[Vegan-commits] r622 - in pkg/vegan: . R inst man

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

Author: psolymos
Date: 2008-12-07 20:33:18 +0100 (Sun, 07 Dec 2008)
New Revision: 622

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/oecosimu.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/adipart.Rd
   pkg/vegan/man/permatfull.Rd
Log:
end of permat update


Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2008-12-07 19:08:53 UTC (rev 621)
+++ pkg/vegan/DESCRIPTION	2008-12-07 19:33:18 UTC (rev 622)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-6
-Date: December 4, 2008
+Version: 1.16-7
+Date: December 7, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2008-12-07 19:08:53 UTC (rev 621)
+++ pkg/vegan/R/oecosimu.R	2008-12-07 19:33:18 UTC (rev 622)
@@ -71,7 +71,7 @@
             for (i in 1:nsimul) {
                 x <- permatfull(comm, fixedmar=control$fixedmar,
                     shuffle=control$shuffle,
-                    reg=control$reg, hab=control$hab,
+                    strata=control$strata,
                     mtype=control$mtype, times=1)
                 tmp <- nestfun(x$perm[[1]])
                 if (is.list(tmp)) {
@@ -85,14 +85,14 @@
             if (control$method %in% c("swap", "tswap")) {
             if (burnin > 0) {
                 m <- permatswap(comm, method=control$method,
-                    reg=control$reg, hab=control$hab,
+                    strata=control$strata,
                     mtype=control$mtype, times=1, 
                     burnin=burnin, thin=0)$perm[[1]]
                 } else m <- comm
             }
             for (i in 1:nsimul) {
                 x <- permatswap(m, method=control$method,
-                    reg=control$reg, hab=control$hab,
+                    strata=control$strata,
                     mtype=control$mtype, times=1, 
                     burnin=0, thin=thin)
                 tmp <- nestfun(x$perm[[1]], ...)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2008-12-07 19:08:53 UTC (rev 621)
+++ pkg/vegan/inst/ChangeLog	2008-12-07 19:33:18 UTC (rev 622)
@@ -2,8 +2,16 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-6
+Version 1.16-7
 
+Version 1.16-6 (closeed Dec 7, 2008)
+
+    * permat*: functions were rationalised, strata argument is
+    used instead of reg and hab, and returned object got several
+    new arguments. The tide of changes affected methods as well,
+    and some other function (adipart, oecosimu). Stratification
+    was tested and corrected.
+
     * permatfull: Jari Oksanen made the C port for the quantitative
     quasiswap algorithm. So the permat* null model family is now
     can be used for a wide array of null model analyses and is

Modified: pkg/vegan/man/adipart.Rd
===================================================================
--- pkg/vegan/man/adipart.Rd	2008-12-07 19:08:53 UTC (rev 621)
+++ pkg/vegan/man/adipart.Rd	2008-12-07 19:33:18 UTC (rev 622)
@@ -87,7 +87,7 @@
 matr <- r2dtable(1, c(3,4,3,7,4,8,7,6), 3:9)[[1]]
 strata <- cbind(1:8, rep(1:4,each=2), rep(1,8))
 ## restricted permutation within habitat classes
-contr <- permat.control(hab = c("a","a","a","b","a","b","b","b"))
+contr <- permat.control(strata = c("a","a","a","b","a","b","b","b"))
 ## Additive diversity partitioning ('oneway')
 x1 <- adipart(matr, strata, index="shannon", nsimul=25, control=contr)
 x1

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2008-12-07 19:08:53 UTC (rev 621)
+++ pkg/vegan/man/permatfull.Rd	2008-12-07 19:33:18 UTC (rev 622)
@@ -18,9 +18,9 @@
 
 \usage{
 permatfull(m, fixedmar = "both", shuffle = "ind", strata = NULL, 
-mtype = "count", times = 100)
+mtype = "count", times = 99)
 permatswap(m, method = "quasiswap", strata = NULL,
-mtype = "count", times = 100, burnin = 10000, thin = 1000)
+mtype = "count", times = 99, burnin = 10000, thin = 1000)
 permat.control(ptype = "full", mtype = "count", method = "quasiswap",
 fixedmar = "both", shuffle = "ind", strata = NULL, 
 burnin = 10000, thin = 1000)