[Dplr-commits] r1032 - in pkg/dplR: . R inst man

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

Author: mvkorpel
Date: 2016-08-09 10:42:23 +0200 (Tue, 09 Aug 2016)
New Revision: 1032

Added:
   pkg/dplR/inst/COPYRIGHTS
Modified:
   pkg/dplR/ChangeLog
   pkg/dplR/DESCRIPTION
   pkg/dplR/R/crn.plot.R
   pkg/dplR/man/crn.plot.Rd
Log:
* Better handling of graphical parameters in crn.plot()
* New file inst/COPYRIGHTS


Modified: pkg/dplR/ChangeLog
===================================================================
--- pkg/dplR/ChangeLog	2016-06-09 19:53:11 UTC (rev 1031)
+++ pkg/dplR/ChangeLog	2016-08-09 08:42:23 UTC (rev 1032)
@@ -1,5 +1,11 @@
 * CHANGES IN dplR VERSION 1.6.5
 
+File: crn.plot.R
+----------------
+
+- Graphical parameters (xlim, ylim, ...) are handled better in crn.plot().
+- Parameter 'ylim2' controls scale of secondary y axis.
+
 File: detrend and detrend.series.Rd
 -----------------
 

Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION	2016-06-09 19:53:11 UTC (rev 1031)
+++ pkg/dplR/DESCRIPTION	2016-08-09 08:42:23 UTC (rev 1032)
@@ -3,7 +3,7 @@
 Type: Package
 Title: Dendrochronology Program Library in R
 Version: 1.6.5
-Date: 2016-06-09
+Date: 2016-08-09
 Authors at R: c(person("Andy", "Bunn", role = c("aut", "cph",
         "cre", "trl"), email = "andy.bunn at wwu.edu"), person("Mikko",
         "Korpela", role = c("aut", "trl")), person("Franco", "Biondi",
@@ -15,7 +15,7 @@
         "Cecile", role = "ctb"), person("Manfred", "Mudelsee", role =
         "ctb"), person("Michael", "Schulz", role = "ctb"))
 Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
-Copyright: Authors and Aalto University (for work of M. Korpela)
+Copyright: Authors and file inst/COPYRIGHTS
 Maintainer: Andy Bunn <andy.bunn at wwu.edu>
 Depends: R (>= 2.15.2)
 Imports: graphics, grDevices, grid, stats, utils, lattice (>= 0.13-6),

Modified: pkg/dplR/R/crn.plot.R
===================================================================
--- pkg/dplR/R/crn.plot.R	2016-06-09 19:53:11 UTC (rev 1031)
+++ pkg/dplR/R/crn.plot.R	2016-08-09 08:42:23 UTC (rev 1032)
@@ -22,23 +22,32 @@
   nCrn <- ncol(crn)
   ## Check to see if the crn has sample depth
   sd.exist <- crn.names[nCrn] == "samp.depth"
+  args0 <- list(...)
+  args1 <- args0
+  args1[["ylim2"]] <- NULL
+  args1[c("x", "y", "type", "axes", "xlab", "ylab")] <-
+      list(yr.vec, as.name("spl"), "n", FALSE, xlab, ylab)
+  args2 <- args1
+  args2[c("main", "sub", "xlab", "ylab")] <- list("", "", "", "")
   if(sd.exist) {
     samp.depth <- crn[[nCrn]]
     nCrn <- nCrn-1
+    text.samp <- gettext("Sample Depth", domain="R-dplR")
+    sdargs <- args2
+    sdargs[["ylim"]] <- args0[["ylim2"]]
+    sdargs[["y"]] <- samp.depth
   }
   if(nCrn > 1) layout(matrix(seq_len(nCrn), nrow=nCrn, ncol=1))
   # strike these?
 #  text.years <- gettext("Years", domain="R-dplR")
 #  text.rwi <- gettext("RWI", domain="R-dplR")
-  text.samp <- gettext("Sample Depth", domain="R-dplR")
   nyrs2 <- nyrs
   for(i in seq_len(nCrn)){
     spl <- crn[[i]]
-    plot(yr.vec, spl, type="n",axes=FALSE,xlab=xlab,ylab=ylab,...)
+    do.call("plot", args1)
     if(sd.exist) {
       par(new=TRUE)
-      plot(yr.vec, samp.depth, type="n",
-           xlab="", ylab="", axes=FALSE)
+      do.call("plot", sdargs)
       xx <- c(yr.vec,max(yr.vec,na.rm=TRUE),min(yr.vec,na.rm=TRUE))
       yy <- c(samp.depth, 0, 0)
       polygon(xx,yy,col=samp.depth.col,border=samp.depth.border.col)
@@ -46,7 +55,7 @@
       mtext(text.samp, side=4, line=1.25)
     }
     par(new=TRUE)
-    plot(yr.vec, spl, type="n",axes=FALSE,xlab="",ylab="")
+    do.call("plot", args2)
     abline(h=abline.pos,lwd=abline.lwd,
            lty=abline.lty,col=abline.col)
     lines(yr.vec, spl, col=crn.line.col,lwd=crn.lwd)

Added: pkg/dplR/inst/COPYRIGHTS
===================================================================
--- pkg/dplR/inst/COPYRIGHTS	                        (rev 0)
+++ pkg/dplR/inst/COPYRIGHTS	2016-08-09 08:42:23 UTC (rev 1032)
@@ -0,0 +1,7 @@
+The code of this package is licensed under GPL 2 or later.
+
+For code contributed by Mikko Korpela:
+* Copyright (C) Aalto University (code introduced in dplR <= 1.6.4)
+* Copyright (C) University of Helsinki (code later than dplR 1.6.4)
+
+Other code in the package is copyright (C) by the corresponding authors.

Modified: pkg/dplR/man/crn.plot.Rd
===================================================================
--- pkg/dplR/man/crn.plot.Rd	2016-06-09 19:53:11 UTC (rev 1031)
+++ pkg/dplR/man/crn.plot.Rd	2016-08-09 08:42:23 UTC (rev 1032)
@@ -48,7 +48,9 @@
   \item{abline.lwd}{ line width for the reference abline (if added)}
   \item{xlab}{ default label for x axis }
   \item{ylab}{ default label for y axis }
-  \item{\dots}{ Additional arguments to pass to \code{\link{plot}} }
+  \item{\dots}{ Additional arguments to pass to \code{\link{plot}}. The
+    scale of the secondary y axis (sample depth) can be controlled with
+    argument \code{ylim2}. }
 }
 \details{
   This makes a plot of one or more tree-ring chronologies.