[Vegan-commits] r2883 - in pkg/vegan: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 16 16:13:14 CEST 2014
Author: jarioksa
Date: 2014-09-16 16:13:14 +0200 (Tue, 16 Sep 2014)
New Revision: 2883
Modified:
pkg/vegan/R/CCorA.R
pkg/vegan/R/adonis.R
pkg/vegan/R/anosim.R
pkg/vegan/R/factorfit.R
pkg/vegan/R/mantel.R
pkg/vegan/R/mantel.partial.R
pkg/vegan/R/mrpp.R
pkg/vegan/R/mso.R
pkg/vegan/R/print.CCorA.R
pkg/vegan/R/print.anosim.R
pkg/vegan/R/print.factorfit.R
pkg/vegan/R/print.mantel.R
pkg/vegan/R/print.mrpp.R
pkg/vegan/R/print.mso.R
pkg/vegan/R/print.permutest.betadisper.R
pkg/vegan/R/print.protest.R
pkg/vegan/R/print.vectorfit.R
pkg/vegan/R/simper.R
pkg/vegan/R/vectorfit.R
pkg/vegan/man/CCorA.Rd
pkg/vegan/man/anosim.Rd
pkg/vegan/man/envfit.Rd
pkg/vegan/man/mantel.Rd
pkg/vegan/man/mrpp.Rd
pkg/vegan/man/procrustes.Rd
Log:
Squashed commit of the following:
commit 33198cba46810c1265f0ba6061225b038272a24f
Merge: 0f86b2b 12aa1f2
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Tue Sep 16 17:05:15 2014 +0300
Merge pull request #39 from jarioksa/adapt-print-to-permute-pkg
Adapt print to permute pkg
commit 12aa1f2555126075ab3fa9fe9ca6a98aa684f73d
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Tue Sep 16 16:06:49 2014 +0300
permutest.betadisper also uses howHead() to show permutations
commit 9526decb88cc91ef7db565cafc0adca06989512b
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 21:37:31 2014 +0300
Document cases when a function returns a "control" item
Some functions return "control" *attributes* with some of their
items: this is not (yet?) documented.
commit 61df5998b0695dee2a5784eee79de083b1eba308
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 21:30:02 2014 +0300
CCorA returns permute "control" and print uses howHead() to show it
commit 31c401289c14af2790fa733e72ba05cb695f1179
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 21:18:34 2014 +0300
simper adds "control" attribute for permutations and summary prints it
commit ecce8c723d5e1b68e251e8c16d167af27b0b5a3e
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 21:08:34 2014 +0300
Add empty line between results and permutation details
commit a0333a2640742df2493ae0a75b16b0b17a27b393
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 19:17:20 2014 +0300
mso adds "control" attribute to the "vario" item and howHead() shows it
commit 711938bd8836a0cdb6210d8c536a8a831986aece
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 18:56:17 2014 +0300
remove dangling '.' from the output
commit 5ca3ecc14686f89b23902f28c4910d3279c6b968
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Mon Sep 15 18:43:45 2014 +0300
adonis adds howHead() to the heading of the anova table
The permutation information is printed similarly as in
anova.cca.
commit 16dc86254cb8d692511bcc71759f03e1bb2f6ec9
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Sep 14 20:19:00 2014 +0300
mrpp printing to the new permute API: no more strata
commit 3728b825dda5303788231414c7f3f1e1735c293e
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Sep 14 19:37:58 2014 +0300
mantel printing to the new permute API: no more strata
commit 03f764df31f5528012cd8e55e9bb77d884741e7e
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Sep 14 09:10:23 2014 +0300
adapt envfit printing to the new permute API: no more strata
commit 808cb0c1a0ddafcea99e1f04de16ef4e9b25dfad
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Sep 14 08:40:37 2014 +0300
print of anosim adapted to the new permute API
No more stores 'strata', but 'control' and uses howHead() to show
its result.
It seems that getPermuteMatrix(..., strata=<name>) does not save the
name of the 'strata', but howHead() just prints "Blocks: strata".
