[Vegan-commits] r2614 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2013-09-10 18:14:13 +0200 (Tue, 10 Sep 2013)
New Revision: 2614

Modified:
   branches/2.0/R/print.betadisper.R
   branches/2.0/R/vegandocs.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/betadisper.Rd
Log:
merge r2600 (tools::: in vegandocs) and r2613 ('medoid' -> 'median' in betadisper)

Modified: branches/2.0/R/print.betadisper.R
===================================================================
--- branches/2.0/R/print.betadisper.R	2013-09-10 07:49:51 UTC (rev 2613)
+++ branches/2.0/R/print.betadisper.R	2013-09-10 16:14:13 UTC (rev 2614)
@@ -13,7 +13,7 @@
     cat(paste("\nNo. of Negative Eigenvalues:", sum(x$eig < 0)))
     cat("\n\n")
     type <- ifelse(isTRUE(all.equal(attr(x, "type"), "median")),
-                   "medoid", "centroid")
+                   "median", "centroid")
     writeLines(strwrap(paste0("Average distance to ", type, ":\n")))
     print.default(tapply(x$distances, x$group, mean), digits = digits)
     cat("\n")

Modified: branches/2.0/R/vegandocs.R
===================================================================
--- branches/2.0/R/vegandocs.R	2013-09-10 07:49:51 UTC (rev 2613)
+++ branches/2.0/R/vegandocs.R	2013-09-10 16:14:13 UTC (rev 2614)
@@ -16,10 +16,9 @@
         ## Try html
         helptype <- getOption("help_type")
         if (length(helptype) && helptype == "html") {
-            if (!tools:::httpdPort)
-                startDynamicHelp()
-            browseURL(paste("http://127.0.0.1:", tools:::httpdPort,
-                            "/library/vegan/doc/NEWS.html", sep=""))
+            browseURL(paste("file://",
+                            system.file(package="vegan", "doc", "NEWS.html"),
+                            sep=""))
         } else {
             file.show(Rd2txt(file.path(system.file(package="vegan"),
                                                "NEWS.Rd"), tempfile()))

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-09-10 07:49:51 UTC (rev 2613)
+++ branches/2.0/inst/ChangeLog	2013-09-10 16:14:13 UTC (rev 2614)
@@ -4,6 +4,8 @@
 
 Version 2.0-9 (opened August 23, 2013)
 
+	* merge 2613: 'medoid' to 'median' in betadisper output and doc.
+	* merge 2600: remove tools::: in vegandocs().
 	* merge 2593: remove stats::: in anova.ccabyaxis().
 	* merge 2590: typos.
 	* merge r2588: remove unneeded utils::: in vegandocs (some remain). 

Modified: branches/2.0/man/betadisper.Rd
===================================================================
--- branches/2.0/man/betadisper.Rd	2013-09-10 07:49:51 UTC (rev 2613)
+++ branches/2.0/man/betadisper.Rd	2013-09-10 16:14:13 UTC (rev 2614)
@@ -260,7 +260,7 @@
 scrs <- scores(mod)
 str(scrs)
 head(scores(mod, 1:4, display = "sites"))
-# group centroids/medoids 
+# group centroids/medians 
 scores(mod, 1:4, display = "centroids")
 # eigenvalues from the underlying principal coordinates analysis
 eigenvals(mod)