[Vegan-commits] r438 - branches/1.13/R branches/1.13/inst pkg/R pkg/inst

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

Author: jarioksa
Date: 2008-06-28 07:15:59 +0200 (Sat, 28 Jun 2008)
New Revision: 438

Modified:
   branches/1.13/R/oecosimu.R
   branches/1.13/inst/ChangeLog
   branches/1.13/inst/NEWS
   pkg/R/oecosimu.R
   pkg/inst/ChangeLog
Log:
oecosimu: p/a transformation also to the primary statistic

Modified: branches/1.13/R/oecosimu.R
===================================================================
--- branches/1.13/R/oecosimu.R	2008-06-24 05:26:10 UTC (rev 437)
+++ branches/1.13/R/oecosimu.R	2008-06-28 05:15:59 UTC (rev 438)
@@ -6,9 +6,9 @@
     method <- match.arg(method, c("r00", "r0", "r1", "r2", "c0",
                                   "swap", "tswap", "backtrack",
                                   "quasiswap"))
+    comm <- ifelse(comm > 0, 1, 0)
     ind <- nestfun(comm, ...)
     simind <- numeric(nsimul)
-    comm <- ifelse(comm > 0, 1, 0)
     if (method %in% c("swap", "tswap")){
         checkbrd <- 1
         if (method == "tswap") {

Modified: branches/1.13/inst/ChangeLog
===================================================================
--- branches/1.13/inst/ChangeLog	2008-06-24 05:26:10 UTC (rev 437)
+++ branches/1.13/inst/ChangeLog	2008-06-28 05:15:59 UTC (rev 438)
@@ -15,6 +15,9 @@
 
 	* merged r427: summary for capscale result similar as for rda.
 
+	* r437 simultaneously with pkg/: oecosimu p/a transforms data also
+	for the original statistic.
+
 Version 1.13-1 (released June 11, 2008)
 
 	* adonis: speed-up and doc updates.

Modified: branches/1.13/inst/NEWS
===================================================================
--- branches/1.13/inst/NEWS	2008-06-24 05:26:10 UTC (rev 437)
+++ branches/1.13/inst/NEWS	2008-06-28 05:15:59 UTC (rev 438)
@@ -15,6 +15,9 @@
       permutation, and this change does not influence the order
       statistic used in permutations.
 
+   - oecosimu: always estimates the original statistic with binary
+     data even when user supplies quantitative data.
+
     - rda (and capscale) use internal scaling constant so that the
       returned site and species scores with scalings 1, 2 or 3
       together provide a biplot approximation of the original

Modified: pkg/R/oecosimu.R
===================================================================
--- pkg/R/oecosimu.R	2008-06-24 05:26:10 UTC (rev 437)
+++ pkg/R/oecosimu.R	2008-06-28 05:15:59 UTC (rev 438)
@@ -6,9 +6,9 @@
     method <- match.arg(method, c("r00", "r0", "r1", "r2", "c0",
                                   "swap", "tswap", "backtrack",
                                   "quasiswap"))
+    comm <- ifelse(comm > 0, 1, 0)
     ind <- nestfun(comm, ...)
     simind <- numeric(nsimul)
-    comm <- ifelse(comm > 0, 1, 0)
     if (method %in% c("swap", "tswap")){
         checkbrd <- 1
         if (method == "tswap") {

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-06-24 05:26:10 UTC (rev 437)
+++ pkg/inst/ChangeLog	2008-06-28 05:15:59 UTC (rev 438)
@@ -16,6 +16,9 @@
 	faster now. In MacBook, 100 swaps with "sipoo" went from 8 sec to
 	0.5 sec, and thinning hardly influenced timing (it used to
 	thin-fold times).
+
+	* oecosimu: takes care that original statistic is found from
+	binary data.
 	
 Version 1.14-5 (closed June 19, 2008)