Modified: pkg/vegan/R/CCorA.R
===================================================================
--- pkg/vegan/R/CCorA.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/CCorA.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -177,7 +177,8 @@
RDA.adj.Rsq=c(Rsquare.adj.Y.X, Rsquare.adj.X.Y),
nperm=nperm, p.Pillai=p.Pillai, p.perm=p.perm, Cy=Cy, Cx=Cx,
corr.Y.Cy=corr.Y.Cy, corr.X.Cx=corr.X.Cx, corr.Y.Cx=corr.Y.Cx,
- corr.X.Cy=corr.X.Cy, call = match.call())
+ corr.X.Cy=corr.X.Cy, control = attr(permat, "control"),
+ call = match.call())
class(out) <- "CCorA"
out
}
Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/adonis.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -147,7 +147,8 @@
rownames(tab) <- c(attr(attr(rhs.frame, "terms"), "term.labels")[u.grps],
"Residuals", "Total")
colnames(tab)[ncol(tab)] <- "Pr(>F)"
- attr(tab, "heading") <- "Terms added sequentially (first to last)\n"
+ attr(tab, "heading") <- c(howHead(attr(p, "control")),
+ "Terms added sequentially (first to last)\n")
class(tab) <- c("anova", class(tab))
out <- list(aov.tab = tab, call = match.call(),
coefficients = beta.spp, coef.sites = beta.sites,
Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/anosim.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -72,11 +72,8 @@
sol$statistic <- as.numeric(statistic)
sol$class.vec <- cl.vec
sol$dis.rank <- x.rank
- sol$dissimilarity <- attr(x, "method")
- if (!missing(strata)) {
- sol$strata <- deparse(substitute(strata))
- sol$stratum.values <- strata
- }
+ sol$dissimilarity <- attr(x, "method")
+ sol$control <- attr(permat, "control")
class(sol) <- "anosim"
sol
}
Modified: pkg/vegan/R/factorfit.R
===================================================================
--- pkg/vegan/R/factorfit.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/factorfit.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -62,10 +62,7 @@
names(pval) <- names(P)
out <- list(centroids = sol, r = r, permutations = permutations,
pvals = pval, var.id = var.id)
- if (!missing(strata)) {
- out$strata <- deparse(substitute(strata))
- out$stratum.values <- strata
- }
+ out$control <- attr(permat, "control")
class(out) <- "factorfit"
out
}
Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/mantel.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -61,11 +61,8 @@
perm <- NULL
}
res <- list(call = match.call(), method = variant, statistic = statistic,
- signif = signif, perm = perm, permutations = permutations)
- if (!missing(strata)) {
- res$strata <- deparse(substitute(strata))
- res$stratum.values <- strata
- }
+ signif = signif, perm = perm, permutations = permutations,
+ control = attr(permat, "control"))
class(res) <- "mantel"
res
}
Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/mantel.partial.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -69,7 +69,8 @@
perm <- NULL
}
res <- list(call = match.call(), method = variant, statistic = statistic,
- signif = signif, perm = perm, permutations = permutations)
+ signif = signif, perm = perm, permutations = permutations,
+ control = attr(permat, "control"))
if (!missing(strata)) {
res$strata <- deparse(substitute(strata))
res$stratum.values <- strata
Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/mrpp.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -43,7 +43,7 @@
stop(gettextf("'permutations' have %d columns, but data have %d rows",
ncol(permutations), N))
-
+ control <- attr(permutations, "control")
if(nrow(permutations)) {
perms <- apply(permutations, 1, function(indx) grouping[indx])
permutations <- ncol(perms)
@@ -76,13 +76,10 @@
permutations <- 0
}
out <- list(call = match.call(), delta = del, E.delta = E.del, CS = CS,
- n = ncl, classdelta = classdel,
- Pvalue = p, A = r2, distance = distance, weight.type = weight.type,
- boot.deltas = m.ds, permutations = permutations)
- if (!missing(strata) && !is.null(strata)) {
- out$strata <- deparse(substitute(strata))
- out$stratum.values <- strata
- }
+ n = ncl, classdelta = classdel, Pvalue = p, A = r2,
+ distance = distance, weight.type = weight.type,
+ boot.deltas = m.ds, permutations = permutations,
+ control = control)
class(out) <- "mrpp"
out
}
Modified: pkg/vegan/R/mso.R
===================================================================
--- pkg/vegan/R/mso.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/mso.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -77,6 +77,7 @@
perm <- sapply(1:nperm, function(take) permfunc(permat[take,]))
object$vario$CA.signif <-
(rowSums(sweep(perm, 1, statistic, ">=")) + 1)/(nperm + 1)
+ attr(object$vario, "control") <- attr(permat, "control")
}
object$call <- match.call()
class(object) <- c("mso", class(object))
Modified: pkg/vegan/R/print.CCorA.R
===================================================================
--- pkg/vegan/R/print.CCorA.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.CCorA.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -10,11 +10,13 @@
cat("Pillai's trace: ", format(x$Pillai, ...), "\n")
cat("\n")
cat("Significance of Pillai's trace:\n")
+
+ cat("from F-distribution: ", format.pval(x$p.Pillai), "\n")
if (x$nperm > 0) {
- cat("based on", x$nperm, "permutations: ")
+ cat("based on permutations: ")
cat(x$p.perm,"\n")
+ cat(howHead(x$control), "\n")
}
- cat("from F-distribution: ", format.pval(x$p.Pillai), "\n\n")
out <- rbind("Eigenvalues" = x$EigenValues, "Canonical Correlations" = x$CanCorr)
colnames(out) <- colnames(x$Cy)
printCoefmat(out, ...)
