[Vegan-commits] r1923 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 2 14:50:07 CEST 2011
Author: jarioksa
Date: 2011-10-02 14:50:06 +0200 (Sun, 02 Oct 2011)
New Revision: 1923
Modified:
pkg/vegan/man/commsim.Rd
pkg/vegan/man/nullmodel.Rd
pkg/vegan/man/permatfull.Rd
pkg/vegan/man/vegandocs.Rd
Log:
deprecation of commsimulator: remove cross references
Modified: pkg/vegan/man/commsim.Rd
===================================================================
--- pkg/vegan/man/commsim.Rd 2011-10-02 06:20:17 UTC (rev 1922)
+++ pkg/vegan/man/commsim.Rd 2011-10-02 12:50:06 UTC (rev 1923)
@@ -66,68 +66,69 @@
The following algorithms are currently predefined:
\itemize{
%% commsimulator
- \item{\code{"r00"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This maintains the number of presences but fills
- these anywhere so that neither species (column) nor
- site (row) totals are preserved. See Wright et al. (1998) for review.}
+
+ \item{\code{"r00"}: }{non-sequential algorithm for binary matrices
+ that maintains the number of presences but fills these anywhere so
+ that neither species (column) nor site (row) totals are
+ preserved. See Wright et al. (1998) for review.}
+
\item{\code{"r0", "r0_old"}: }{non-sequential algorithm for binary
- matrices described in the page of \code{\link{commsimulator}}.
- This maintains the site (row) frequencies, fills presences
- anywhere on the row with no respect to species (column)
+ matrices that maintains the site (row) frequencies, fills
+ presences anywhere on the row with no respect to species (column)
frequencies. Methods \code{"r0"} and \code{"r0_old"} implement the
same method, but use different random number sequences; use
\code{"r0_old"} is you want to reproduce reusult in \pkg{vegan
- 2.0-0} or older. See Wright et al. (1998) for a review.}
- \item{\code{"r1"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This maintains the site (row) frequencies,
- uses column marginal frequencies as probabilities.
- It tries to simulate original species frequencies,
- but it is not strictly constrained. See Wright et al. (1998) for review.}
- \item{\code{"r2"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This maintains the site (row) frequencies,
- uses squared column sums as as probabilities.
- It tries to simulate original species frequencies,
- but it is not strictly constrained. See Wright et al. (1998) for review.}
- \item{\code{"c0"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This method maintains species frequencies,
- but does not honour site (row) frequencies (Jonsson 2001). }
- \item{\code{"swap"}: }{sequential algorithm for binary matrices
- described in the page of \code{\link{commsimulator}}.
- This changes the matrix structure, but does not influence
- marginal sums (Gotelli & Entsminger 2003).
- This inspects 2 x 2 submatrices so long that a swap can be done.}
- \item{\code{"tswap"}: }{sequential algorithm for binary matrices
- described in the page of \code{\link{commsimulator}}.
- Same as the \code{"swap"} algorithm, but it
- is trying a fixed number of times and doing zero to
- many swaps at one step (according th thin argument in later call,
- see Examples). This approach was suggested by
- \enc{Miklós}{Miklos} & Podani (2004) because they found that ordinary swap
- may lead into biased sequences,
- since some columns or rows may be more easily swapped.}
- \item{\code{"quasiswap"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This method implements a
- method where matrix is first filled honouring row and
- column totals, but with integers that may be larger than one.
- Then the method inspects random 2x2 matrices and performs a
- quasiswap on them. Quasiswap is similar to ordinary swap,
- but it also can reduce numbers above one to ones maintaining
- marginal totals (\enc{Miklós}{Miklos} & Podani 2004). }
- \item{\code{"backtracking"}: }{non-sequential algorithm for binary matrices described
- in the page of \code{\link{commsimulator}}.
- This method implements a filling method with constraints
- both for row and column frequencies (Gotelli & Entsminger 2001).
- The matrix is first filled randomly using row and column frequencies
- as probabilities. Typically row and column sums are reached before
- all incidences are filled in. After that begins "backtracking",
- where some of the points are removed, and then filling is
- started again, and this backtracking is done so may times that
- all incidences will be filled into matrix.}
+ 2.0-0} or older using \code{commsimulator} (now deprecated). See
+ Wright et al. (1998) for a review.}
+
+ \item{\code{"r1"}: }{non-sequential algorithm for binary matrices
+ that maintains the site (row) frequencies, uses column marginal
+ frequencies as probabilities. It tries to simulate original
+ species frequencies, but it is not strictly constrained. See
+ Wright et al. (1998) for review.}
+
+ \item{\code{"r2"}: }{non-sequential algorithm for binary matrices
+ that maintains the site (row) frequencies, uses squared column
+ sums as as probabilities. It tries to simulate original species
+ frequencies, but it is not strictly constrained. See Wright et
+ al. (1998) for review.}
+
+ \item{\code{"c0"}: }{non-sequential algorithm for binary matrices
+ that maintains species frequencies, but does not honour site (row)
+ frequencies (Jonsson 2001). }
+
+ \item{\code{"swap"}: }{sequential algorithm for binary matrices that
+ changes the matrix structure, but does not influence marginal sums
+ (Gotelli & Entsminger 2003). This inspects \eqn{2 \times 2}{2 by
+ 2} submatrices so long that a swap can be done.}
+
+ \item{\code{"tswap"}: }{sequential algorithm for binary matrices.
