[Vegan-commits] r2297 - in pkg/vegan: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 26 15:40:11 CEST 2012
Author: jarioksa
Date: 2012-09-26 15:40:10 +0200 (Wed, 26 Sep 2012)
New Revision: 2297
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/anova.cca.Rd
pkg/vegan/man/bgdispersal.Rd
pkg/vegan/man/capscale.Rd
pkg/vegan/man/cascadeKM.Rd
pkg/vegan/man/cca.Rd
pkg/vegan/man/cca.object.Rd
pkg/vegan/man/designdist.Rd
pkg/vegan/man/mantel.Rd
pkg/vegan/man/mantel.correlog.Rd
pkg/vegan/man/screeplot.cca.Rd
pkg/vegan/man/varpart.Rd
pkg/vegan/man/vegdist.Rd
Log:
upgrade docs to Legendre & Legendre (2012)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/inst/ChangeLog 2012-09-26 13:40:10 UTC (rev 2297)
@@ -28,6 +28,9 @@
This has been wrong since the introduction of radlattice in r551
(2008-11-09). Now radlattice also check that it gets the "radfit"
object it can handle.
+
+ * Rd: documentation files upgraded to the third English edition
+ (2012) of Legendre & Legendre.
Version 2.1-19 (closed September 16, 2012)
Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/anova.cca.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -162,7 +162,7 @@
only when \code{model = "direct"}.
}
\references{
- Legendre, P. and Legendre, L. (1998). \emph{Numerical Ecology}. 2nd
+ Legendre, P. and Legendre, L. (2012). \emph{Numerical Ecology}. 3rd
English ed. Elsevier.
Legendre, P., Oksanen, J. and ter Braak, C.J.F. (2011). Testing the
Modified: pkg/vegan/man/bgdispersal.Rd
===================================================================
--- pkg/vegan/man/bgdispersal.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/bgdispersal.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -6,7 +6,7 @@
\description{ This function computes coefficients of dispersal direction
between geographically connected areas, as defined by Legendre and
-Legendre (1984), and also described in Legendre and Legendre (1998,
+Legendre (1984), and also described in Legendre and Legendre (2012,
section 13.3.4). }
\usage{
@@ -72,7 +72,7 @@
freshwater fishes in the Québec
peninsula. \emph{Can. J. Fish. Aquat. Sci.} \strong{41}: 1781-1802.
- Legendre, P. and L. Legendre. 1998. \emph{Numerical ecology}, 2nd
+ Legendre, P. and L. Legendre. 2012. \emph{Numerical ecology}, 3rd
English edition. Elsevier Science BV, Amsterdam.
Sokal, R. R. and F. J. Rohlf. 1995. \emph{Biometry. The principles and
Modified: pkg/vegan/man/capscale.Rd
===================================================================
--- pkg/vegan/man/capscale.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/capscale.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -56,7 +56,7 @@
that all eigenvalues are non-negative in the underlying
Principal Co-ordinates Analysis (see \code{\link{cmdscale}}
for details). This implements \dQuote{correction method 2} of
- Legendre & Legendre (1998, p. 434). The negative eigenvalues are
+ Legendre & Legendre (2012, p. 503). The negative eigenvalues are
caused by using semi-metric or non-metric dissimilarities with
basically metric \code{\link{cmdscale}}. They are harmless and
ignored in \code{capscale}, but you also can avoid warnings with
@@ -164,7 +164,7 @@
analysis: testing multispecies responses in multifactorial ecological
experiments. \emph{Ecological Monographs} 69, 1--24.
- Legendre, P. & Legendre, L. (1998). \emph{Numerical Ecology}. 2nd English
+ Legendre, P. & Legendre, L. (2012). \emph{Numerical Ecology}. 3rd English
Edition. Elsevier
}
\author{ Jari Oksanen }
Modified: pkg/vegan/man/cascadeKM.Rd
===================================================================
--- pkg/vegan/man/cascadeKM.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/cascadeKM.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -117,7 +117,7 @@
distance matrix. (3) The first principal coordinate is used as the new
order of the objects in the graph. A simplified algorithm is used to
compute the first principal coordinate only, using the iterative
- algorithm described in Legendre & Legendre (1998, Table 9.10). The
+ algorithm described in Legendre & Legendre (2012). The
full distance matrix among objects is never computed; this avoids
the problem of storing it when the number of objects is
large. Distance values are computed as they are needed by the
@@ -157,7 +157,7 @@
methods used in multivariate analysis. \emph{Biometrika} \strong{53}:
325-338.
