[Vegan-commits] r2457 - in branches/2.0: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 1 18:30:51 CET 2013
Author: jarioksa
Date: 2013-03-01 18:30:51 +0100 (Fri, 01 Mar 2013)
New Revision: 2457
Modified:
branches/2.0/R/nestedtemp.R
branches/2.0/R/points.cca.R
branches/2.0/R/print.monoMDS.R
branches/2.0/R/text.cca.R
branches/2.0/inst/ChangeLog
branches/2.0/man/plot.cca.Rd
Log:
merge small fixes to vegan 2.0-7 (2448 partly, 2449, 2452, 2453)
- print metaMDS explains clearer the stopping criteria (r2448, 2449)
- plot/text.cca gained argument axis.bp = TRUE (r2452)
- nestedtemp failed with fill < 0.38% (r2453)
Modified: branches/2.0/R/nestedtemp.R
===================================================================
--- branches/2.0/R/nestedtemp.R 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/R/nestedtemp.R 2013-03-01 17:30:51 UTC (rev 2457)
@@ -48,7 +48,23 @@
fillfun <- function(x, p) 1 - (1-(1-x)^p)^(1/p)
intfun <- function(p, fill)
integrate(fillfun, lower=0, upper=1, p=p)$value - fill
- p <- uniroot(intfun, c(0,20), fill=fill)$root
+ ## 'p' will depend on 'fill', and fill = 0.0038 correspond to p =
+ ## 20. Sometimes the fill is lower, and therefore we try() to see
+ ## if we need to move the bracket up. We should need to do this
+ ## very rarely.
+ lo <- 0
+ hi <- 20
+ repeat{
+ sol <- try(uniroot(intfun, c(lo,hi), fill=fill), silent = TRUE)
+ if (inherits(sol, "try-error")) {
+ if (hi > 640) # bail out
+ stop(gettextf("matrix is too sparse, fill is %g"), fill)
+ lo <- hi
+ hi <- hi + hi
+ } else
+ break
+ }
+ p <- sol$root
## row coordinates of the fill line for all matrix entries
out <- matrix(0, nrow=length(r), ncol=length(c))
for (i in 1:length(r))
Modified: branches/2.0/R/points.cca.R
===================================================================
--- branches/2.0/R/points.cca.R 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/R/points.cca.R 2013-03-01 17:30:51 UTC (rev 2457)
@@ -1,6 +1,6 @@
`points.cca` <-
function (x, display = "sites", choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, const, ...)
+ arrow.mul, head.arrow = 0.05, select, const, axis.bp = TRUE, ...)
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
@@ -28,10 +28,12 @@
arrows(0, 0, pts[, 1], pts[, 2], length = head.arrow,
...)
pts <- pts * 1.1
- axis(3, at = c(-arrow.mul, 0, arrow.mul), labels = rep("",
- 3))
- axis(4, at = c(-arrow.mul, 0, arrow.mul), labels = c(-1,
- 0, 1))
+ if (axis.bp) {
+ axis(3, at = c(-arrow.mul, 0, arrow.mul),
+ labels = rep("", 3))
+ axis(4, at = c(-arrow.mul, 0, arrow.mul),
+ labels = c(-1, 0, 1))
+ }
return(invisible())
}
points(pts, ...)
Modified: branches/2.0/R/print.monoMDS.R
===================================================================
--- branches/2.0/R/print.monoMDS.R 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/R/print.monoMDS.R 2013-03-01 17:30:51 UTC (rev 2457)
@@ -31,10 +31,10 @@
cat(", rotated to principal components")
cat("\n")
stoplab <- switch(x$icause,
- "Maximum number of iteration reached",
- "Stress nearly zero",
- "Stress nearly unchanged",
- "Scale factor of gradient nearly zero")
+ "Maximum number of iterations (maxit) reached",
+ "Stress nearly zero (< smin)",
+ "Stress nearly unchanged (ratio > sratmax)",
+ "Scale factor of gradient nearly zero (< sfgrmin)")
cat("Stopped after ", x$iters, " iterations: ", stoplab, "\n", sep="")
invisible(x)
}
Modified: branches/2.0/R/text.cca.R
===================================================================
--- branches/2.0/R/text.cca.R 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/R/text.cca.R 2013-03-01 17:30:51 UTC (rev 2457)
@@ -1,6 +1,6 @@
`text.cca` <-
function (x, display = "sites", labels, choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, const, ...)
+ arrow.mul, head.arrow = 0.05, select, const, axis.bp = TRUE, ...)
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
@@ -30,10 +30,12 @@
arrows(0, 0, pts[, 1], pts[, 2], length = head.arrow,
...)
pts <- pts * 1.1
- axis(3, at = c(-arrow.mul, 0, arrow.mul), labels = rep("",
- 3))
- axis(4, at = c(-arrow.mul, 0, arrow.mul), labels = c(-1,
- 0, 1))
+ if (axis.bp) {
+ axis(side = 3, at = c(-arrow.mul, 0, arrow.mul),
+ labels = rep("", 3))
+ axis(side = 4, at = c(-arrow.mul, 0, arrow.mul),
+ labels = c(-1, 0, 1))
+ }
}
text(pts, labels = rownames(pts), ...)
invisible()
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/inst/ChangeLog 2013-03-01 17:30:51 UTC (rev 2457)
@@ -4,6 +4,10 @@
Version 2.0-7 (opened February 17, 2013)
+ * merge r2453: nestedtemp failed with fill < 0.38%
+ * merge r2452: plot/text.cca gained axis.bp = TRUE argument.
+ * merge r2448 (partly), 2449: print.monoMDS clearer about
+ convergence. Only this part merged: metaMDSiter untouched.
* merge r2443: edit cca.object.Rd.
* merge r2434: return wcmdscale object always with non-default
arguments.
Modified: branches/2.0/man/plot.cca.Rd
===================================================================
--- branches/2.0/man/plot.cca.Rd 2013-03-01 03:56:33 UTC (rev 2456)
+++ branches/2.0/man/plot.cca.Rd 2013-03-01 17:30:51 UTC (rev 2457)
@@ -21,9 +21,9 @@
\method{plot}{cca}(x, choices = c(1, 2), display = c("sp", "wa", "cn"),
scaling = 2, type, xlim, ylim, const, ...)
\method{text}{cca}(x, display = "sites", labels, choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, const, ...)
+ arrow.mul, head.arrow = 0.05, select, const, axis.bp = TRUE, ...)
\method{points}{cca}(x, display = "sites", choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, const, ...)
+ arrow.mul, head.arrow = 0.05, select, const, axis.bp = TRUE, ...)
\method{scores}{cca}(x, choices=c(1,2), display=c("sp","wa","cn"), scaling=2, ...)
\method{scores}{rda}(x, choices=c(1,2), display=c("sp","wa","cn"), scaling=2,
const, ...)
@@ -74,6 +74,7 @@
\samp{decision-vegan.pdf} with \code{\link{vegandocs}} for details
and discussion). If \code{const} is a vector of two items, the first
is used for species, and the second item for site scores.}
+ \item{axis.bp}{Draw \code{\link{axis}} for biplot arrows.}
\item{axes}{Number of axes in summaries.}
\item{digits}{Number of digits in output.}
\item{n, head, tail}{Number of rows printed from the head and tail of
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