[Vegan-commits] r2877 - in pkg/vegan: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 28 10:50:50 CEST 2014
Author: jarioksa
Date: 2014-08-28 10:50:50 +0200 (Thu, 28 Aug 2014)
New Revision: 2877
Modified:
pkg/vegan/R/betadisper.R
pkg/vegan/R/biplot.CCorA.R
pkg/vegan/R/bstick.cca.R
pkg/vegan/R/decorana.R
pkg/vegan/R/ordipointlabel.R
pkg/vegan/R/ordispider.R
pkg/vegan/R/ordisurf.R
pkg/vegan/R/points.cca.R
pkg/vegan/R/read.cep.R
pkg/vegan/R/scores.default.R
pkg/vegan/R/text.cca.R
pkg/vegan/R/tolerance.cca.R
pkg/vegan/man/dune.taxon.Rd
Log:
Merge branch 'master' into r-forge-svn-local
Modified: pkg/vegan/R/betadisper.R
===================================================================
--- pkg/vegan/R/betadisper.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/betadisper.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -68,7 +68,7 @@
n <- n - sum(gr.na)
## update labels
labs <- labs[!gr.na]
- warning("Missing observations due to 'group' removed.")
+ warning("missing observations due to 'group' removed")
}
## remove NA's in d
if(any(x.na <- apply(x, 1, function(x) any(is.na(x))))) {
@@ -78,7 +78,7 @@
n <- n - sum(x.na)
## update labels
labs <- labs[!x.na]
- warning("Missing observations due to 'd' removed.")
+ warning("missing observations due to 'd' removed")
}
x <- x + t(x)
x <- dblcen(x)
Modified: pkg/vegan/R/biplot.CCorA.R
===================================================================
--- pkg/vegan/R/biplot.CCorA.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/biplot.CCorA.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -22,11 +22,11 @@
epsilon <- sqrt(.Machine$double.eps)
if(length(which(x$Eigenvalues > epsilon)) == 1)
- stop("Plot of axes (", paste(plot.axes, collapse=","),
- ") not drawn because the solution has a single dimension.")
+ stop("plot of axes (", paste(plot.axes, collapse=","),
+ ") not drawn because the solution has a single dimension")
if(max(plot.axes) > length(which(x$Eigenvalues > epsilon)))
- stop("Plot of axes (", paste(plot.axes, collapse=","),
- ") not drawn because the solution has fewer dimensions.")
+ stop("plot of axes (", paste(plot.axes, collapse=","),
+ ") not drawn because the solution has fewer dimensions")
if (missing(xlabs))
xlabs <- rownames(x$Cy)
Modified: pkg/vegan/R/bstick.cca.R
===================================================================
--- pkg/vegan/R/bstick.cca.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/bstick.cca.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -4,7 +4,7 @@
if(!inherits(n, c("rda", "cca")))
stop("'n' not of class \"cca\" or \"rda\"")
if(!is.null(n$CCA) && n$CCA$rank > 0)
- stop("'bstick' only for unconstrained models.")
+ stop("'bstick' only for unconstrained models")
## No idea how to define bstick for capscale with negative
## eigenvalues
if (inherits(n, "capscale") && !is.null(n$CA$imaginary.rank))
Modified: pkg/vegan/R/decorana.R
===================================================================
--- pkg/vegan/R/decorana.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/decorana.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -8,11 +8,11 @@
ZEROEIG <- 1e-7 # consider as zero eigenvalue
veg <- as.matrix(veg)
if (any(rowSums(veg) <= 0))
- stop("All row sums must be >0 in the community matrix: remove empty sites.")
+ stop("all row sums must be >0 in the community matrix: remove empty sites")
if (any(veg < 0))
stop("'decorana' cannot handle negative data entries")
if (any(colSums(veg) <= 0))
- warning("Some species were removed because they were missing in the data.")
+ warning("some species were removed because they were missing in the data")
nr <- nrow(veg)
nc <- ncol(veg)
mk <- mk + 4
Modified: pkg/vegan/R/ordipointlabel.R
===================================================================
--- pkg/vegan/R/ordipointlabel.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/ordipointlabel.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -15,7 +15,7 @@
if(isTRUE(all.equal(length(display), 1L))) {
xy[[1]] <- .checkSelect(select, xy[[1]])
} else {
- warning("'select' does not apply when plotting more than one set of scores.\n'select' was ignored.")
