[Vegan-commits] r1885 - in pkg/vegan: R man tests/Examples

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

Author: jarioksa
Date: 2011-09-25 19:56:29 +0200 (Sun, 25 Sep 2011)
New Revision: 1885

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/man/oecosimu.Rd
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
oecosimu can take either a method name or a commsim function: get back custom function in examples

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2011-09-24 23:56:14 UTC (rev 1884)
+++ pkg/vegan/R/oecosimu.R	2011-09-25 17:56:29 UTC (rev 1885)
@@ -73,7 +73,7 @@
         names(indstat) <- statistic
     if (!is.list(ind))
         ind <- list(statistic = ind)
-    ind$oecosimu <- list(z = z, pval = p, simulated=simind, method=method,
+    ind$oecosimu <- list(z = z, pval = p, simulated=simind, method=nm$commsim$method,
                          statistic = indstat, alternative = alternative)
     class(ind) <- c("oecosimu", class(ind))
     ind

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2011-09-24 23:56:14 UTC (rev 1884)
+++ pkg/vegan/man/oecosimu.Rd	2011-09-25 17:56:29 UTC (rev 1885)
@@ -38,7 +38,9 @@
     community as the first argument, and returns either a plain number or
     the result in list item with the name defined in argument
   \code{statistic}. See Examples for defining your own functions.}
-  \item{method}{Null model method. See details.}
+  \item{method}{Null model method: either a name (character string) of
+    a method defined in \code{\link{make.commsim}} or a
+    \code{\link{commsim}} function. See Details and Examples.}
   \item{nsimul}{Number of simulated null communities.}
   \item{burnin}{Number of null communities discarded before proper
   analysis in sequential methods \code{"swap"} and \code{"tswap"}.}
@@ -256,7 +258,18 @@
 meandist <- function(x) mean(vegdist(x, "bray"))
 mbc1 <- oecosimu(dune, meandist, "r2dtable")
 mbc1
+
+## Define your own null model as a 'commsim' function: shuffle cells
+## in each row
+foo <- function(x, n, nr, nc, ...) {
+   out <- array(0, c(nr, nc, n))
+   for (k in seq_len(n))
+      out[,,k] <- apply(x, 2, function(z) sample(z, length(z)))
+   out
 }
+cf <- commsim("myshuffle", foo, isSeq = FALSE, binary = FALSE, mode = "double")
+oecosimu(dune, meandist, cf)
+}
 \keyword{ multivariate }
 \keyword{ datagen }
 

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-09-24 23:56:14 UTC (rev 1884)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-09-25 17:56:29 UTC (rev 1885)
@@ -4330,8 +4330,27 @@
 ---
 Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
 > 
+> ## Define your own null model as a 'commsim' function: shuffle cells
+> ## in each row
+> foo <- function(x, n, nr, nc, ...) {
++    out <- array(0, c(nr, nc, n))
++    for (k in seq_len(n))
++       out[,,k] <- apply(x, 2, function(z) sample(z, length(z)))
++    out
++ }
+> cf <- commsim("myshuffle", foo, isSeq = FALSE, binary = FALSE, mode = "double")
+> oecosimu(dune, meandist, cf)
+oecosimu with 99 simulations
+simulation method myshuffle
+alternative hypothesis: true mean is not equal to the statistic
+
+          statistic       z    2.5%     50%  97.5% Pr(sim.)   
+statistic   0.64565 3.44557 0.62994 0.63487 0.6418     0.01 **
+---
+Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
 > 
 > 
+> 
 > cleanEx()
 
 detaching ‘package:lattice’
@@ -4984,7 +5003,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1074dd0a0>
+<environment: 0x107a4cd50>
 
 Estimated degrees of freedom:
 6.4351  total = 7.435071 
@@ -5000,7 +5019,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x10696c9c8>
+<environment: 0x107008a38>
 
 Estimated degrees of freedom:
 6.1039  total = 7.103853 
@@ -5156,7 +5175,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1073b3118>
+<environment: 0x105ce1950>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -5169,7 +5188,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x10715aa30>
+<environment: 0x105b6bc68>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -5182,7 +5201,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x107d26cd8>
+<environment: 0x106f04f10>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -7441,7 +7460,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1072c38d0>
+<environment: 0x105b7de68>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -7917,7 +7936,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  110.662 1.469 112.859 0 0 
+Time elapsed:  112.312 1.473 115.297 0 0 
 > grDevices::dev.off()
 null device 
           1