Modified: pkg/vegan/R/print.anosim.R
===================================================================
--- pkg/vegan/R/print.anosim.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.anosim.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -1,4 +1,4 @@
-"print.anosim" <-
+`print.anosim` <-
function (x, digits = max(3, getOption("digits") - 3), ...)
{
cat("\nCall:\n")
@@ -10,10 +10,8 @@
if (nperm) {
cat(" Significance:", format.pval(x$signif),
"\n\n")
- cat("Based on ", nperm, " permutations")
+ cat(howHead(x$control))
}
- if (!is.null(x$strata))
- cat(", stratified within", x$strata)
- cat("\n\n")
+ cat("\n")
invisible(x)
}
Modified: pkg/vegan/R/print.factorfit.R
===================================================================
--- pkg/vegan/R/print.factorfit.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.factorfit.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -1,4 +1,4 @@
-"print.factorfit" <-
+`print.factorfit` <-
function (x, ...)
{
cat("Centroids:\n")
@@ -7,10 +7,7 @@
out <- cbind(r2 = x$r, "Pr(>r)" = x$pvals)
if (x$permutations) {
printCoefmat(out, has.Pvalue = TRUE, ...)
- cat("P values based on", x$permutations, "permutations")
- if (!is.null(x$strata))
- cat(", stratified within", x$strata)
- cat(".\n")
+ cat(howHead(x$control))
}
else printCoefmat(out, na.print = "", ...)
invisible(x)
Modified: pkg/vegan/R/print.mantel.R
===================================================================
--- pkg/vegan/R/print.mantel.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.mantel.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -16,11 +16,9 @@
out <- quantile(x$perm, c(0.9, 0.95, 0.975, 0.99))
cat("Upper quantiles of permutations (null model):\n")
print(out, digits = 3)
- cat("\nBased on", nperm, "permutations")
- if (!is.null(x$strata))
- cat(", stratified within", x$strata)
+ cat(howHead(x$control))
}
- cat("\n\n")
+ cat("\n")
invisible(x)
}
Modified: pkg/vegan/R/print.mrpp.R
===================================================================
--- pkg/vegan/R/print.mrpp.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.mrpp.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -28,9 +28,7 @@
cat("Significance of delta:", format.pval(x$Pvalue),
"\n")
}
- cat("Based on ", nperm, " permutations")
- if (!is.null(x$strata))
- cat(", stratified within", x$strata)
- cat("\n\n")
+ cat(howHead(x$control))
+ cat("\n")
invisible(x)
}
Modified: pkg/vegan/R/print.mso.R
===================================================================
--- pkg/vegan/R/print.mso.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.mso.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -4,6 +4,8 @@
NextMethod("print", x, digits = digits, ...)
cat("mso variogram:\n\n")
print(x$vario, digits = digits, ...)
+ if(!is.null(attr(x$vario, "control")))
+ cat("\n", howHead(attr(x$vario, "control")), "\n", sep="")
invisible(x)
}
Modified: pkg/vegan/R/print.permutest.betadisper.R
===================================================================
--- pkg/vegan/R/print.permutest.betadisper.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.permutest.betadisper.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -5,7 +5,7 @@
cat("\n")
writeLines(strwrap("Permutation test for homogeneity of multivariate dispersions\n"))
##cat("\n")
- print(x$control)
+ cat(howHead(x$control))
nc <- dim(x$tab)[2]
cn <- colnames(x$tab)
has.P <- substr(cn[nc], 1, 3) == "Pr("
Modified: pkg/vegan/R/print.protest.R
===================================================================
--- pkg/vegan/R/print.protest.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.protest.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -8,7 +8,7 @@
cat("Correlation in a symmetric Procrustes rotation: ")
cat(formatC(x$t0, digits = digits), "\n")
cat("Significance: ")
- cat(format.pval(x$signif),"\n")
+ cat(format.pval(x$signif),"\n\n")
cat(howHead(x$control))
cat("\n")
invisible(x)
Modified: pkg/vegan/R/print.vectorfit.R
===================================================================
--- pkg/vegan/R/print.vectorfit.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/print.vectorfit.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -5,10 +5,7 @@
printCoefmat(out, na.print = "",
zap.ind = seq_len(ncol(out)-2), ...)