+ Same as the \code{"swap"} algorithm, but it is trying a fixed
+ number of times and doing zero to many swaps at one step
+ (according th thin argument in later call, see Examples). This
+ approach was suggested by \enc{Miklós}{Miklos} & Podani (2004)
+ because they found that ordinary swap may lead into biased
+ sequences, since some columns or rows may be more easily swapped.}
+
+ \item{\code{"quasiswap"}: }{non-sequential algorithm for binary
+ matrices that implements a method where matrix is first filled
+ honouring row and column totals, but with integers that may be
+ larger than one. Then the method inspects random \eqn{2 \times
+ 2}{2 by 2} matrices and performs a quasiswap on them. Quasiswap is
+ similar to ordinary swap, but it also can reduce numbers above one
+ to ones maintaining marginal totals (\enc{Miklós}{Miklos} & Podani
+ 2004). }
+
+ \item{\code{"backtracking"}: }{non-sequential algorithm for binary
+ matrices that implements a filling method with constraints both
+ for row and column frequencies (Gotelli & Entsminger 2001). The
+ matrix is first filled randomly using row and column frequencies
+ as probabilities. Typically row and column sums are reached before
+ all incidences are filled in. After that begins "backtracking",
+ where some of the points are removed, and then filling is started
+ again, and this backtracking is done so may times that all
+ incidences will be filled into matrix.}
+
%% permatswap
\item{\code{"swap_count"}: }{sequential algorithm for count matrices
described in the page of \code{\link{permatswap}}.
@@ -312,8 +313,8 @@
Jari Oksanen and Peter Solymos
}
\seealso{
-\code{\link{commsimulator}}, \code{\link{permatfull}},
-\code{\link{permatswap}}, \code{\link{oecosimu}}.
+\code{\code{\link{permatfull}}, \code{\link{permatswap}},
+\code{\link{oecosimu}}.
}
\examples{
## write the r00 algorithm
Modified: pkg/vegan/man/nullmodel.Rd
===================================================================
--- pkg/vegan/man/nullmodel.Rd 2011-10-02 06:20:17 UTC (rev 1922)
+++ pkg/vegan/man/nullmodel.Rd 2011-10-02 12:50:06 UTC (rev 1923)
@@ -142,7 +142,6 @@
\seealso{
\code{\link{commsim}}, \code{\link{make.commsim}},
\code{\link{permatfull}}, \code{\link{permatswap}}
-\code{\link{commsimulator}}
}
\examples{
x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd 2011-10-02 06:20:17 UTC (rev 1922)
+++ pkg/vegan/man/permatfull.Rd 2011-10-02 12:50:06 UTC (rev 1923)
@@ -48,7 +48,7 @@
\item{method}{Character for method used for the swap algorithm
(\code{"swap"}, \code{"tswap"}, \code{"quasiswap"},
\code{"backtrack"}) as described for function
- \code{\link{commsimulator}}. If \code{mtype="count"} the
+ \code{\link{make.commsim}}. If \code{mtype="count"} the
\code{"quasiswap"}, \code{"swap"}, \code{"swsh"} and
\code{"abuswap"} methods are available (see details).}
\item{shuffle}{Character, indicating whether individuals
@@ -82,8 +82,8 @@
\code{\link{r2dtable}} function is used that is based on Patefield's
(1981) algorithm. For presence absence data, matrix fill should be
necessarily fixed, and \code{permatfull} is a wrapper for the function
- \code{\link{commsimulator}}. The \code{r00, r0, c0, quasiswap}
- algorithms of \code{\link{commsimulator}} are used for \code{"none",
+ \code{\link{make.commsim}}. The \code{r00, r0, c0, quasiswap}
+ algorithms of \code{\link{make.commsim}} are used for \code{"none",
"rows", "columns", "both"} values of the \code{fixedmar} argument,
respectively
@@ -101,7 +101,7 @@
kept constant. \code{permatswap} uses different kinds of swap
algorithms, and row and columns sums are fixed in all cases. For
presence-absence data, the \code{swap} and \code{tswap} methods of
- \code{\link{commsimulator}} can be used. For count data, a special
+ \code{\link{make.commsim}} can be used. For count data, a special
swap algorithm ('swapcount') is implemented that results in permuted
matrices with fixed marginals and matrix fill at the same time.
@@ -203,7 +203,7 @@
\references{ Original references for presence-absence algorithms are
- given on help page of \code{\link{commsimulator}}.
+ given on help page of \code{\link{make.commsim}}.
Hardy, O. J. (2008) Testing the spatial phylogenetic structure of
local communities: statistical performances of different null models
@@ -219,7 +219,7 @@
\email{solymos at ualberta.ca} and Jari Oksanen}
\seealso{ For other functions to permute matrices:
-\code{\link{commsimulator}}, \code{\link{r2dtable}},
+\code{\link{make.commsim}}, \code{\link{r2dtable}},
\code{\link{sample}}, \code{\link[bipartite]{swap.web}}.
For the use of these permutation algorithms: \code{\link{oecosimu}},
Modified: pkg/vegan/man/vegandocs.Rd
===================================================================
--- pkg/vegan/man/vegandocs.Rd 2011-10-02 06:20:17 UTC (rev 1922)
+++ pkg/vegan/man/vegandocs.Rd 2011-10-02 12:50:06 UTC (rev 1923)
@@ -46,7 +46,7 @@
design decisions in \pkg{vegan}. Currently this discusses
implementing nestedness temperature (\code{\link{nestedtemp}}),
backtracking algorithm in community null models
- (\code{\link{commsimulator}}), scaling of RDA results, and why WA
+ (\code{\link{make.commsim}}), scaling of RDA results, and why WA
scores are used as default instead of LC scores in constrained
ordination.
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