[Vegan-commits] r644 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 19 10:28:01 CET 2008
Author: jarioksa
Date: 2008-12-19 10:28:01 +0100 (Fri, 19 Dec 2008)
New Revision: 644
Modified:
pkg/vegan/man/adipart.Rd
pkg/vegan/man/dispindmorisita.Rd
pkg/vegan/man/permCheck.Rd
pkg/vegan/man/permatfull.Rd
pkg/vegan/man/permuted.index2.Rd
Log:
Fixing unescaped $ in doc files following R-Devel message by
Brian Ripley on 'Misuse of $<matn expressions>$ in Rd files'
(https://stat.ethz.ch/pipermail/r-devel/2008-December/051634.html)
Modified: pkg/vegan/man/adipart.Rd
===================================================================
--- pkg/vegan/man/adipart.Rd 2008-12-19 09:07:53 UTC (rev 643)
+++ pkg/vegan/man/adipart.Rd 2008-12-19 09:28:01 UTC (rev 644)
@@ -50,11 +50,17 @@
\value{
An object of class 'adipart' with same structure as 'oecosimu' objects.
}
+
\references{
-Lande, R. 1996. Statistics and partitioning of species diversity, and similarity among multiple communities. \emph{Oikos}, 76, 5-13.
+ Lande, R. 1996. Statistics and partitioning of species
+diversity, and similarity among multiple communities. \emph{Oikos}, 76,
+5-13.
-Crist, T.O., Veech, J.A., Gering, J.C. and Summerville, K.S. 2003. Partitioning species diversity across landscapes and regions: a hierarchical analysis of $\alpha$, $\beta$, and $\gamma$-diversity. \emph{Am. Nat.}, 162, 734-743.
-}
+Crist, T.O., Veech, J.A., Gering, J.C. and Summerville,
+K.S. 2003. Partitioning species diversity across landscapes and regions:
+a hierarchical analysis of \eqn{\alpha}, \eqn{\beta}, and
+\eqn{\gamma}-diversity. \emph{Am. Nat.}, 162, 734-743. }
+
\author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}}
\seealso{See \code{\link{permatfull}}, \code{\link{permatswap}} and \code{\link{permat.control}} for permutation settings, and \code{\link{oecosimu}} for calculating confidence levels.}
\examples{
Modified: pkg/vegan/man/dispindmorisita.Rd
===================================================================
--- pkg/vegan/man/dispindmorisita.Rd 2008-12-19 09:07:53 UTC (rev 643)
+++ pkg/vegan/man/dispindmorisita.Rd 2008-12-19 09:28:01 UTC (rev 644)
@@ -18,15 +18,31 @@
\code{Imor = n * (sum(xi^2) - sum(xi)) / (sum(xi)^2 - sum(xi))}
-where $xi$ is the count of individuals in sample $i$, and $n$ is the number of samples ($i$ = 1, 2, \ldots, $n$). $Imor$ has values from 0 to $n$. In uniform (hyperdispersed) patterns its value falls between 0 and 1, in clumped patterns it falls between 1 and $n$. For incresing sample sizes (i.e. joining neighbouring quadrats), $Imor$ goes to $n$ as the quadrat size approaches clump size. For random patterns, $Imor$ = 1 and counts in the samples follow Poisson frequency distribution.
+where \eqn{xi} is the count of individuals in sample \eqn{i}, and \eqn{n} is the
+number of samples (\eqn{i = 1, 2, \ldots, n}). \eqn{Imor} has values from 0 to
+\eqn{n}. In uniform (hyperdispersed) patterns its value falls between 0 and
+1, in clumped patterns it falls between 1 and \eqn{n}. For incresing sample
+sizes (i.e. joining neighbouring quadrats), \eqn{Imor} goes to \eqn{n} as the
+quadrat size approaches clump size. For random patterns, \eqn{Imor = 1} and
+counts in the samples follow Poisson frequency distribution.
