[Analogue-commits] r298 - in pkg: . R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 16 13:15:37 CET 2013
Author: gsimpson
Date: 2013-01-16 13:15:36 +0100 (Wed, 16 Jan 2013)
New Revision: 298
Modified:
pkg/DESCRIPTION
pkg/R/fitted.timetrack.R
pkg/R/plot.timetrack.R
pkg/inst/ChangeLog
pkg/man/timetrack.Rd
pkg/tests/Examples/analogue-Ex.Rout.save
Log:
user-friendly improvements to timetrack; move to 0.11-0 for development
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/DESCRIPTION 2013-01-16 12:15:36 UTC (rev 298)
@@ -1,7 +1,7 @@
Package: analogue
Type: Package
Title: Analogue and weighted averaging methods for palaeoecology
-Version: 0.10-0
+Version: 0.11-0
Date: $Date$
Depends: R (>= 2.15.0), stats, graphics, vegan (>= 1.17-12), lattice, grid,
MASS, princurve, mgcv
Modified: pkg/R/fitted.timetrack.R
===================================================================
--- pkg/R/fitted.timetrack.R 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/R/fitted.timetrack.R 2013-01-16 12:15:36 UTC (rev 298)
@@ -1,6 +1,6 @@
`fitted.timetrack` <-
function(object, type = c("passive", "ordination"),
- model = NULL, ...)
+ model = NULL, choices = 1:2, ...)
{
if(missing(type))
type <- "passive"
@@ -9,9 +9,10 @@
if(is.null(object$ordination$CCA)) "CA" else "CCA"
}
if(isTRUE(all.equal(type, "passive"))) {
- fit <- fitted(unclass(object), ...)
+ fit <- fitted(unclass(object), ...)[, choices, drop = FALSE]
} else {
- fit <- fitted(object$ordination, model = model, ...)
+ fit <- fitted(object$ordination, model = model,
+ ...)[, choices, drop = FALSE]
}
- return(fit)
+ fit
}
Modified: pkg/R/plot.timetrack.R
===================================================================
--- pkg/R/plot.timetrack.R 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/R/plot.timetrack.R 2013-01-16 12:15:36 UTC (rev 298)
@@ -1,10 +1,24 @@
-`plot.timetrack` <- function(x, choices = 1:2,
+`plot.timetrack` <- function(x, choices = 1:2, order,
+ ptype = c("l", "p", "o", "b"),
pch = c(1,2),
col = c("black","red"),
+ lty = "solid", lwd = 1,
...) {
+ ptype <- match.arg(ptype)
plt <- plot(x$ord, choices = choices, scaling = x$scaling,
type = "p", display = "sites", ...,
pch = pch[1], col = col[1])
- ##points(fitted(x)[, choices])
- lines(fitted(x)[, choices], pch = pch[2], col = col[2])
+ pass <- fitted(x, type = "passive", choices = choices)
+ if(!missing(order)) {
+ if(length(order) != NROW(pass))
+ stop("'length(order)' not equal to number of passive samples.")
+ pass[order, ]
+ }
+ if(ptype %in% c("l", "o", "b")) {
+ lines(pass, pch = pch[2], col = col[2],
+ lty = lty, lwd = lwd, type = ptype, ...)
+ } else {
+ points(pass, pch = pch[2], col = col[2], ...)
+ }
+ invisible()
}
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/inst/ChangeLog 2013-01-16 12:15:36 UTC (rev 298)
@@ -1,5 +1,14 @@
analogue Change Log
+Version 0.11-0
+
+ * timetrack: fitted method gains argument `choices` with
+ default `1:2` for extracting the ordinary or passive
+ samples scores on `choices` axes. `plot` method can now draw
+ the passive samples as a line, points or both. The `plot`
+ method also gains an argument `order` that can be used to
+ reorder the passive samples into correct temporal ordering.
+
Version 0.10-0
* Release: Version 0.9-11 plus a minor documentation fix
Modified: pkg/man/timetrack.Rd
===================================================================
--- pkg/man/timetrack.Rd 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/man/timetrack.Rd 2013-01-16 12:15:36 UTC (rev 298)
@@ -17,10 +17,12 @@
rank = "full", model = c("CCA", "CA"), \dots)
\method{fitted}{timetrack}(object, type = c("passive", "ordination"),
- model = NULL, \dots)
+ model = NULL, choices = 1:2, \dots)
-\method{plot}{timetrack}(x, choices = 1:2, pch = c(1,2),
- col = c("black","red"), \dots)
+\method{plot}{timetrack}(x, choices = 1:2, order,
+ ptype = c("l", "p", "o", "b"), pch = c(1,2),
+ col = c("black","red"), lty = "solid", lwd = 1,
+ \dots)
}
\arguments{
@@ -53,12 +55,22 @@
\item{type}{character; which fitted values should be returned?}
\item{choices}{numeric; the length-2 vector of ordination axes to
plot.}
+ \item{order}{numeric; vector of indices to use to reorder the passive
+ samples. Useful to get passive samples into temporal order for
+ plotting with a line.}
+ \item{ptype}{character; controls how the time track should be
+ drawn. Default is draw the passive samples connected by a line in
+ the order in which they appear in the data. With \code{ptype = "p"}
+ no line is drawn. The other two types have their usual meaning from
+ \code{\link{plot.default}}.}
\item{pch}{The length-2 vector of plotting characters. The first
element is used for the ordination samples, the second for the
passive samples.}
\item{col}{The length-2 vector of plotting colours. The first
element is used for the ordination samples, the second for the
passive samples.}
+ \item{lty, lwd}{graphical parameters for the plotted time track for
+ \code{ptype != "p"}.}
\item{\dots}{arguments passed to other methods.
\code{timetrack} passes arguments on to \code{tran} and the
ordination function given in \code{method}. \code{fitted} passes
@@ -143,7 +155,12 @@
mod
## Plot the timetrack
-plot(mod)
+plot(mod, ptype = "b", col = c("forestgreen", "orange"), lwd = 2)
+
+## Other options (reorder the time track)
+ord <- rev(seq_len(nrow(rlgh)))
+plot(mod, choices = 2:3, order = ord, ptype = "b",
+ col = c("forestgreen", "orange"), lwd = 2)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save 2013-01-03 12:29:41 UTC (rev 297)
+++ pkg/tests/Examples/analogue-Ex.Rout.save 2013-01-16 12:15:36 UTC (rev 298)
@@ -31,7 +31,7 @@
Loading required package: princurve
Loading required package: mgcv
This is mgcv 1.7-22. For overview type 'help("mgcv-package")'.
-This is analogue 0.10-0
+This is analogue 0.11-0
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -6925,10 +6925,15 @@
>
> ## Plot the timetrack
-> plot(mod)
+> plot(mod, ptype = "b", col = c("forestgreen", "orange"), lwd = 2)
>
+> ## Other options (reorder the time track)
+> ord <- rev(seq_len(nrow(rlgh)))
+> plot(mod, choices = 2:3, order = ord, ptype = "b",
++ col = c("forestgreen", "orange"), lwd = 2)
>
>
+>
> cleanEx()
> nameEx("tran")
> ### * tran
@@ -7365,7 +7370,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 22.741 0.267 23.803 0 0
+Time elapsed: 21.537 0.227 22.33 0 0
> grDevices::dev.off()
null device
1
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