- Legendre, P. & L. Legendre. 1998. \emph{Numerical ecology}, 2nd
+ Legendre, P. & L. Legendre. 2012. \emph{Numerical ecology}, 3rd
English edition. Elsevier Science BV, Amsterdam.
Milligan, G. W. & M. C. Cooper. 1985. An examination of procedures for
Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/cca.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -60,7 +60,7 @@
Functions \code{cca} and \code{rda} are similar to popular
proprietary software \code{Canoco}, although the implementation is
completely different. The functions are based on Legendre &
- Legendre's (1998) algorithm: in \code{cca}
+ Legendre's (2012) algorithm: in \code{cca}
Chi-square transformed data matrix is subjected to weighted linear
regression on constraining variables, and the fitted values are
submitted to correspondence analysis performed via singular value
@@ -170,7 +170,7 @@
\references{ The original method was by ter Braak, but the current
implementations follows Legendre and Legendre.
- Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
+ Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
ed. Elsevier.
McCune, B. (1997) Influence of noisy environmental data on canonical
Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/cca.object.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -192,7 +192,7 @@
\code{cca.object} as well).
}
\references{
- Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
+ Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
ed. Elsevier.
}
\author{ Jari Oksanen }
Modified: pkg/vegan/man/designdist.Rd
===================================================================
--- pkg/vegan/man/designdist.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/designdist.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -65,7 +65,7 @@
The function \code{designdist} can implement most dissimilarity
indices in \code{\link{vegdist}} or elsewhere, and it can also be
used to implement many other indices, amongst them, most of those
- described in Legendre & Legendre (1998). It can also be used to
+ described in Legendre & Legendre (2012). It can also be used to
implement all indices of beta diversity described in Koleff et
al. (2003), but there also is a specific function
\code{\link{betadiver}} for the purpose.
@@ -85,7 +85,7 @@
diversity for presence--absence data. \emph{J. Animal Ecol.}
\strong{72}, 367--382.
- Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd
+ Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd
English ed. Elsevier
}
\author{ Jari Oksanen }
Modified: pkg/vegan/man/mantel.Rd
===================================================================
--- pkg/vegan/man/mantel.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/mantel.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -75,15 +75,15 @@
\references{ The test is due to Mantel, of course, but the
current implementation is based on Legendre and Legendre.
- Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
+ Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
Edition. Elsevier.
}
\note{
- Legendre & Legendre (1998) say that partial Mantel correlations
- often are difficult to interpret.
- }
+ Legendre & Legendre (2012, Box 10.4) warn against using partial
+ Mantel correlations.
+}
\author{Jari Oksanen }
Modified: pkg/vegan/man/mantel.correlog.Rd
===================================================================
--- pkg/vegan/man/mantel.correlog.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/mantel.correlog.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -7,8 +7,8 @@
\description{
Function \code{mantel.correlog} computes a multivariate
Mantel correlogram. Proposed by Sokal (1986) and Oden and Sokal
- (1986), the method is also described in Legendre and Legendre (1998,
- pp. 736-738).
+ (1986), the method is also described in Legendre and Legendre (2012,
+ pp. 819--821).
}
\usage{
@@ -119,7 +119,7 @@
\references{
- Legendre, P. and L. Legendre. 1998. Numerical ecology, 2nd English
+ Legendre, P. and L. Legendre. 2012. Numerical ecology, 3rd English
edition. Elsevier Science BV, Amsterdam.
