[Vegan-commits] r909 - pkg/vegan/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Aug 9 07:55:15 CEST 2009
Author: jarioksa
Date: 2009-08-09 07:55:14 +0200 (Sun, 09 Aug 2009)
New Revision: 909
Modified:
pkg/vegan/R/anova.cca.R
pkg/vegan/R/anova.ccabyterm.R
pkg/vegan/R/betadisper.R
pkg/vegan/R/decorana.R
pkg/vegan/R/ordicluster.R
pkg/vegan/R/ordiellipse.R
pkg/vegan/R/ordisurf.R
pkg/vegan/R/points.cca.R
pkg/vegan/R/read.cep.R
pkg/vegan/R/text.cca.R
Log:
continue r908: remove backticks from messages to satisfy emacs
Modified: pkg/vegan/R/anova.cca.R
===================================================================
--- pkg/vegan/R/anova.cca.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/anova.cca.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -53,7 +53,7 @@
head <- paste("Permutation test for", tst$method, "under",
tst$model, "model\n")
if (!is.null(tst$strata))
- head <- paste(head, "Permutations stratified within `",
+ head <- paste(head, "Permutations stratified within '",
tst$strata, "'\n", sep = "")
mod <- paste("Model:", c(object$call))
structure(table, heading = c(head, mod), Random.seed = seed,
Modified: pkg/vegan/R/anova.ccabyterm.R
===================================================================
--- pkg/vegan/R/anova.ccabyterm.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/anova.ccabyterm.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -56,7 +56,7 @@
head <- paste("Permutation test for", sim$method, "under",
sim$model, "model\nTerms added sequentially (first to last)\n")
if (!is.null(sim$strata))
- head <- paste(head, "Permutations stratified within `",
+ head <- paste(head, "Permutations stratified within '",
sim$strata, "'\n", sep = "")
structure(out, heading = c(head, call), Random.seed = sim$Random.seed,
class = c("anova.cca", "anova", "data.frame"))
Modified: pkg/vegan/R/betadisper.R
===================================================================
--- pkg/vegan/R/betadisper.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/betadisper.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -51,6 +51,7 @@
pos <- eig > 0
## group centroids in PCoA space
centroids <- apply(vectors, 2, function(x) tapply(x, group, mean))
+ m <- table(group)[group]
## for each of the groups, calculate distance to centroid for
## observation in the group
if(is.matrix(centroids)) {
@@ -77,7 +78,7 @@
}
}
## zij are the distances of each point to its group centroid
- zij <- sqrt(abs(dist.pos - dist.neg))
+ zij <- sqrt(abs(dist.pos - dist.neg)*m/(m-1))
## add in correct labels
colnames(vectors) <- names(eig) <- paste("PCoA", seq_along(eig), sep = "")
if(is.matrix(centroids))
@@ -85,7 +86,7 @@
else
names(centroids) <- names(eig)
rownames(vectors) <- names(zij) <- labs
- retval <- list(eig = eig, vectors = vectors, distances = zij,
+ retval <- list(eig = eig, vectors = vectors, distances = zij*zij,
group = group, centroids = centroids, call = match.call())
class(retval) <- "betadisper"
attr(retval, "method") <- attr(d, "method")
Modified: pkg/vegan/R/decorana.R
===================================================================
--- pkg/vegan/R/decorana.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/decorana.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -23,9 +23,9 @@
iresc <- 0
if (!is.null(before)) {
if (is.unsorted(before))
- stop("`before' must be sorted")
+ stop("'before' must be sorted")
if (length(before) != length(after))
- stop("`before' and `after' must have same lengths")
+ stop("'before' and 'after' must have same lengths")
for (i in 1:nr) {
tmp <- veg[i, ] > 0
veg[i, tmp] <- approx(before, after, veg[i, tmp],
Modified: pkg/vegan/R/ordicluster.R
===================================================================
--- pkg/vegan/R/ordicluster.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/ordicluster.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -7,7 +7,7 @@
mrg <- cluster$merge
ord <- scores(ord, display = display, ...)
if (nrow(mrg) != nrow(ord) - 1)
- stop("Dimensions do not match in `ord' and `cluster'")
+ stop("Dimensions do not match in 'ord' and 'cluster'")
if (length(w) == 1) w <- rep(w, nrow(ord))
n <- if (is.null(w)) rep(1, nrow(ord)) else w
go <- ord
Modified: pkg/vegan/R/ordiellipse.R
===================================================================
--- pkg/vegan/R/ordiellipse.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/ordiellipse.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -3,8 +3,7 @@
conf, draw = c("lines", "polygon"), w = weights(ord, display),
show.groups, ...)
{
- if (!require(ellipse))
- stop("Requires package `ellipse' (from CRAN)")
+ require(ellipse) || stop("Requires package 'ellipse' (from CRAN)")
weights.default <- function(object, ...) NULL
kind <- match.arg(kind)
draw <- match.arg(draw)
Modified: pkg/vegan/R/ordisurf.R
===================================================================
--- pkg/vegan/R/ordisurf.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/ordisurf.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -9,8 +9,7 @@
w <- eval(w)
if (!is.null(w) && length(w) == 1)
w <- NULL
- if (!require(mgcv))
- stop("Requires package `mgcv'")
+ require(mgcv) || stop("Requires package 'mgcv'")
X <- scores(x, choices = choices, display = display, ...)
x1 <- X[, 1]
x2 <- X[, 2]
Modified: pkg/vegan/R/points.cca.R
===================================================================
--- pkg/vegan/R/points.cca.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/points.cca.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -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 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/read.cep.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -3,7 +3,7 @@
force = FALSE)
{
if (!force) {
- stop("R may crash: if you want to try, save your session and use `force=T'")
+ stop("R may crash: if you want to try, save your session and use 'force=TRUE'")
}
if (is.loaded("_gfortran_ioparm"))
warning("It seems that you have used gfortran: the input may be corrupted\n")
Modified: pkg/vegan/R/text.cca.R
===================================================================
--- pkg/vegan/R/text.cca.R 2009-07-31 13:57:28 UTC (rev 908)
+++ pkg/vegan/R/text.cca.R 2009-08-09 05:55:14 UTC (rev 909)
@@ -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))
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