[Vegan-commits] r2801 - in pkg/vegan: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 3 18:34:58 CET 2013
Author: jarioksa
Date: 2013-12-03 18:34:58 +0100 (Tue, 03 Dec 2013)
New Revision: 2801
Modified:
pkg/vegan/NAMESPACE
pkg/vegan/R/add1.cca.R
pkg/vegan/R/ccanova.R
pkg/vegan/R/drop1.cca.R
pkg/vegan/R/ordiR2step.R
pkg/vegan/R/ordistep.R
pkg/vegan/man/add1.cca.Rd
pkg/vegan/man/ccanova.Rd
Log:
stage 3 of new anova.cca: start adapting functions dependent on anova.cca and fix things flagged in R CMD build
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/NAMESPACE 2013-12-03 17:34:58 UTC (rev 2801)
@@ -30,7 +30,7 @@
vectorfit, vegandocs, vegdist, vegemite, veiledspec, wascores,
wcmdscale, wisconsin)
## Export temporary function later intended to replace anova.cca()
-export(anovacca) ## <-- REMOVE THIS WHEN anova.cca IS UPGRADED <--!!!
+export(ccanova) ## <-- REMOVE THIS WHEN ccanova IS REMOVED <--!!!
## export pasteCall for 'permute'
export(pasteCall)
## export anova.cca for 'BiodiversityR': this should be fixed there
Modified: pkg/vegan/R/add1.cca.R
===================================================================
--- pkg/vegan/R/add1.cca.R 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/R/add1.cca.R 2013-12-03 17:34:58 UTC (rev 2801)
@@ -1,6 +1,6 @@
`add1.cca`<-
function(object, scope, test = c("none", "permutation"),
- pstep = 100, perm.max = 200, ...)
+ permutations = how(nperm = 199), ...)
{
if (inherits(object, "prc"))
stop("'step'/'add1' cannot be used for 'prc' objects")
@@ -27,7 +27,7 @@
else
nfit <- update(object,
as.formula(paste(". ~ . +", tt)))
- tmp <- anova(nfit, step = pstep, perm.max = perm.max, ...)
+ tmp <- anova(nfit, permutations = permutations, ...)
adds[i+1,] <- unlist(tmp[1,3:5])
}
colnames(adds) <- colnames(tmp)[3:5]
Modified: pkg/vegan/R/ccanova.R
===================================================================
--- pkg/vegan/R/ccanova.R 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/R/ccanova.R 2013-12-03 17:34:58 UTC (rev 2801)
@@ -1,4 +1,4 @@
-`anova.cca` <-
+`ccanova` <-
function (object, alpha = 0.05, beta = 0.01, step = 100, perm.max = 9999,
by = NULL, ...)
{
Modified: pkg/vegan/R/drop1.cca.R
===================================================================
--- pkg/vegan/R/drop1.cca.R 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/R/drop1.cca.R 2013-12-03 17:34:58 UTC (rev 2801)
@@ -1,6 +1,6 @@
`drop1.cca` <-
function(object, scope, test = c("none", "permutation"),
- pstep = 100, perm.max = 200, ...)
+ permutations = how(nperm = 199), ...)
{
if (inherits(object, "prc"))
stop("'step'/'drop1' cannot be used for 'prc' objects")
@@ -13,8 +13,8 @@
scope <- rn
else if (!is.character(scope))
scope <- drop.scope(scope)
- adds <- anova(object, by = "margin", step = pstep,
- perm.max = perm.max, scope = scope, ...)
+ adds <- anova(object, by = "margin", scope = scope,
+ permutations = permutations, ...)
nr <- nrow(adds)
out <- cbind(out, rbind(NA, adds[rn,3:5]))
class(out) <- cl
Modified: pkg/vegan/R/ordiR2step.R
===================================================================
--- pkg/vegan/R/ordiR2step.R 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/R/ordiR2step.R 2013-12-03 17:34:58 UTC (rev 2801)
@@ -4,7 +4,7 @@
`ordiR2step` <-
function(object, scope, direction = c("both", "forward"),
- Pin = 0.05, R2scope = TRUE, pstep = 100, perm.max = 1000,
+ Pin = 0.05, R2scope = TRUE, permutations = how(nperm=499),
trace = TRUE, ...)