if (x$permutations) {
- cat("P values based on", x$permutations, "permutations")
- if (!is.null(x$strata))
- cat(", stratified within", x$strata)
- cat(".\n")
+ cat(howHead(x$control))
}
invisible(x)
}
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/simper.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -100,6 +100,7 @@
if (isParal && !isMulticore && !hasClus)
stopCluster(parallel)
attr(outlist, "permutations") <- nperm
+ attr(outlist, "control") <- attr(perm, "control")
class(outlist) <- "simper"
outlist
}
@@ -141,6 +142,7 @@
}
attr(out, "digits") <- digits
attr(out, "permutations") <- attr(object, "permutations")
+ attr(out, "control") <- attr(object, "control")
class(out) <- "summary.simper"
out
}
@@ -167,8 +169,8 @@
symbols = c("***", "**", "*", ".", " ")), "legend")
cat("---\nSignif. codes: ", leg, "\n")
}
- if ((np <- attr(x, "permutations")) > 0)
- cat("P-values based on", np, "permutations\n")
+ if (!is.null(attr(x, "control")))
+ cat(howHead(attr(x, "control")))
invisible(x)
}
Modified: pkg/vegan/R/vectorfit.R
===================================================================
--- pkg/vegan/R/vectorfit.R 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/R/vectorfit.R 2014-09-16 14:13:14 UTC (rev 2883)
@@ -54,10 +54,7 @@
else pvals <- NULL
sol <- list(arrows = heads, r = r, permutations = permutations,
pvals = pvals)
- if (!missing(strata)) {
- sol$strata <- deparse(substitute(strata))
- sol$stratum.values <- strata
- }
+ sol$control <- attr(permat, "control")
class(sol) <- "vectorfit"
sol
}
Modified: pkg/vegan/man/CCorA.Rd
===================================================================
--- pkg/vegan/man/CCorA.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/CCorA.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -105,6 +105,8 @@
\item{ corr.X.Cx }{ Scores of X variables in X biplot, computed as cor(X,Cx). }
\item{ corr.Y.Cx }{ cor(Y,Cy) available for plotting variables Y in space of X manually. }
\item{ corr.X.Cy }{ cor(X,Cx) available for plotting variables X in space of Y manually. }
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
\item{ call }{ Call to the CCorA function. }
}
Modified: pkg/vegan/man/anosim.Rd
===================================================================
--- pkg/vegan/man/anosim.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/anosim.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -85,6 +85,8 @@
\item{dis.rank}{Rank of dissimilarity entry.}
\item{dissimilarity}{The name of the dissimilarity index: the
\code{"method"} entry of the \code{dist} object.}
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
}
\references{
Clarke, K. R. (1993). Non-parametric multivariate analysis of changes
Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/envfit.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -162,6 +162,8 @@
\item{centroids}{Class centroids from \code{factorfit}.}
\item{r}{Goodness of fit statistic: Squared correlation coefficient}
\item{permutations}{Number of permutations.}
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
\item{pvals}{Empirical P-values for each variable.}
Function \code{envfit} returns a list of class \code{envfit} with
Modified: pkg/vegan/man/mantel.Rd
===================================================================
--- pkg/vegan/man/mantel.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/mantel.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -73,6 +73,8 @@
permuted values can be inspected with \code{\link{density.mantel}}
function.}
\item{permutations}{Number of permutations.}
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
}
\references{ The test is due to Mantel, of course, but the
current implementation is based on Legendre and Legendre.
Modified: pkg/vegan/man/mrpp.Rd
===================================================================
--- pkg/vegan/man/mrpp.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/mrpp.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -148,6 +148,8 @@
calculated from each of the permuted datasets. The distribution of
this item can be inspected with \code{\link{density.mrpp}} function.}
\item{permutations}{The number of permutations used.}
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
}
\references{
B. McCune and J. B. Grace. 2002. \emph{Analysis of Ecological
Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd 2014-09-16 07:13:05 UTC (rev 2882)
+++ pkg/vegan/man/procrustes.Rd 2014-09-16 14:13:14 UTC (rev 2883)
@@ -165,6 +165,8 @@
function.}
\item{signif}{`Significance' of \code{t}}
\item{permutations}{Number of permutations.}
+ \item{control}{A list of control values for the permutations
+ as returned by the function \code{\link[permute]{how}}.}
\item{control}{the list passed to argument \code{control} describing
the permutation design.}
}
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