[Vegan-commits] r833 - in branches/1.15: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 28 15:09:39 CEST 2009
Author: jarioksa
Date: 2009-05-28 15:09:38 +0200 (Thu, 28 May 2009)
New Revision: 833
Modified:
branches/1.15/DESCRIPTION
branches/1.15/R/anova.ccabyaxis.R
branches/1.15/R/anova.ccabymargin.R
branches/1.15/R/anova.ccabyterm.R
branches/1.15/R/kendall.global.R
branches/1.15/R/ordilattice.getEnvfit.R
branches/1.15/R/orditkplot.R
branches/1.15/R/ordixyplot.R
branches/1.15/R/panel.ordi.R
branches/1.15/R/taxa2dist.R
branches/1.15/inst/ChangeLog
branches/1.15/man/metaMDS.Rd
Log:
merged some fixes between r809 andr832 to branches for possible 1.15-3 release
Modified: branches/1.15/DESCRIPTION
===================================================================
--- branches/1.15/DESCRIPTION 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/DESCRIPTION 2009-05-28 13:09:38 UTC (rev 833)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 1.15-2
-Date: April 15, 2009
+Version: 1.15-3
+Date: May 28, 2009
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson,
Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
Modified: branches/1.15/R/anova.ccabyaxis.R
===================================================================
--- branches/1.15/R/anova.ccabyaxis.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/anova.ccabyaxis.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -26,20 +26,20 @@
bigperm <- out$N.Perm[1]
environment(object$terms) <- environment()
if (rnk > 1) {
- for (i in 2:rnk) {
- zz <- paste(paste("Condition(", axnam[1:(i - 1)],
+ for (.ITRM in 2:rnk) {
+ zz <- paste(paste("Condition(", axnam[1:(.ITRM - 1)],
")"), collapse = "+")
fla <- update(formula(object), paste(". ~ . +", zz))
sol <- update(object, fla, data = newdata)
assign(".Random.seed", seed, envir = .GlobalEnv)
- out[i, ] <- as.matrix(anova(sol, first = TRUE, ...))[1,
+ out[.ITRM, ] <- as.matrix(anova(sol, first = TRUE, ...))[1,
]
- if (out[i, "N.Perm"] > bigperm) {
- bigperm <- out[i, "N.Perm"]
+ if (out[.ITRM, "N.Perm"] > bigperm) {
+ bigperm <- out[.ITRM, "N.Perm"]
bigseed <- get(".Random.seed", envir = .GlobalEnv,
inherits = FALSE)
}
- if (out[i, "Pr(>F)"] > cutoff)
+ if (out[.ITRM, "Pr(>F)"] > cutoff)
break
}
}
Modified: branches/1.15/R/anova.ccabymargin.R
===================================================================
--- branches/1.15/R/anova.ccabymargin.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/anova.ccabymargin.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -10,12 +10,12 @@
trms <- trms[keep]
ntrms <- length(trms)
bigperm <- 0
- for (i in 1:ntrms) {
+ for (.ITRM in 1:ntrms) {
fla <- formula(object)
## Put all trms except current into Condition() and update
## formula
if (length(alltrms) > 1) {
- keeptrms <- alltrms[!(alltrms==trms[i])]
+ keeptrms <- alltrms[!(alltrms==trms[.ITRM])]
updfla <- paste("Condition(",paste(keeptrms, collapse="+"), ")")
fla <- update(fla, paste(". ~ . + ", updfla))
}
@@ -29,12 +29,12 @@
bigseed <- get(".Random.seed", envir = .GlobalEnv,
inherits = FALSE)
}
- if (i == 1) {
+ if (.ITRM == 1) {
seed <- attr(tmp, "Random.seed")
sol <- tmp
}
else {
- sol <- rbind(sol[1:(i-1),], as.matrix(tmp[1,]), sol[i,])
+ sol <- rbind(sol[1:(.ITRM-1),], as.matrix(tmp[1,]), sol[.ITRM,])
}
assign(".Random.seed", seed, envir = .GlobalEnv)
}
Modified: branches/1.15/R/anova.ccabyterm.R
===================================================================
--- branches/1.15/R/anova.ccabyterm.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/anova.ccabyterm.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -21,21 +21,21 @@
pchi[ntrm, ] <- sim$num
df[ntrm:(ntrm + 1)] <- sim$df
chi[ntrm:(ntrm + 1)] <- sim$chi
- for (i in ntrm:2) {
+ for (.ITRM in ntrm:2) {
if (ntrm < 2)
break
assign(".Random.seed", sim$Random.seed, envir = .GlobalEnv)
- fla <- as.formula(paste(" . ~ . -", trmlab[i]))
+ fla <- as.formula(paste(" . ~ . -", trmlab[.ITRM]))
object <- update(object, fla)
if (is.null(object$CCA))
break
sim <- permutest.cca(object, permutations = step, ...)
