[Vegan-commits] r2534 - in pkg/vegan: R inst man

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

Author: gsimpson
Date: 2013-06-21 06:20:10 +0200 (Fri, 21 Jun 2013)
New Revision: 2534

Modified:
   pkg/vegan/R/ordisurf.R
   pkg/vegan/R/plot.ordisurf.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordisurf.Rd
Log:
all setting lwd for contours

Modified: pkg/vegan/R/ordisurf.R
===================================================================
--- pkg/vegan/R/ordisurf.R	2013-06-21 04:02:11 UTC (rev 2533)
+++ pkg/vegan/R/ordisurf.R	2013-06-21 04:20:10 UTC (rev 2534)
@@ -21,7 +21,7 @@
               fx = FALSE, add = FALSE, display = "sites", w = weights(x),
               main, nlevels = 10, levels, npoints = 31, labcex = 0.6,
               bubble = FALSE, cex = 1, select = TRUE, method = "REML",
-              gamma = 1, plot = TRUE, ...)
+              gamma = 1, plot = TRUE, lwd.cl = par("lwd"), ...)
 {
     weights.default <- function(object, ...) NULL
     if(!missing(thinplate)) {
@@ -156,7 +156,8 @@
            (select && !isTRUE(all.equal(as.numeric(summary(mod)$edf), 0))))
             contour(xn1, xn2, matrix(fit, nrow=GRID), col = col, add = TRUE,
                     levels = levels, labcex = labcex,
-                    drawlabels = !is.null(labcex) && labcex > 0)
+                    drawlabels = !is.null(labcex) && labcex > 0,
+                    lwd = lwd.cl)
     }
     mod$grid <- list(x = xn1, y = xn2, z = matrix(fit, nrow = GRID))
     class(mod) <- c("ordisurf", class(mod))

Modified: pkg/vegan/R/plot.ordisurf.R
===================================================================
--- pkg/vegan/R/plot.ordisurf.R	2013-06-21 04:02:11 UTC (rev 2533)
+++ pkg/vegan/R/plot.ordisurf.R	2013-06-21 04:20:10 UTC (rev 2534)
@@ -1,6 +1,7 @@
 `plot.ordisurf` <- function(x, what = c("contour","persp","gam"),
                             add = FALSE, bubble = FALSE, col = "red", cex = 1,
-                            nlevels = 10, levels, labcex = 0.6, ...) {
+                            nlevels = 10, levels, labcex = 0.6,
+                            lwd.cl = par("lwd"), ...) {
     what <- match.arg(what)
     y <- x$model$y
     x1 <- x$model$x1
@@ -23,7 +24,8 @@
             levels <- pretty(range(x$grid$z, finite = TRUE), nlevels)
         contour(X, Y, Z, col = col, add = TRUE,
                 levels = levels, labcex = labcex,
-                drawlabels = !is.null(labcex) && labcex > 0)
+                drawlabels = !is.null(labcex) && labcex > 0,
+                lwd = lwd.cl)
     } else if(isTRUE(all.equal(what, "persp"))) {
         persp(X, Y, Z, col = col, cex = cex, ...)
     } else {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-06-21 04:02:11 UTC (rev 2533)
+++ pkg/vegan/inst/ChangeLog	2013-06-21 04:20:10 UTC (rev 2534)
@@ -20,6 +20,9 @@
 	* ordipointlabel: now uses `ordiArgAbsorber()` to stop the warnings
 	about non-graphical paramters being passed to plotting functions.
 
+	* ordisurf: can now pass in a line width for the contours via
+	argument `lwd.cl`.
+
 Version 2.1-30 (opened May 5, 2013)
 
 	* bioenv: can now use Mahalanobis, Manhattan and Gower distances

Modified: pkg/vegan/man/ordisurf.Rd
===================================================================
--- pkg/vegan/man/ordisurf.Rd	2013-06-21 04:02:11 UTC (rev 2533)
+++ pkg/vegan/man/ordisurf.Rd	2013-06-21 04:20:10 UTC (rev 2534)
@@ -17,7 +17,7 @@
          display = "sites", w = weights(x), main, nlevels = 10,
          levels, npoints = 31, labcex = 0.6, bubble = FALSE,
          cex = 1, select = TRUE, method = "REML", gamma = 1,
-         plot = TRUE, ...)
+         plot = TRUE, lwd.cl = par("lwd"), ...)
 
 \method{ordisurf}{formula}(formula, data, ...)
 
@@ -25,7 +25,7 @@
 
 \method{plot}{ordisurf}(x, what = c("contour","persp","gam"),
      add = FALSE, bubble = FALSE, col = "red", cex = 1,
-     nlevels = 10, levels, labcex = 0.6, \dots)
+     nlevels = 10, levels, labcex = 0.6, lwd.cl = par("lwd"), \dots)
 }
 
 \arguments{
@@ -108,6 +108,8 @@
   \item{plot}{logical; should any plotting be done by
     \code{ordisurf}? Useful if all you want is the fitted response
     surface model.}
+  \item{lwd.cl}{numeric; the \code{lwd} (line width) parameter to use
+    when drawing the contour lines.}
   \item{formula, data}{Alternative definition of the fitted model as
     \code{x ~ y}, where left-hand side is the ordination \code{x} and
     right-hand side the single fitted continuous variable