[Vegan-commits] r2546 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2013-07-09 15:32:28 +0200 (Tue, 09 Jul 2013)
New Revision: 2546

Modified:
   branches/2.0/R/oecosimu.R
   branches/2.0/R/print.oecosimu.R
   branches/2.0/R/raupcrick.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/oecosimu.Rd
Log:
merge r2495,8: test direction in oecosimu

Modified: branches/2.0/R/oecosimu.R
===================================================================
--- branches/2.0/R/oecosimu.R	2013-07-09 13:22:12 UTC (rev 2545)
+++ branches/2.0/R/oecosimu.R	2013-07-09 13:32:28 UTC (rev 2546)
@@ -102,8 +102,8 @@
     z <- (indstat - means)/sd
     if (any(sd < sqrt(.Machine$double.eps)))
         z[sd < sqrt(.Machine$double.eps)] <- 0
-    pless <- rowSums(indstat <= simind, na.rm = TRUE)
-    pmore <- rowSums(indstat >= simind, na.rm = TRUE)
+    pless <- rowSums(indstat >= simind, na.rm = TRUE)
+    pmore <- rowSums(indstat <= simind, na.rm = TRUE)
     if (any(is.na(simind))) {
         warning("some simulated values were NA and were removed")
         nsimul <- nsimul - rowSums(is.na(simind))

Modified: branches/2.0/R/print.oecosimu.R
===================================================================
--- branches/2.0/R/print.oecosimu.R	2013-07-09 13:22:12 UTC (rev 2545)
+++ branches/2.0/R/print.oecosimu.R	2013-07-09 13:32:28 UTC (rev 2546)
@@ -13,10 +13,10 @@
         cat("options: ", paste(names(att), att, collapse=", "))
     }
     alt.char <- switch(x$oecosimu$alternative,
-                       two.sided = "not equal to",
+                       two.sided = "less or greater than",
                        less = "less than",
                        greater = "greater than")
-    cat("\nalternative hypothesis: simulated median is", alt.char, "the statistic")
+    cat("\nalternative hypothesis: statistic is", alt.char, "simulated values")
     ## dim attribute is always there, but print all others
 
     cat("\n\n")

Modified: branches/2.0/R/raupcrick.R
===================================================================
--- branches/2.0/R/raupcrick.R	2013-07-09 13:22:12 UTC (rev 2545)
+++ branches/2.0/R/raupcrick.R	2013-07-09 13:32:28 UTC (rev 2546)
@@ -12,7 +12,7 @@
     ## but is much slower
     sol <- oecosimu(comm, function(x) tcrossprod(x)[tri], method = null,
                     nsimul = nsimul,
-                    alternative = if (chase) "greater" else "less")
+                    alternative = if (chase) "less" else "greater")
     ## Chase et al. way, or the standard way
     if (chase)
         out <- 1 - sol$oecosimu$pval

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-07-09 13:22:12 UTC (rev 2545)
+++ branches/2.0/inst/ChangeLog	2013-07-09 13:32:28 UTC (rev 2546)
@@ -11,7 +11,9 @@
 	* merge r2534: lwd in ordisurf.
 	* merge r2533: ordipointlabel uses ordiArgAbsorber.
 	* merge r2504: notation in adipart.Rd.
+	* merge r2498: adapt raupcrick to r2495.
 	* merge r2497: avoid visible ~ in .Rnw.
+	* merge r2495: fix twisted test direction in oecosimu.
 	* merge r2490 thru 2493: ordisurf new options.
 	* merge r2484 thru 2486: betadisper fixes (centroid with one
 	group, call it medoid).

Modified: branches/2.0/man/oecosimu.Rd
===================================================================
--- branches/2.0/man/oecosimu.Rd	2013-07-09 13:22:12 UTC (rev 2545)
+++ branches/2.0/man/oecosimu.Rd	2013-07-09 13:32:28 UTC (rev 2546)
@@ -251,7 +251,11 @@
 ## Use the first eigenvalue of correspondence analysis as an index
 ## of structure: a model for making your own functions.
 data(sipoo)
-out <- oecosimu(sipoo, decorana, "swap", burnin=100, thin=10, statistic="evals")
+## Traditional nestedness statistics (number of checkerboard units)
+oecosimu(sipoo, nestedchecker, "r0")
+## sequential model, one-sided test, a vector statistic
+out <- oecosimu(sipoo, decorana, "swap", burnin=100, thin=10, 
+   statistic="evals", alt = "greater")
 out
 ## Inspect the swap sequence as a time series object
 plot(as.ts(out))