Mantel, N. 1967. The detection of disease clustering and a generalized
Modified: pkg/vegan/man/screeplot.cca.Rd
===================================================================
--- pkg/vegan/man/screeplot.cca.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/screeplot.cca.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -81,7 +81,7 @@
Function \code{bstick} gives the brokenstick values which are ordered
random proportions, defined as \eqn{p_i = (tot/n) \sum_{x=i}^n
- (1/x)}{p[i] = tot/n sum(from x=i to n) 1/x} (Legendre & Legendre 1998), where
+ (1/x)}{p[i] = tot/n sum(from x=i to n) 1/x} (Legendre & Legendre 2012), where
\eqn{tot} is the total and \eqn{n} is the number of brokenstick
components (cf. \code{\link{radfit}}). Broken stick has
been recommended as a stopping rule in principal component analysis
@@ -113,7 +113,7 @@
analysis: a comparison of heuristical and statistical
approaches. \emph{Ecology} 74, 2204--2214.
- Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
+ Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English
ed. Elsevier.
}
\note{Function \code{screeplot} is generic from \code{R} version
Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/varpart.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -168,7 +168,7 @@
Borcard, D., P. Legendre & P. Drapeau. 1992. Partialling out the spatial
component of ecological variation. Ecology 73: 1045--1055.
-Legendre, P. & L. Legendre. 1998. Numerical ecology, 2nd English edition.
+Legendre, P. & L. Legendre. 2012. Numerical ecology, 3rd English edition.
Elsevier Science BV, Amsterdam.
(b) Reference on transformations for species data
Modified: pkg/vegan/man/vegdist.Rd
===================================================================
--- pkg/vegan/man/vegdist.Rd 2012-09-26 07:07:56 UTC (rev 2296)
+++ pkg/vegan/man/vegdist.Rd 2012-09-26 13:40:10 UTC (rev 2297)
@@ -170,26 +170,24 @@
are divided by \eqn{\log(2)}{log(2)} so that the results will be in
the conventional range \eqn{0 \dots 1}.
- Raup--Crick dissimilarity (\code{method = "raup"}) is a
- probabilistic index based on presence/absence data. It is defined
- as \eqn{1 - prob(j)}, or based on the probability of observing at
- least \eqn{j} species in shared in compared communities. Legendre &
- Legendre (1998) suggest using simulations to assess the probability,
- but the current function uses analytic result from hypergeometric
- distribution (\code{\link{phyper}}) instead. This probability (and
- the index) is dependent on the number of species missing in both
+ Raup--Crick dissimilarity (\code{method = "raup"}) is a probabilistic
+ index based on presence/absence data. It is defined as \eqn{1 -
+ prob(j)}, or based on the probability of observing at least \eqn{j}
+ species in shared in compared communities. The current function uses
+ analytic result from hypergeometric distribution
+ (\code{\link{phyper}}) to find the probablities. This probability
+ (and the index) is dependent on the number of species missing in both
sites, and adding all-zero species to the data or removing missing
- species from the data will influence the index. The probability
- (and the index) may be almost zero or almost one for a wide range of
+ species from the data will influence the index. The probability (and
+ the index) may be almost zero or almost one for a wide range of
parameter values. The index is nonmetric: two communities with no
shared species may have a dissimilarity slightly below one, and two
- identical communities may have dissimilarity slightly above
- zero. The index uses equal occurrence probabilities for all species,
- but Raup and Crick originally suggested that sampling probabilities
- should be proportional to species frequencies (Chase et al. 2011). A
- simulation approach with unequal species sampling probabilities is
- implemented in \code{\link{raupcrick}} function following Chase et
- al. (2011).
+ identical communities may have dissimilarity slightly above zero. The
+ index uses equal occurrence probabilities for all species, but Raup
+ and Crick originally suggested that sampling probabilities should be
+ proportional to species frequencies (Chase et al. 2011). A simulation
+ approach with unequal species sampling probabilities is implemented in
+ \code{\link{raupcrick}} function following Chase et al. (2011).
Chao index tries to take into account the number of unseen species
pairs, similarly as in \code{method = "chao"} in
@@ -274,9 +272,6 @@
Krebs, C. J. (1999). \emph{Ecological Methodology.} Addison Wesley Longman.
- Legendre, P, & Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
- Edition. Elsevier.
-
Mountford, M. D. (1962). An index of similarity and its application to
classification problems. In: P.W.Murphy (ed.),
\emph{Progress in Soil Zoology}, 43--50. Butterworths.
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