{
direction <- match.arg(direction)
@@ -78,7 +78,7 @@
if (R2scope) R2.adds[best] <= R2.all else TRUE) {
## Second criterion: added variable is significant
tst <- add1(object, scope = adds[best], test="permu",
- pstep = pstep, perm.max = perm.max,
+ permutations = permutations,
alpha = Pin, trace = FALSE, ...)
if (trace) {
print(tst[-1,])
@@ -95,7 +95,7 @@
}
}
if (NROW(anotab) > 0) {
- anotab <- rbind(anotab, "<All variables>" = c(R2.all, rep(NA, 5)))
+ anotab <- rbind(anotab, "<All variables>" = c(R2.all, rep(NA, 4)))
class(anotab) <- c("anova", class(anotab))
object$anova <- anotab
}
Modified: pkg/vegan/R/ordistep.R
===================================================================
--- pkg/vegan/R/ordistep.R 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/R/ordistep.R 2013-12-03 17:34:58 UTC (rev 2801)
@@ -1,6 +1,6 @@
`ordistep` <-
function(object, scope, direction =c("both", "backward", "forward"),
- Pin = 0.05, Pout = 0.1, pstep = 100, perm.max = 1000,
+ Pin = 0.05, Pout = 0.1, permutations = how(nperm = 199),
steps=50, trace = TRUE, ...)
{
if (!inherits(object, "cca"))
@@ -43,17 +43,18 @@
change <- NULL
## Consider dropping
if (backward && length(scope$drop)) {
- aod <- drop1(object, scope = scope$drop, test="perm", pstep = pstep,
- perm.max = perm.max, alpha = Pout, trace = trace, ...)
+ aod <- drop1(object, scope = scope$drop, test="perm",
+ permutations = permutations,
+ alpha = Pout, trace = trace, ...)
aod <- aod[-1,]
- o <- order(-aod[,5], aod[,4], aod[,2])
+ o <- order(-aod[,4], aod[,2])
aod <- aod[o,]
rownames(aod) <- paste("-", rownames(aod), sep = " ")
if (trace) {
cat("\n")
print(aod)
}
- if (is.na(aod[1,5]) || aod[1,5] > Pout) {
+ if (is.na(aod[1,4]) || aod[1,4] > Pout) {
anotab <- rbind(anotab, aod[1,])
change <- rownames(aod)[1]
object <- eval.parent(update(object, paste("~ .", change)))
@@ -70,14 +71,14 @@
aod <- add1(object, scope = scope$add, test = "perm", pstep = pstep,
perm.max = perm.max, alpha = Pin, trace = trace, ...)
aod <- aod[-1,]
- o <- order(aod[,5], aod[,4], aod[,2])
+ o <- order(aod[,4], aod[,2])
aod <- aod[o,]
rownames(aod) <- paste("+", rownames(aod), sep = " ")
if (trace) {
cat("\n")
print(aod)
}
- if (!is.na(aod[1,5]) && aod[1,5] <= Pin) {
+ if (!is.na(aod[1,4]) && aod[1,4] <= Pin) {
anotab <- rbind(anotab, aod[1,])
change <- rownames(aod)[1]
object <- eval.parent(update(object, paste( "~ .",change)))
Modified: pkg/vegan/man/add1.cca.Rd
===================================================================
--- pkg/vegan/man/add1.cca.Rd 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/man/add1.cca.Rd 2013-12-03 17:34:58 UTC (rev 2801)
@@ -9,9 +9,9 @@
}
\usage{
\method{add1}{cca}(object, scope, test = c("none", "permutation"),
- pstep = 100, perm.max = 200, ...)
+ permutations = how(nperm=199), ...)
\method{drop1}{cca}(object, scope, test = c("none", "permutation"),
- pstep = 100, perm.max = 200, ...)
+ permutations = how(nperm=199), ...)
}
\arguments{
@@ -20,9 +20,12 @@
\item{scope}{ A formula giving the terms to be considered for adding
or dropping; see \code{\link{add1}} for details.}
\item{test}{ Should a permutation test be added using \code{\link{anova.cca}}. }
- \item{pstep}{Number of permutations in one step, passed as argument
- \code{step} to \code{\link{anova.cca}}.}
- \item{perm.max}{ Maximum number of permutation in \code{\link{anova.cca}}. }
+
+ \item{permutations}{Permutation scheme as defined in
+ \code{\link[permute]{ho}}; the default defines a simple
+ permutations (and could also be expressed as a single number). Any
+ structure accepted by \code{\link{anova.cca}} acn be used.}
+
\item{\dots}{Other arguments passed to \code{\link{add1.default}},
\code{\link{drop1.default}}, and \code{\link{anova.cca}}.}
}
Modified: pkg/vegan/man/ccanova.Rd
===================================================================
--- pkg/vegan/man/ccanova.Rd 2013-12-03 17:13:16 UTC (rev 2800)
+++ pkg/vegan/man/ccanova.Rd 2013-12-03 17:34:58 UTC (rev 2801)
@@ -33,7 +33,7 @@
\details{
Function \code{ccanova} is a deprecated version of \code{anova.cca}.
- The new \code{link{\anova.cca}} function is completely
+ The new \code{link{anova.cca}} function is completely
rewritten. With the same random number seed and the same number of
permutations, the results are mostly identical. The only difference
is that marginal tests (\code{by = "margin"}) are implemented
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