[Vegan-commits] r1899 - pkg/vegan/R

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

Author: psolymos
Date: 2011-09-27 03:18:22 +0200 (Tue, 27 Sep 2011)
New Revision: 1899

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/R/simulate.nullmodel.R
Log:
fix for oecosimu, removing message on thin/burnin

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2011-09-27 01:04:17 UTC (rev 1898)
+++ pkg/vegan/R/oecosimu.R	2011-09-27 01:18:22 UTC (rev 1899)
@@ -26,13 +26,12 @@
         if (inherits(comm, "nullmodel")) {
             nm <- comm
             comm <- comm$data
-            method <- nm$commsim$method
         } else {
-            method <- make.commsim(method)$method
             nm <- nullmodel(comm, method)
             if (nm$commsim$binary)
                 comm <- nm$data
         }
+        method <- nm$commsim$method
     }
     
     ind <- nestfun(comm, ...)

Modified: pkg/vegan/R/simulate.nullmodel.R
===================================================================
--- pkg/vegan/R/simulate.nullmodel.R	2011-09-27 01:04:17 UTC (rev 1898)
+++ pkg/vegan/R/simulate.nullmodel.R	2011-09-27 01:18:22 UTC (rev 1899)
@@ -21,11 +21,11 @@
         x <- object$state
     } else {
         x <- m
-        if (thin != 1)
-            message("non-sequential model: 'thin' set to 1")
+#        if (thin != 1)
+#            message("non-sequential model: 'thin' set to 1")
         thin <- 1L
-        if (burnin != 0)
-            message("non-sequential model: 'burnin' set to 0")
+#        if (burnin != 0)
+#            message("non-sequential model: 'burnin' set to 0")
         burnin <- 0L
     }
     perm <- object$commsim$fun(x=x,