[Vegan-commits] r2738 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2013-11-21 19:26:38 +0100 (Thu, 21 Nov 2013)
New Revision: 2738

Modified:
   pkg/vegan/R/anovacca.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/anovacca.Rd
Log:
update anovacca interface and add by = 'margin'

Modified: pkg/vegan/R/anovacca.R
===================================================================
--- pkg/vegan/R/anovacca.R	2013-11-21 18:04:39 UTC (rev 2737)
+++ pkg/vegan/R/anovacca.R	2013-11-21 18:26:38 UTC (rev 2738)
@@ -1,7 +1,9 @@
 `anovacca` <-
     function(object, ..., permutations = how(nperm=999), by = NULL,
-             strata = NULL) 
+             model = c("reduced", "direct", "full"),
+             parallel = getOption("mc.cores"), strata = NULL) 
 {
+    model <- match.arg(model)
     if (!exists(".Random.seed", envir = .GlobalEnv,
                 inherits = FALSE)) 
         runif(1)
@@ -32,15 +34,7 @@
     dotargs <- list(...)
     ## we do not want to give dotargs to anova.ccalist, but we
     ## evaluate 'parallel' and 'model' here
-    if (is.null(dotargs$model))
-        model <- "reduced"
-    else
-        model <- dotargs$model
-    if (is.null(dotargs$parallel))
-        parallel <- NULL
-    else
-        parallel <- dotargs$parallel
-    if (length(dotargs)) {
+     if (length(dotargs)) {
         isCCA <- sapply(dotargs, function(z) inherits(z, "cca"))
         if (any(isCCA)) {
             dotargs <- dotargs[isCCA]
@@ -55,13 +49,16 @@
     }
     ## by cases
     if (!is.null(by)) {
-        by <- match.arg(by, c("terms", "margin"))
+        by <- match.arg(by, c("terms", "margin", "axis"))
         sol <- switch(by,
                       "terms" = anovacca.byterm(object,
                       permutations = permutations,
                       model = model, parallel = parallel),
                       "margin" = anovacca.bymargin(object,
                       permutations = permutations,
+                      model = model, parallel = parallel),
+                      "axis" = anovacca.byaxis(object,
+                      permutations = permutations,
                       model = model, parallel = parallel))
         return(sol)
     }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-11-21 18:04:39 UTC (rev 2737)
+++ pkg/vegan/inst/ChangeLog	2013-11-21 18:26:38 UTC (rev 2738)
@@ -18,8 +18,15 @@
 	models in anova.ccalist. Case by = "margin" directly calls
 	permutest.cca and gets the significances from differences of
 	residual variation similarly as anova.ccalist. Case by = "axis" is
-	not yet implemented.
+	is implemented as a marginal model.
 
+	Simple permutations give identical results for "term" and "axis"
+	cases, but by = "margin" is different. Marginal models were
+	implemented as partial models with other parameters partialled out
+	in vegan 2.0 and earlier, but the current implementation is an
+	anova.ccalist model where the parameter in question was removed
+	and model compared against the complete model.
+
 	* commsim: documentation (commsim.Rd) was restructured so that
 	nullmodels were collected under separate sections with a brief
 	introductory text and shorter specific text of the

Modified: pkg/vegan/man/anovacca.Rd
===================================================================
--- pkg/vegan/man/anovacca.Rd	2013-11-21 18:04:39 UTC (rev 2737)
+++ pkg/vegan/man/anovacca.Rd	2013-11-21 18:26:38 UTC (rev 2738)
@@ -23,7 +23,8 @@
 
 \usage{
 anovacca(object, ..., permutations = how(nperm=999),
-      by = NULL, strata = NULL)
+      by = NULL, model = c("reduced", "direct", "full"), 
+      parallel = getOption("mc.cores"), strata = NULL)
 }
 
 \arguments{
@@ -46,6 +47,10 @@
     the terms (each marginal term analysed in a model with all other
     variables). Not yet implemented.}
 
+  \item{model}{Model}
+
+  \item{parallel}{Parallel processing}
+
   \item{strata}{An integer vector or factor specifying the strata for
     permutation. If supplied, observations are permuted only within
     the specified strata. It is an error to use this when