-The deviation from this random expectation can be tested based on critical values of the Chi-squared distribution with degrees of freedom $n-1$. Confidence interval around 1 can be calculated by the clumped $Mclu$ and uniform $Muni$ indices (Hairston et al. 1971, Krebs 1999) (Chi2Lower and Chi2Upper refers to e.g. 0.025 and 0.975 quantile values of the Chi-squared distribution with $n-1$ degrees of freedom, respectively, for \code{alpha = 0.05}):
+The deviation from this random expectation can be tested based on
+critical values of the Chi-squared distribution with degrees of freedom
+\eqn{n-1}. Confidence interval around 1 can be calculated by the clumped
+\eqn{Mclu} and uniform \eqn{Muni}indices (Hairston et al. 1971, Krebs 1999)
+(Chi2Lower and Chi2Upper refers to e.g. 0.025 and 0.975 quantile values
+of the Chi-squared distribution with \eqn{n-1} degrees of freedom,
+respectively, for \code{alpha = 0.05}):
\code{Mclu = (Chi2Upper - n + sum(xi)) / (sum(xi) - 1)}
\code{Muni = (Chi2Lower - n + sum(xi)) / (sum(xi) - 1)}
-Smith-Gill (1975) proposed the standardization of the Morisita index to rescale the [0, n] interval into [-1, 1], and setting up -0.5 and 0.5 values as confidence limits around random distribution with rescaled value 0. To rescale the Morisita index, one of the following four apply to calculate the standardized index $Imst$:
+Smith-Gill (1975) proposed the standardization of the Morisita index to
+rescale the [0, n] interval into [-1, 1], and setting up -0.5 and 0.5
+values as confidence limits around random distribution with rescaled
+value 0. To rescale the Morisita index, one of the following four apply
+to calculate the standardized index \eqn{Imst}:
(a) \code{Imor >= Mclu > 1}: \code{Imst = 0.5 + 0.5 (Imor - Mclu) / (n - Mclu)},
@@ -36,27 +52,44 @@
(d) \code{1 > Muni > Imor}: \code{Imst = -0.5 + 0.5 (Imor - Muni) / Muni}.
}
-\value{
-Returns a data frame with as many rows as the number of columns in the input data, and with four columns. Columns are: \code{imor} unstandardized Morisita index, \code{mclu} the cumpedness index, \code{muni} the uniform index, \code{imst} standardized Morisita index.
+
+\value{ Returns a data frame with as many rows as the number of columns
+in the input data, and with four columns. Columns are: \code{imor}
+unstandardized Morisita index, \code{mclu} the cumpedness index,
+\code{muni} the uniform index, \code{imst} standardized Morisita index.
}
+
\references{
-Morisita, M. 1959. Measuring of the dispersion of individuals and analysis of the distributional patterns.
-\emph{Mem. Fac. Sci. Kyushu Univ. Ser. E} 2, 215--235.
+
+Morisita, M. 1959. Measuring of the dispersion of individuals and
+analysis of the distributional patterns. \emph{Mem. Fac. Sci. Kyushu
+Univ. Ser. E} 2, 215--235.
Morisita, M. 1962. Id-index, a measure of dispersion of individuals.
\emph{Res. Popul. Ecol.} 4, 1--7.
-Smith-Gill, S. J. 1975. Cytophysiological basis of disruptive pigmentary patterns in the leopard frog, \emph{Rana pipiens}. II.
-Wild type and mutant cell specific patterns. \emph{J. Morphol.} 146, 35--54.
+Smith-Gill, S. J. 1975. Cytophysiological basis of disruptive pigmentary
+patterns in the leopard frog, \emph{Rana pipiens}. II. Wild type and
+mutant cell specific patterns. \emph{J. Morphol.} 146, 35--54.
-Hairston, N. G., Hill, R. and Ritte, U. 1971. The interpretation of aggregation patterns. In: Patil, G. P., Pileou, E. C. and Waters, W. E. eds. \emph{Statistical Ecology 1: Spatial Patterns and Statistical Distributions}. Penn. State Univ. Press, University Park.
+Hairston, N. G., Hill, R. and Ritte, U. 1971. The interpretation of
+aggregation patterns. In: Patil, G. P., Pileou, E. C. and Waters,
+W. E. eds. \emph{Statistical Ecology 1: Spatial Patterns and Statistical
+Distributions}. Penn. State Univ. Press, University Park.
-Krebs, C. J. 1999. \emph{Ecological Methodology}. 2nd ed. Benjamin Cummings Publishers.
-}
+Krebs, C. J. 1999. \emph{Ecological Methodology}. 2nd ed. Benjamin
+Cummings Publishers. }
+
\author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}}
-\note{
-A common error found in several papers is that when standardizing as in the case (b), the denominator is given as \code{Muni - 1}. This reult in a hiatus in the [0, 0.5] interval of the standardized index. The root of this typo is the book of Krebs (1999), see the Errata for the book (Page 217, \url{http://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf}).
+
+\note{ A common error found in several papers is that when standardizing
+as in the case (b), the denominator is given as \code{Muni - 1}. This
+reult in a hiatus in the [0, 0.5] interval of the standardized
+index. The root of this typo is the book of Krebs (1999), see the Errata
+for the book (Page 217,
+\url{http://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf}).