- pchi[i, ] <- pchi[i, ] - sim$num
- chi[i] <- chi[i] - sim$chi[1]
- df[i] <- df[i] - sim$df[1]
- pchi[i - 1, ] <- sim$num
- chi[i - 1] <- sim$chi[1]
- df[i - 1] <- sim$df[1]
+ pchi[.ITRM, ] <- pchi[.ITRM, ] - sim$num
+ chi[.ITRM] <- chi[.ITRM] - sim$chi[1]
+ df[.ITRM] <- df[.ITRM] - sim$df[1]
+ pchi[.ITRM - 1, ] <- sim$num
+ chi[.ITRM - 1] <- sim$chi[1]
+ df[.ITRM - 1] <- sim$df[1]
}
Fval <- chi/df/(chi[ntrm + 1]/df[ntrm + 1])
Fval[ntrm + 1] <- NA
Modified: branches/1.15/R/kendall.global.R
===================================================================
--- branches/1.15/R/kendall.global.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/kendall.global.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -47,7 +47,8 @@
p.i <- n.per.gr[i]
if(p.i < 2) stop("There is a single variable in group ",gr.lev[i])
##CC# Correction factors for tied ranks (eq. 3.3)
- t.ranks <- apply(R[,gr[[i]]], 2, function(x) summary(as.factor(x)))
+ t.ranks <- apply(R[,gr[[i]]], 2,
+ function(x) summary(as.factor(x), maxsum=n))
T. <- sum(unlist(lapply(t.ranks, function(x) sum((x^3)-x))))
##CC# Compute the Sum of squares of the uncentred ranks (S) (eq. 3.1)
Modified: branches/1.15/R/ordilattice.getEnvfit.R
===================================================================
--- branches/1.15/R/ordilattice.getEnvfit.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/ordilattice.getEnvfit.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -1,7 +1,7 @@
`ordilattice.getEnvfit` <-
function(formula, object, envfit, choices = 1:3, ...)
{
- if (!missing(envfit))
+ if (!missing(envfit) && !is.null(envfit))
object <- envfit
bp <- scores(object, display = "bp", choices = choices)
cn <- scores(object, display = "cn", choices = choices)
Modified: branches/1.15/R/orditkplot.R
===================================================================
--- branches/1.15/R/orditkplot.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/orditkplot.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -323,9 +323,9 @@
labfnt <- labfnt[take]
## Ranges and pretty values for axes
if (missing(xlim))
- xlim <- range(sco[,1])
+ xlim <- range(sco[,1], na.rm = TRUE)
if (missing(ylim))
- ylim <- range(sco[,2])
+ ylim <- range(sco[,2], na.rm = TRUE)
xpretty <- pretty(xlim)
ypretty <- pretty(ylim)
## Extend ranges by 4%
Modified: branches/1.15/R/ordixyplot.R
===================================================================
--- branches/1.15/R/ordixyplot.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/ordixyplot.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -15,6 +15,8 @@
formula <- as.formula(paste(v[2], "~", v[1]))
}
if ("biplot" %in% type && (!is.null(x$CCA) || !missing(envfit))) {
+ if (missing(envfit))
+ envfit <- NULL
env <- localOrdilattice.getEnvfit(formula, x, envfit, choices, ...)
if (!is.null(env$arrows)) {
mul <- apply(p[,colnames(env$arrows)], 2, range)/apply(env$arrows, 2, range)
Modified: branches/1.15/R/panel.ordi.R
===================================================================
--- branches/1.15/R/panel.ordi.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/panel.ordi.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -4,11 +4,11 @@
panel.xyplot(x, y, type = type, ...)
tp <- trellis.par.get()
if ("biplot" %in% type && !is.null(biplot$arrows)) {
- panel.arrows(0, 0, biplot$arrows[,1], biplot$arrows[,2],
+ panel.arrows(0, 0, biplot$arrows[,2], biplot$arrows[,1],
col=tp$superpose.symbol$col, ...)
}
if ("biplot" %in% type && !is.null(biplot$centres)) {
- panel.xyplot(biplot$centres[,1], biplot$centres[,2],
+ panel.xyplot(biplot$centres[,2], biplot$centres[,1],
col = tp$plot.symbol$col,
pch = "+", cex = 3*tp$plot.symbol$cex, lwd=2,
...)
Modified: branches/1.15/R/taxa2dist.R
===================================================================
--- branches/1.15/R/taxa2dist.R 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/R/taxa2dist.R 2009-05-28 13:09:38 UTC (rev 833)
@@ -37,7 +37,7 @@
warning("Labels are wrong: needed ", nrow(x), " got ", length(labels))
attr(out, "Labels") <- as.character(labels)
}
- if (!check && any(out) <= 0)
+ if (!check && any(out <= 0))
warning("you used 'check=FALSE' and some distances are zero -- was this intended?")
out
}
Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/inst/ChangeLog 2009-05-28 13:09:38 UTC (rev 833)
@@ -3,6 +3,26 @@
VEGAN STABLE VERSIONS
+Version 1.15-3 (opened 28 May, 2009)
+
+ * merged r832: wrong reference in metaMDS.Rd.
+
+ * merged r827: kendall.global: could get wrong counts of ties in
+ large data sets.
+
+ * merged r823: fixed wrong test of output validity in taxa2dist.
+
+ * merged r815: anova.cca(..., by = ) name clash if data were
+ indexed with 'i' in fitted model.
+
+ * merged r812: ordixyplot mixed x and y axes for biplot arrows and
+ env centres.
+
+ * merged r811: orditkplot copes with NA and NaN scores.
+
+ * merged r810: ordixyplot failed in constrained ordination (broken
+ in r108 in Nov 2007).
+
Version 1.15-2 (released to CRAN: 15 April, 2009)
* spantree.Rd: example plots use type = "t". Parallel change with
Modified: branches/1.15/man/metaMDS.Rd
===================================================================
--- branches/1.15/man/metaMDS.Rd 2009-05-27 16:15:25 UTC (rev 832)
+++ branches/1.15/man/metaMDS.Rd 2009-05-28 13:09:38 UTC (rev 833)
@@ -223,8 +223,8 @@
distance. \emph{Vegetatio} 69, 57--68.
Minchin, P.R. (1987) An evaluation of relative robustness
- of techniques for ecological ordinations. \emph{Vegetatio} 71,
- 145-156.
+ of techniques for ecological ordinations. \emph{Vegetatio} 69,
+ 89--107.
}
\author{ Jari Oksanen }
More information about the Vegan-commits
mailing list