[Vegan-commits] r1605 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-05-26 15:14:10 +0200 (Thu, 26 May 2011)
New Revision: 1605

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/oecosimu.Rd
Log:
revert r1557: no tie split in order statistics in oecosimu

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2011-05-26 11:34:31 UTC (rev 1604)
+++ pkg/vegan/R/oecosimu.R	2011-05-26 13:14:10 UTC (rev 1605)
@@ -2,7 +2,7 @@
     function(comm, nestfun, method, nsimul=99,
              burnin=0, thin=1, statistic = "statistic",
              alternative = c("two.sided", "less", "greater"),
-             tiesplit = FALSE, ...)
+             ...)
 {
     alternative <- match.arg(alternative)
     nestfun <- match.fun(nestfun)
@@ -103,18 +103,14 @@
         z[sd < sqrt(.Machine$double.eps)] <- 0
     pless <- rowSums(indstat <= simind, na.rm = TRUE)
     pmore <- rowSums(indstat >= simind, na.rm = TRUE)
-    if (tiesplit)
-        ties <- rowSums(indstat == simind, na.rm = TRUE)/2
-    else
-        ties <- 0
     if (any(is.na(simind))) {
         warning("some simulated values were NA and were removed")
         nsimul <- nsimul - rowSums(is.na(simind))
     }
     p <- switch(alternative,
-                two.sided = 2*(pmin(pless, pmore) - ties),
-                less = pless - ties,
-                greater = pmore - ties)
+                two.sided = 2*pmin(pless, pmore),
+                less = pless,
+                greater = pmore)
     p <- pmin(1, (p + 1)/(nsimul + 1))
 
     ## ADDITION: if z is NA then it is not correct to calculate p values

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-05-26 11:34:31 UTC (rev 1604)
+++ pkg/vegan/inst/ChangeLog	2011-05-26 13:14:10 UTC (rev 1605)
@@ -2,14 +2,22 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.18-30 (opened April 27, 2011)
+Version 1.18-31 (opened May 26, 2011)
 
+	* oecosimu: reverted r1557 of version 1.18-26, or splitting tied
+	values. This was introduced because Chase et al. (Ecosphere 2011,
+	http://www.esajournals.org/doi/pdf/10.1890/ES10-00117.1) used this
+	in their Raup-Crick index. This is against established practice in
+	order statistics and therefore we cancelled this.
+
+Version 1.18-30 (closed May 26, 2011)
+
 	* opened with the release of vegan 1.17-10 on April 27, 2011.
 
 	* nobs: documented nobs() methods for vegan. These seem to be
 	needed in R 2.13.0 and should be released soon (there is no need
 	to add R >= 2.13.0 dependence as long as we do not use these
-	functions ourselves within released vegan code).
+ 	functions ourselves within released vegan code).
 
 	* treeheight: dramatic simplification and speed-up of the code.
 

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2011-05-26 11:34:31 UTC (rev 1604)
+++ pkg/vegan/man/oecosimu.Rd	2011-05-26 13:14:10 UTC (rev 1605)
@@ -21,7 +21,7 @@
 \usage{
 oecosimu(comm, nestfun, method, nsimul = 99, burnin = 0, thin = 1,
    statistic = "statistic", alternative = c("two.sided", "less", "greater"),
-   tiesplit = FALSE, ...)
+   ...)
 commsimulator(x, method, thin=1)
 \method{as.ts}{oecosimu}(x, ...)
 \method{as.mcmc}{oecosimu}(x)
@@ -53,9 +53,6 @@
     or \code{"less"}. You can specify just the initial letter.}
   \item{data}{Ignored argument of the generic function.}
   \item{xlab}{Label of the x-axis.}
-  \item{tiesplit}{Tied values of simulations are split so that half of them are
-    regarded as fulfilling the condition of \code{alternative}. This is not 
-    usually done, but some published examples use splitting.}
   \item{\dots}{Other arguments to functions.}
 }