[Vegan-commits] r669 - in pkg/vegan: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 20 10:47:14 CET 2009
Author: jarioksa
Date: 2009-01-20 10:47:14 +0100 (Tue, 20 Jan 2009)
New Revision: 669
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/R/kendall.global.R
pkg/vegan/R/kendall.post.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/kendall.global.Rd
Log:
kendall: uses all p.adjust alternatives; version to 1.16-10
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2009-01-20 09:20:18 UTC (rev 668)
+++ pkg/vegan/DESCRIPTION 2009-01-20 09:47:14 UTC (rev 669)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 1.16-9
-Date: Januay 7, 2009
+Version: 1.16-10
+Date: Januay 20, 2009
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson,
Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
Modified: pkg/vegan/R/kendall.global.R
===================================================================
--- pkg/vegan/R/kendall.global.R 2009-01-20 09:20:18 UTC (rev 668)
+++ pkg/vegan/R/kendall.global.R 2009-01-20 09:47:14 UTC (rev 669)
@@ -7,7 +7,7 @@
### copyleft - Guillaume Blanchet and Pierre Legendre, October 2008
################################################################################
- mult <- match.arg(mult, c("sidak", "holm", "bonferroni"))
+ mult <- match.arg(mult, c("sidak", p.adjust.methods))
##CC# Make sure Y is a matrix and find number of rows and columns of Y
Y <- as.matrix(Y)
@@ -85,15 +85,10 @@
prob.F.corr <- NA
for(i in 1:ngr) prob.F.corr = c(prob.F.corr, (1-(1-prob.F.gr[i])^ngr))
prob.F.corr <- prob.F.corr[-1]
+ } else {
+ perm.corr <- p.adjust(prob.perm.gr, method=mult)
+ prob.F.corr <- p.adjust(prob.F.gr, method=mult)
}
- if(mult == "holm") {
- perm.corr <- p.adjust(prob.perm.gr, method="holm")
- prob.F.corr <- p.adjust(prob.F.gr, method="holm")
- }
- if(mult == "bonferroni") {
- perm.corr <- p.adjust(prob.perm.gr, method="bonferroni")
- prob.F.corr <- p.adjust(prob.F.gr, method="bonferroni")
- }
}
## Create a data frame containing the results
if(ngr == 1) {
Modified: pkg/vegan/R/kendall.post.R
===================================================================
--- pkg/vegan/R/kendall.post.R 2009-01-20 09:20:18 UTC (rev 668)
+++ pkg/vegan/R/kendall.post.R 2009-01-20 09:47:14 UTC (rev 669)
@@ -6,9 +6,9 @@
###
### copyleft - Guillaume Blanchet and Pierre Legendre, October 2008
################################################################################
+
+ mult <- match.arg(mult, c("sidak", p.adjust.methods))
- mult <- match.arg(mult, c("sidak", "holm", "bonferroni"))
-
##CC# Make sure Y is a matrix and find number of rows and columns of Y
Y <- as.matrix(Y)
n <- nrow(Y)
@@ -102,9 +102,9 @@
vec.corr = NA
for(i in 1:p) vec.corr = c(vec.corr, (1-(1-vec[i])^p))
vec.corr <- vec.corr[-1]
+ } else {
+ vec.corr <- p.adjust(vec, method=mult)
}
- if(mult == "holm") vec.corr <- p.adjust(vec, method="holm")
- if(mult == "bonferroni") vec.corr <- p.adjust(vec, method="bonferroni")
if(ngr > 1) {
vec.gr <- vector("list",ngr)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2009-01-20 09:20:18 UTC (rev 668)
+++ pkg/vegan/inst/ChangeLog 2009-01-20 09:47:14 UTC (rev 669)
@@ -2,8 +2,13 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 1.16-9 (opened Jan 7, 2009)
+Version 1.6-10 (openen Jan 20, 2009)
+ * kendall.post, kendall.global: knows now all P value adjustment
+ methods of 'p.adjust()' plus "sidak".
+
+Version 1.16-9 (closed Jan 20, 2009)
+
* kendall.post: added one line that was accidentally lost in
editing.
Modified: pkg/vegan/man/kendall.global.Rd
===================================================================
--- pkg/vegan/man/kendall.global.Rd 2009-01-20 09:20:18 UTC (rev 668)
+++ pkg/vegan/man/kendall.global.Rd 2009-01-20 09:47:14 UTC (rev 669)
@@ -35,10 +35,11 @@
group. }
\item{nperm}{ Number of permutations to be performed. Default is
999. }
- \item{mult}{ Correct P-values for multiple testing. The methods are
- "holm", "sidak", and "bonferroni". The Bonferroni correction is
- overly conservative; it is not recommended. It is included to
- allow comparisons with the other methods. }
+ \item{mult}{Correct P-values for multiple testing using the
+ alternatives described in \code{\link{p.adjust}} and in addition
+ \code{"sidak"} (see Details). The Bonferroni correction is overly
+ conservative; it is not recommended. It is included to allow
+ comparisons with the other methods.}
}
\details{
\code{Y} must contain quantitative data. They will be transformed to
@@ -81,25 +82,11 @@
The corrections used for multiple testing are applied to the list of
P-values (P); they take into account the number of tests (k) carried
out simulatenously (number of groups in \code{kendall.global}, or
- number of species in \code{kendall.post}).
-
- The Holm correction is computed after ordering the P-values in a
- list with the smallest value to the left. Compute adjusted P-values
- as:
- \eqn{P_{corr} = (k-i+1) P}{P_corr = (k-i+1)*P}
-
- where i is the position in the ordered list. Final step: from left
- to right, if an adjusted \eqn{P_corr} in the ordered list is smaller
- than the one occurring at its left, make the smallest one equal to
- the largest one.
-
- The \enc{Šidák}{Sidak} correction is:
-
- \eqn{P_{corr} = 1 - (1 - P)^k}
-
- The Bonferonni correction is:
-
- \eqn{P_{corr} = k P}{P_corr = k*P}
+ number of species in \code{kendall.post}). The corrections are
+ performed using funtion \code{\link{p.adjust}}; see that function
+ for the describtion of the correction methods. In addition, there is
+ \enc{Šidák}{Sidak} correction which defined as
+ \eqn{P_{corr} = 1 -(1 - P)^k}.
}
\value{
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