}
+
\examples{
data(dune)
x <- dispindmorisita(dune)
Modified: pkg/vegan/man/permCheck.Rd
===================================================================
--- pkg/vegan/man/permCheck.Rd 2008-12-19 09:07:53 UTC (rev 643)
+++ pkg/vegan/man/permCheck.Rd 2008-12-19 09:28:01 UTC (rev 644)
@@ -102,12 +102,12 @@
the number of observations and the permutation design. In such cases,
\code{nperm} is reduced to equal the number of possible permutations,
and complete enumeration of all permutations is turned on
- (\code{control$complete} is set to \code{TRUE}).
+ (\code{control\$complete} is set to \code{TRUE}).
Alternatively, if the number of possible permutations is low, and less
- than \code{control$minperm}, it is better to enumerate all possible
+ than \code{control\$minperm}, it is better to enumerate all possible
permutations, and as such complete enumeration of all permutations is
- turned on (\code{control$complete} is set to \code{TRUE}).
+ turned on (\code{control\$complete} is set to \code{TRUE}).
Function \code{numPerms} returns the number of permutations for the
passed \code{object} and the selected permutation
Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd 2008-12-19 09:07:53 UTC (rev 643)
+++ pkg/vegan/man/permatfull.Rd 2008-12-19 09:28:01 UTC (rev 644)
@@ -69,7 +69,7 @@
The 'quasiswapcount' algorithm (\code{method="quasiswap"} and \code{mtype="count"}) uses the same trick as Carsten Dormann's \code{\link[bipartite]{swap.web}} function in the package 'bipartite'. First, a random matrix is generated by the \code{\link{r2dtable}} function retaining row and column sums. Than the original matrix fill is reconstructed by sequential steps to increase or decrease matrix fill in the random matrix. These steps are based on swaping 2x2 submatrices (see 'swapcount' algorithm for details) to maintain row and column totals. This algorithm generates independent matrices in each step, so \code{burnin} and \code{thin} arguments are not considered. This is the default method, because this is not sequential (as 'swapcount' is) so independence of subsequent matrices does not have to be checked.
-The 'swapcount' algorithm (\code{method="swap"} and \code{mtype="count"}) tries to find 2x2 submatrices (identified by 2 random row and 2 random column indices), that can be swapped in order to leave column and row totals and fill unchanged. First, the algorithm finds the largest value in the submatrix that can be swapped ($d$) and whether in diagonal or antidiagonal way. Submatrices that contain values larger than zero in either diagonal or antidiagonal position can be swapped. Swap means that the values in diagonal or antidiagonal positions are decreased by $d$, while remaining cells are increased by $d$. A swap is made only if fill doesn't change. This algorithm is sequential, subsequent matrices are not independent, because swaps modify little if the matrix is large. In these cases many burnin steps and thinning is needed to get independent random matrices. Although this algorithm is implemented in C, large burmin and thin values can slow it down considerably.
+The 'swapcount' algorithm (\code{method="swap"} and \code{mtype="count"}) tries to find 2x2 submatrices (identified by 2 random row and 2 random column indices), that can be swapped in order to leave column and row totals and fill unchanged. First, the algorithm finds the largest value in the submatrix that can be swapped (\eqn{d}) and whether in diagonal or antidiagonal way. Submatrices that contain values larger than zero in either diagonal or antidiagonal position can be swapped. Swap means that the values in diagonal or antidiagonal positions are decreased by \eqn{d}, while remaining cells are increased by \eqn{d}. A swap is made only if fill doesn't change. This algorithm is sequential, subsequent matrices are not independent, because swaps modify little if the matrix is large. In these cases many burnin steps and thinning is needed to get independent random matrices. Although this algorithm is implemented in C, large burmin and thin values can slow it down considerably.
Constraints on row/colum sums, matrix fill, total sum and sums within
strata can be checked by the \code{summary} method. \code{plot} method is for
Modified: pkg/vegan/man/permuted.index2.Rd
===================================================================
--- pkg/vegan/man/permuted.index2.Rd 2008-12-19 09:07:53 UTC (rev 643)
+++ pkg/vegan/man/permuted.index2.Rd 2008-12-19 09:28:01 UTC (rev 644)
@@ -83,8 +83,8 @@
within a function implementing a permutation test. The main purpose of
\code{permute} is to return the correct permutation in each iteration
of the loop, either a random permutation from the current design or
- the next permutation from \code{control$all.perms} if it is not
- \code{NULL} and \code{control$complete} is \code{TRUE}.
+ the next permutation from \code{control\$all.perms} if it is not
+ \code{NULL} and \code{control\$complete} is \code{TRUE}.
}
\value{
For \code{permuted.index2} a vector of length \code{n} containing a
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