+ warning("'select' does not apply when plotting more than one set of scores--\n'select' was ignored")
}
}
if (length(display) > 1) {
Modified: pkg/vegan/R/ordispider.R
===================================================================
--- pkg/vegan/R/ordispider.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/ordispider.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -42,16 +42,19 @@
kk <- complete.cases(pts)
for (is in inds) {
gr <- out[groups == is & kk]
- if (length(gr) > 1) {
- X <- pts[gr, ]
+ if (length(gr)) {
+ X <- pts[gr, , drop = FALSE]
W <- w[gr]
- ave <- switch(spiders,
- "centroid" = apply(X, 2, weighted.mean, w = W),
- "median" = ordimedian(X, rep(1, nrow(X)))
- )
+ if (length(gr) > 1) {
+ ave <- switch(spiders,
+ "centroid" = apply(X, 2, weighted.mean, w = W),
+ "median" = ordimedian(X, rep(1, nrow(X))))
+ ordiArgAbsorber(ave[1], ave[2], X[, 1], X[, 2],
+ FUN = segments, ...)
+ } else {
+ ave <- X
+ }
spids[,gr] <- ave
- ordiArgAbsorber(ave[1], ave[2], X[, 1], X[, 2],
- FUN = segments, ...)
if (label) {
cntrs <- rbind(cntrs, ave)
names <- c(names, is)
Modified: pkg/vegan/R/ordisurf.R
===================================================================
--- pkg/vegan/R/ordisurf.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/ordisurf.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -25,7 +25,7 @@
{
weights.default <- function(object, ...) NULL
if(!missing(thinplate)) {
- warning("Use of 'thinplate' is deprecated and will soon be removed;\nuse 'isotropic' instead.")
+ warning("use of 'thinplate' is deprecated and will soon be removed;\nuse 'isotropic' instead")
isotropic <- thinplate
}
## GRID no user-definable - why 31?
@@ -48,9 +48,9 @@
x2 <- X[, 2]
## handle fx - allow vector of length up to two
if(!(missfx <- missing(fx)) && missing(knots))
- warning("Requested fixed d.f. splines but without specifying 'knots'.\nSwitching to 'fx = FALSE'.")
+ warning("requested fixed d.f. splines but without specifying 'knots':\nswitching to 'fx = FALSE'")
if (length(fx) > 2L)
- warning("Length of 'fx' supplied exceeds '2'. Using the first two.")
+ warning("length of 'fx' supplied exceeds '2': using the first two")
## expand fx robustly, no matter what length supplied
fx <- rep(fx, length.out = 2)
## can't have `fx = TRUE` and `select = TRUE`
@@ -59,17 +59,17 @@
warning("'fx = TRUE' requested; using 'select = FALSE'")
select <- FALSE
} else if(!miss.select && isTRUE(select)){
- stop("Fixed d.f. splines ('fx = TRUE') incompatible with 'select = TRUE'")
+ stop("fixed d.f. splines ('fx = TRUE') incompatible with 'select = TRUE'")
}
}
## handle knots - allow vector of length up to two
if (length(knots) > 2L)
- warning("Length of 'knots' supplied exceeds '2'. Using the first two.")
+ warning("length of 'knots' supplied exceeds '2': using the first two")
## expand knots robustly, no matter what length supplied
knots <- rep(knots, length.out = 2)
## handle the bs - we only allow some of the possible options
if (length(bs) > 2L)
- warning("Number of basis types supplied exceeds '2'. Only using the first two.")
+ warning("number of basis types supplied exceeds '2': only using the first two")
bs <- rep(bs, length.out = 2)
## check allowed types
BS <- c("tp","ts","cr","cs","ds","ps","ad")
@@ -83,7 +83,7 @@
}
## can't use "cr", "cs", "ps" in 2-d smoother with s()
if(isTRUE(isotropic) && any(bs %in% c("cr", "cs", "ps"))) {
- stop("Bases \"cr\", \"cs\", and \"ps\" not allowed in isotropic smooths.")
