[Vegan-commits] r1330 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-10-12 20:41:06 +0200 (Tue, 12 Oct 2010)
New Revision: 1330

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/R/print.oecosimu.R
   pkg/vegan/inst/ChangeLog
Log:
na.rm = TRUE for handling simulated statistics in oecosimu

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2010-10-12 18:15:06 UTC (rev 1329)
+++ pkg/vegan/R/oecosimu.R	2010-10-12 18:41:06 UTC (rev 1330)
@@ -95,12 +95,16 @@
         }
     }
     ## end of addition
-    sd <- apply(simind, 1, sd)
-    z <- (indstat - rowMeans(simind))/sd
+    sd <- apply(simind, 1, sd, na.rm = TRUE)
+    z <- (indstat - rowMeans(simind, na.rm = TRUE))/sd
     if (any(sd < sqrt(.Machine$double.eps)))
         z[sd < sqrt(.Machine$double.eps)] <- 0
-    pless <- rowSums(indstat <= simind)
-    pmore <- rowSums(indstat >= simind)
+    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))
+    }
     p <- switch(alternative,
                 two.sided = 2*pmin(pless, pmore),
                 less = pless,

Modified: pkg/vegan/R/print.oecosimu.R
===================================================================
--- pkg/vegan/R/print.oecosimu.R	2010-10-12 18:15:06 UTC (rev 1329)
+++ pkg/vegan/R/print.oecosimu.R	2010-10-12 18:41:06 UTC (rev 1330)
@@ -25,10 +25,15 @@
                     two.sided = c(0.025, 0.5, 0.975),
                     less = c(0, 0.5, 0.95),
                     greater = c(0.05, 0.5, 1))
-    qu <- apply(x$oecosimu$simulated, 1, quantile, probs=probs)
+    qu <- apply(x$oecosimu$simulated, 1, quantile, probs=probs, na.rm = TRUE)
     m <- cbind("statistic" = x$oecosimu$statistic,
                "z" = x$oecosimu$z, t(qu),
                "Pr(sim.)"=x$oecosimu$pval)
     printCoefmat(m, ...)
+    if (any(is.na(x$oecosimu$simulated))) {
+        nacount <- rowSums(is.na(x$oecosimu$simulated))
+        cat("\nNumber of NA cases removed from simulations:\n",
+            nacount, "\n")
+    }
     invisible(x)   
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-10-12 18:15:06 UTC (rev 1329)
+++ pkg/vegan/inst/ChangeLog	2010-10-12 18:41:06 UTC (rev 1330)
@@ -7,6 +7,10 @@
 	* treedive: handles trivial cases of zero (diversity NA) or one
 	species (diversity 0). 
 
+	* oecosimu: handles NA values as na.rm = TRUE in simulations for
+	cases where these are produced by the function to evaluate
+	statistics.
+
 	* nestednodf: Gustavo Carvalho sent a new upgraded version which
 	also implements a new quantitative method of Almeida-Neto & Ulrich
 	(Env Mod Software, in press; 2010). Based on feature request #1097