[Analogue-commits] r314 - in pkg: R inst man

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2013-03-21 23:07:02 +0100 (Thu, 21 Mar 2013)
New Revision: 314

Modified:
   pkg/R/plot.timetrack.R
   pkg/inst/ChangeLog
   pkg/man/timetrack.Rd
Log:
allow 'lc' scores in plot.timetrack

Modified: pkg/R/plot.timetrack.R
===================================================================
--- pkg/R/plot.timetrack.R	2013-03-21 22:04:39 UTC (rev 313)
+++ pkg/R/plot.timetrack.R	2013-03-21 22:07:02 UTC (rev 314)
@@ -1,12 +1,15 @@
-`plot.timetrack` <- function(x, choices = 1:2, order,
+`plot.timetrack` <- function(x, choices = 1:2, 
+                             display = c("wa","lc"),
+                             order,
                              ptype = c("l", "p", "o", "b"),
                              pch = c(1,2),
                              col = c("black","red"),
                              lty = "solid", lwd = 1,
                              ...) {
     ptype <- match.arg(ptype)
+    display <- match.arg(display)
     plt <- plot(x$ord, choices = choices, scaling = x$scaling,
-                type = "p", display = "sites", ...,
+                type = "p", display = display, ...,
                 pch = pch[1], col = col[1])
     pass <- fitted(x, type = "passive", choices = choices)
     if(!missing(order)) {

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2013-03-21 22:04:39 UTC (rev 313)
+++ pkg/inst/ChangeLog	2013-03-21 22:07:02 UTC (rev 314)
@@ -1,5 +1,11 @@
 analogue Change Log
 
+Version 0.11-2
+
+	* timetrack: plot method now allows plotting of "lc" or "wa"
+	site scores for the base ordination. The latter is the default
+	to maintain backwards compatability.
+
 Version 0.11-1
 
 	* scores.prcurve: new function to extract "axis" scores for

Modified: pkg/man/timetrack.Rd
===================================================================
--- pkg/man/timetrack.Rd	2013-03-21 22:04:39 UTC (rev 313)
+++ pkg/man/timetrack.Rd	2013-03-21 22:07:02 UTC (rev 314)
@@ -19,10 +19,9 @@
 \method{fitted}{timetrack}(object, type = c("passive", "ordination"),
        model = NULL, choices = 1:2, \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)
+\method{plot}{timetrack}(x, choices = 1:2, display = c("wa", "lc"),
+     order, ptype = c("l", "p", "o", "b"), pch = c(1,2),
+     col = c("black","red"), lty = "solid", lwd = 1, \dots)
 }
 
 \arguments{
@@ -55,6 +54,8 @@
   \item{type}{character; which fitted values should be returned?}
   \item{choices}{numeric; the length-2 vector of ordination axes to
     plot.}
+  \item{display}{character; which type of sites scores to display? See
+    \code{\link{scores.cca}} for details.}
   \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.}