in case of 
-  asking Beals smoothing for a single species.
+  The function returns a transformed data matrix or a vector if Beals smoothing 
+  is requested for a single species.
 }
 \references{
   
-Beals, E.W. 1984. Bray-Curtis-ordination: an effective strategy for
-analysis of multivariate ecological data.  \emph{Adv. Ecol. Res.} 14:
-1--55.
+Beals, E.W. 1984. Bray-Curtis ordination: an effective strategy for
+analysis of multivariate ecological data. Pp. 1--55 in: MacFadyen, A. &
+E.D. Ford [eds.] \emph{Advances in Ecological Research, 14}. Academic
+Press, London.
 
 De \enc{Cáceres}{Caceres}, M. & Legendre, P. 2008. Beals smoothing
 revisited. \emph{Oecologia} 156: 657--669.
@@ -103,8 +104,8 @@
 habitats in metapopulation studies using co-occurrence of species. \emph{Oikos}
 105: 408--414.
 
-Swan, J.M.A. (1970) An examination of some ordination problems by use of
-simulated vegetational data. \emph{Ecology} 51, 89--102. 
+Swan, J.M.A. 1970. An examination of some ordination problems by use of
+simulated vegetational data. \emph{Ecology} 51: 89--102. 
 
 }
 \author{Miquel De \enc{Cáceres}{Caceres} and Jari Oksanen}