[Vegan-commits] r2802 - in pkg/vegan: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 3 19:37:39 CET 2013
Author: jarioksa
Date: 2013-12-03 19:37:39 +0100 (Tue, 03 Dec 2013)
New Revision: 2802
Modified:
pkg/vegan/R/add1.cca.R
pkg/vegan/R/drop1.cca.R
pkg/vegan/R/ordistep.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/add1.cca.Rd
pkg/vegan/man/anova.cca.Rd
pkg/vegan/man/ordistep.Rd
Log:
stage 4 or new anova.cca: Pass examples in R CMD check, but still fail in inst/tests
Modified: pkg/vegan/R/add1.cca.R
===================================================================
--- pkg/vegan/R/add1.cca.R 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/R/add1.cca.R 2013-12-03 18:37:39 UTC (rev 2802)
@@ -15,7 +15,7 @@
if (!is.character(scope))
scope <- add.scope(object, update.formula(object, scope))
ns <- length(scope)
- adds <- matrix(0, ns+1, 3)
+ adds <- matrix(0, ns+1, 2)
adds[1, ] <- NA
for (i in 1:ns) {
tt <- scope[i]
@@ -28,9 +28,9 @@
nfit <- update(object,
as.formula(paste(". ~ . +", tt)))
tmp <- anova(nfit, permutations = permutations, ...)
- adds[i+1,] <- unlist(tmp[1,3:5])
+ adds[i+1,] <- unlist(tmp[1,3:4])
}
- colnames(adds) <- colnames(tmp)[3:5]
+ colnames(adds) <- colnames(tmp)[3:4]
out <- cbind(out, adds)
class(out) <- cl
}
Modified: pkg/vegan/R/drop1.cca.R
===================================================================
--- pkg/vegan/R/drop1.cca.R 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/R/drop1.cca.R 2013-12-03 18:37:39 UTC (rev 2802)
@@ -16,7 +16,7 @@
adds <- anova(object, by = "margin", scope = scope,
permutations = permutations, ...)
nr <- nrow(adds)
- out <- cbind(out, rbind(NA, adds[rn,3:5]))
+ out <- cbind(out, rbind(NA, adds[rn,3:4]))
class(out) <- cl
}
out
Modified: pkg/vegan/R/ordistep.R
===================================================================
--- pkg/vegan/R/ordistep.R 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/R/ordistep.R 2013-12-03 18:37:39 UTC (rev 2802)
@@ -68,8 +68,9 @@
}
## Consider adding
if (forward && length(scope$add)) {
- aod <- add1(object, scope = scope$add, test = "perm", pstep = pstep,
- perm.max = perm.max, alpha = Pin, trace = trace, ...)
+ aod <- add1(object, scope = scope$add, test = "perm",
+ permutations = permutations,
+ alpha = Pin, trace = trace, ...)
aod <- aod[-1,]
o <- order(aod[,4], aod[,2])
aod <- aod[o,]
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/inst/ChangeLog 2013-12-03 18:37:39 UTC (rev 2802)
@@ -4,10 +4,21 @@
Version 2.1-40 (opened December 3, 2013)
- * anova.cca: Function is now based on the new code, and the old
- (deprecated) code is called ccanova. Except several functions to
- fail while they depend on the old interface (certainly add1.cca,
- drop1.cca, ordistep, ordiR2step).
+ * anova.cca: Function is now based on the new code, but the old is
+ avaialable in a function called ccanova. The API changes:
+ arguments 'step' and 'perm.max' are gone and replaced with
+ 'permutations' that accepts a how() object defining permutations,
+ or a single number like previously or a permutation matrix. The
+ new anova.cca adds an option of analysing a sequence of ordination
+ models. This also means that '...' is now the second argument and
+ the names of all arguments must be written in full. This change
+ can be expected to cause trouble outside vegan. Currently the
+ tests in examples are passed, but tests fail (looks like being
+ caused by the change in API).
+
+ * add1.cca, drop1.cca, ordistep, ordiR2step: functions were
+ adapted to new anova.cca and this brought along similar changes in
+ API.
Version 2.1-39 (closed December 3, 2013)
Modified: pkg/vegan/man/add1.cca.Rd
===================================================================
--- pkg/vegan/man/add1.cca.Rd 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/man/add1.cca.Rd 2013-12-03 18:37:39 UTC (rev 2802)
@@ -22,7 +22,7 @@
\item{test}{ Should a permutation test be added using \code{\link{anova.cca}}. }
\item{permutations}{Permutation scheme as defined in
- \code{\link[permute]{ho}}; the default defines a simple
+ \code{\link[permute]{how}}; 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.}
Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/man/anova.cca.Rd 2013-12-03 18:37:39 UTC (rev 2802)
@@ -73,6 +73,8 @@
used to select the marginal terms for testing. The default is to
test all marginal terms in \code{\link{drop.scope}}.}
+ \item{first}{Analyse only significance of the first axis.}
+
\item{\dots}{Parameters passed to other functions. \code{anova.cca}
passes all arguments to \code{permutest.cca}. In \code{anova} with
\code{by = "axis"} you can use argument \code{cutoff} (defaults
Modified: pkg/vegan/man/ordistep.Rd
===================================================================
--- pkg/vegan/man/ordistep.Rd 2013-12-03 17:34:58 UTC (rev 2801)
+++ pkg/vegan/man/ordistep.Rd 2013-12-03 18:37:39 UTC (rev 2802)
@@ -16,10 +16,10 @@
}
\usage{
ordistep(object, scope, direction = c("both", "backward", "forward"),
- Pin = 0.05, Pout = 0.1, pstep = 100, perm.max = 1000, steps = 50,
+ Pin = 0.05, Pout = 0.1, permutation = how(nperm = 199), steps = 50,
trace = TRUE, ...)
ordiR2step(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, ...)
}
%- maybe also 'usage' for other objects documented here.
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