[Vegan-commits] r2612 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2013-09-10 09:36:36 +0200 (Tue, 10 Sep 2013)
New Revision: 2612

Modified:
   pkg/vegan/R/simulate.rda.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/simulate.rda.Rd
Log:
implement correlated simulation for cca, and clearly skip for capscale

Modified: pkg/vegan/R/simulate.rda.R
===================================================================
--- pkg/vegan/R/simulate.rda.R	2013-09-10 06:12:46 UTC (rev 2611)
+++ pkg/vegan/R/simulate.rda.R	2013-09-10 07:36:36 UTC (rev 2612)
@@ -91,8 +91,11 @@
 ### still guarantee that all marginal totals are positive.
 
 `simulate.cca` <-
-    function(object, nsim = 1, seed = NULL, indx = NULL, rank = "full", ...)
+    function(object, nsim = 1, seed = NULL, indx = NULL, rank = "full",
+             correlated = FALSE, ...)
 {
+    if (is.null(indx) && correlated)
+        require(MASS) || stop("simulate options require MASS package")
     ## Handle RNG: code directly from stats::simulate.lm
     if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) 
         runif(1)
@@ -124,11 +127,17 @@
     ## Residual Xbar need weighting and back-weighting
     Xbar <- sweep(object$CA$Xbar, 1, sq.r, "*")
     ## Simulation
+    if (correlated)
+        dev <- cov(Xbar)
+    else
+        dev <- outer(rep(1, nrow(ftd)), apply(Xbar, 2, sd))
     ans <- array(0, c(dim(ftd), nsim))
     for (i in seq_len(nsim)) {
         if (is.null(indx)) {
-            tmp <- matrix(rnorm(length(ftd), 
-               sd = outer(rep(1,nrow(ftd)), apply(Xbar, 2, sd))), 
+            if (correlated)
+                tmp <- mvrnorm(nrow(ftd), numeric(ncol(ftd)), Sigma = dev)
+            else
+                tmp <- matrix(rnorm(length(ftd), sd = dev), 
                           nrow = nrow(ftd))
             ans[,,i] <- as.matrix(ftd + sweep(tmp, 1, sq.r, "/"))
         }
@@ -176,8 +185,11 @@
 ### component.
 
 `simulate.capscale` <-
-    function(object, nsim = 1, seed = NULL, indx = NULL, rank = "full", ...) 
+    function(object, nsim = 1, seed = NULL, indx = NULL, rank = "full",
+             correlated = FALSE, ...) 
 {
+    if (is.null(indx) && correlated)
+        warning("argument 'correlated' does not work and will be ignored")
     ## Handle RNG: code directly from stats::simulate.lm
     if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) 
         runif(1)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-09-10 06:12:46 UTC (rev 2611)
+++ pkg/vegan/inst/ChangeLog	2013-09-10 07:36:36 UTC (rev 2612)
@@ -11,6 +11,14 @@
 	further are oblique to the corresponding axis. In any case they
 	will have zero correlation to all subsequent dimensions.
 
+	* simulate.rda, simulate.cca: gained argument 'correlated' for
+	using covariances of species in generating correlated multivariate
+	normal residuals in parametric simulations. The covariances are
+	estimated from the residual ordination of species. The argument
+	defaults FALSE which implements the old parametric simulation
+	where each species is simulated independently.  The argument has
+	no effect in capscale() which stores no information on species.
+	
 Version 2.1-34 (closed September 5, 2013)
 
 	* DESCRIPTION: dependent on R >= 2.14.0.

Modified: pkg/vegan/man/simulate.rda.Rd
===================================================================
--- pkg/vegan/man/simulate.rda.Rd	2013-09-10 06:12:46 UTC (rev 2611)
+++ pkg/vegan/man/simulate.rda.Rd	2013-09-10 07:36:36 UTC (rev 2612)
@@ -45,8 +45,9 @@
   \item{correlated}{Are species regarded as correlated in parametric
     simulation or when \code{indx} is not given? If
     \code{correlated = TRUE}, multivariate Gaussian random error is
-    generated, and if \code{FALSE}, Gaussian random error is
-    generated separately for each species. }
+    generated, and if \code{FALSE}, Gaussian random error is generated
+    separately for each species. The argument has no effect in
+    \code{\link{capscale}} which has no information on species.}
 
   \item{\dots}{additional optional arguments (ignored). }
 }