[Vegan-commits] r744 - in pkg/vegan: R man

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

Author: psolymos
Date: 2009-03-15 15:51:51 +0100 (Sun, 15 Mar 2009)
New Revision: 744

Modified:
   pkg/vegan/R/permat.control.R
   pkg/vegan/R/permatswap.R
   pkg/vegan/man/permatfull.Rd
Log:
conflicting default behaviour of oecosimu and permatswap in now parallel


Modified: pkg/vegan/R/permat.control.R
===================================================================
--- pkg/vegan/R/permat.control.R	2009-03-14 16:26:38 UTC (rev 743)
+++ pkg/vegan/R/permat.control.R	2009-03-15 14:51:51 UTC (rev 744)
@@ -1,5 +1,5 @@
 `permat.control` <-
-function(ptype="full", mtype="count", method="quasiswap", fixedmar="both", shuffle="both", strata=NULL, burnin=10000, thin=1000)
+function(ptype="full", mtype="count", method="quasiswap", fixedmar="both", shuffle="both", strata=NULL, burnin=0, thin=1)
 {
 list(ptype=ptype, mtype=mtype, method=method, fixedmar=fixedmar, shuffle=shuffle, strata=strata, burnin=burnin, thin=thin)
 }

Modified: pkg/vegan/R/permatswap.R
===================================================================
--- pkg/vegan/R/permatswap.R	2009-03-14 16:26:38 UTC (rev 743)
+++ pkg/vegan/R/permatswap.R	2009-03-15 14:51:51 UTC (rev 744)
@@ -1,6 +1,6 @@
 ## permatswap function
 `permatswap` <-
-function(m, method="quasiswap", fixedmar="both", shuffle="both", strata=NULL, mtype="count", times=99, burnin = 10000, thin = 1000)
+function(m, method="quasiswap", fixedmar="both", shuffle="both", strata=NULL, mtype="count", times=99, burnin = 0, thin = 1)
 {
 ## internal function
 indshuffle <- function(x)

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2009-03-14 16:26:38 UTC (rev 743)
+++ pkg/vegan/man/permatfull.Rd	2009-03-15 14:51:51 UTC (rev 744)
@@ -19,10 +19,10 @@
 permatfull(m, fixedmar = "both", shuffle = "both", strata = NULL, 
 mtype = "count", times = 99)
 permatswap(m, method = "quasiswap", fixedmar="both", shuffle = "both",
-strata = NULL, mtype = "count", times = 99, burnin = 10000, thin = 1000)
+strata = NULL, mtype = "count", times = 99, burnin = 0, thin = 1)
 permat.control(ptype = "full", mtype = "count", method = "quasiswap",
 fixedmar = "both", shuffle = "both", strata = NULL, 
-burnin = 10000, thin = 1000)
+burnin = 0, thin = 1)
 \method{print}{permat}(x, digits = 3, ...)
 \method{summary}{permat}(object, ...)
 \method{print}{summary.permat}(x, digits = 2, ...)