+ stop("bases \"cr\", \"cs\", and \"ps\" not allowed in isotropic smooths")
}
## Build formula
if (knots[1] <= 0) {
Modified: pkg/vegan/R/points.cca.R
===================================================================
--- pkg/vegan/R/points.cca.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/points.cca.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -4,7 +4,7 @@
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
- stop("Only one 'display' item can be added in one command.")
+ stop("only one 'display' item can be added in one command")
pts <- scores(x, choices = choices, display = display, scaling = scaling,
const)
if (!missing(select))
Modified: pkg/vegan/R/read.cep.R
===================================================================
--- pkg/vegan/R/read.cep.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/read.cep.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -12,7 +12,7 @@
if (trace)
cat("File", file, "\n")
if (file.access(file, 4) < 0) {
- stop("File does not exist or is not readable.")
+ stop("file does not exist or is not readable")
}
on.exit(.Fortran("cepclose", PACKAGE = "vegan"))
cep <- .Fortran("cephead", file = file, kind = integer(1),
@@ -66,8 +66,8 @@
PACKAGE = "vegan"))
if (cd$ier) {
if (cd$ier == 1)
- stop("Too many non-zero entries: increase maxdata.")
- else stop("Unknown and obscure error: don't know what to do.")
+ stop("too many non-zero entries: increase maxdata")
+ else stop("unknown and obscure error: I do not know what to do")
}
if (trace)
cat("Read", cd$nsp, "species, ", cd$nst, "sites.\n")
Modified: pkg/vegan/R/scores.default.R
===================================================================
--- pkg/vegan/R/scores.default.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/scores.default.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -39,11 +39,21 @@
}
else if (is.numeric(x)) {
X <- as.matrix(x)
- ## as.matrix() changes 1-row scores into 1-col matrix: this is
+ ## as.matrix() changes a score vector to 1-col matrix: this is
## a hack which may fail sometimes (but probably less often
## than without this hack):
- if (ncol(X) == 1 && nrow(X) == length(choices))
- X <- t(X)
+
+ ## Removed this hack after an issue raised by
+ ## vanderleidebastiani in github. He was worried for getting
+ ## an error when 'choices' were not given with genuinely 1-dim
+ ## (1-col) results. At a second look, it seems that this hack
+ ## will fail both with missing 'choices', and also often with
+ ## 'choices' given because 'choices' are only applied later,
+ ## so that nrow(X) > length(choices). Only vectors (dim arg
+ ## missing) should fail here. Let's see...
+
+ ##if (ncol(X) == 1 && nrow(X) == length(choices))
+ ## X <- t(X)
}
if (is.null(rownames(X))) {
root <- substr(display, 1, 4)
Modified: pkg/vegan/R/text.cca.R
===================================================================
--- pkg/vegan/R/text.cca.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/text.cca.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -4,7 +4,7 @@
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
- stop("Only one 'display' item can be added in one command.")
+ stop("only one 'display' item can be added in one command")
pts <- scores(x, choices = choices, display = display, scaling = scaling,
const)
if (!missing(labels))
Modified: pkg/vegan/R/tolerance.cca.R
===================================================================
--- pkg/vegan/R/tolerance.cca.R 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/R/tolerance.cca.R 2014-08-28 08:50:50 UTC (rev 2877)
@@ -27,7 +27,7 @@
which = c("species","sites"),
scaling = 2, useN2 = FALSE, ...) {
if(inherits(x, "rda"))
- stop("Tolerances only available for unimodal ordinations.")
+ stop("tolerances only available for unimodal ordinations")
if(missing(which))
which <- "species"
## reconstruct species/response matrix Y - up to machine precision!
Modified: pkg/vegan/man/dune.taxon.Rd
===================================================================
--- pkg/vegan/man/dune.taxon.Rd 2014-08-25 10:34:01 UTC (rev 2876)
+++ pkg/vegan/man/dune.taxon.Rd 2014-08-28 08:50:50 UTC (rev 2877)
@@ -23,7 +23,7 @@
\details{
The classification of vascular plants is based on APG (2009), and
- that of mosses from Hill et al. (2006).
+ that of mosses on Hill et al. (2006).
}
\references{
APG [Angiosperm Phylogeny Group] (2009) An update of the Angiosperm
More information about the Vegan-commits
mailing list