[Vegan-commits] r1308 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-09-17 11:53:44 +0200 (Fri, 17 Sep 2010)
New Revision: 1308

Removed:
   pkg/vegan/R/anova.ccalist.R
Modified:
   pkg/vegan/inst/ChangeLog
Log:
remove anova.ccalist()

Deleted: pkg/vegan/R/anova.ccalist.R
===================================================================
--- pkg/vegan/R/anova.ccalist.R	2010-09-17 09:48:06 UTC (rev 1307)
+++ pkg/vegan/R/anova.ccalist.R	2010-09-17 09:53:44 UTC (rev 1308)
@@ -1,70 +0,0 @@
-### A test of concept function for significance test of two (or more)
-### cca, rda or capscale models. A "test of concept" means that there
-### are no sanity chekcs, but only the basic code with assumption that
-### input is correct.
-
-### The idea is to run permutest with the same random number seed and
-### take the difference of permutation results (denominator and
-### numerator of pseudo-F) and take P-values of that.  Assume the two
-### models are m1 <- cca(y ~ x1) and m2 <- cca(y ~ x1 + x2). Currently
-### the difference can be analysed as a partial model, where the
-### common part is partialled out m12 <- cca(y ~ Condition(x1) +
-### x2). The direct difference of two models suggested here does not
-### produce the same results except with model = "direct", because the
-### partial model will permute residuals after conditions.
-`anova.ccalist` <- function(object, ...)
-{
-    objects <- list(object, ...)
-    nmodels <- length(objects)
-    ## Collect statistics
-    N <- nrow(object$CA$u)
-    ranks <- sapply(objects, function(x)
-                    if (is.null(x$CCA$qrank)) 0 else x$CCA$qrank)
-    resdf <- N - ranks - 1
-    resdev <- sapply(objects, deviance)
-    moddev <- c(NA, -diff(resdev))
-    moddf <- c(NA, diff(ranks))
-    ##Collect tests
-    mods <- list()
-    for(i in 1:nmodels) {
-        if (i > 1)
-            ## juggling for Null model y ~ 1
-            if (!is.null(mods[[i-1]]$Random.seed))
-                assign(".Random.seed", mods[[i-1]]$Random.seed,
-                       envir = .GlobalEnv)
-        if (!is.null(objects[[i]]$CCA) && !is.null(objects[[i]]$CA))
-            mods[[i]] <- permutest(objects[[i]])
-        else {
-            if (is.null(objects[[i]]$CCA)) {
-                mods[[i]] <- list(num = 0,
-                                 den = objects[[i]]$CA$tot.chi/(N-1))
-            } else {
-                mods[[i]] <- list(num = objects[[i]]$CCA$tot.chi/moddf[i],
-                                  den = 0)
-            }
-        }
-    }
-    ## Differences of permutations. In permutation F values, numerator
-    ## is taken from each model, but all use the same denominator from
-    ## the largest model.
-    bigmodel <- which.min(resdf)
-    F <- moddev/moddf/resdev[bigmodel]*resdf[bigmodel]
-    den <- mods[[bigmodel]]$den/mods[[bigmodel]]$df[2]
-    Pval <- rep(NA, nmodels)
-    for (i in 2:nmodels) {
-        F.perm <- abs(mods[[i]]$num - mods[[i-1]]$num)/abs(moddf[i])/abs(den)
-        Pval[i] <- (sum(F.perm >= F[i]) + 1)/(length(F.perm) + 1)
-    }   
-    ## ANOVA table 
-    table <- data.frame(resdf, resdev, moddf, moddev, F, Pval)
-    dimnames(table) <- list(1:nmodels, c("Res.Df", "RSS", "Df", "Sum of Sq",
-                                         "F", "Pr(>F)"))
-    variables <- sapply(objects,
-                        function(x) paste(deparse(formula(x)), collapse="\n"))
-    title <- "Analysis of Variance Table\n"
-    topnote <- paste("Model ", format(1:nmodels), ": ", variables,
-                     sep = "", collapse = "\n")
-    table <- structure(table, heading = c(title, topnote))
-    class(table) <- c("anova.cca", "anova", class(table))
-    table
-}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-09-17 09:48:06 UTC (rev 1307)
+++ pkg/vegan/inst/ChangeLog	2010-09-17 09:53:44 UTC (rev 1308)
@@ -9,6 +9,12 @@
 	not yet seen a case where a terms is dropped. Abandoned dangerous
 	practice of getting the R2.all directly from a fitted model of the
 	'scope' since this may have different lhs.
+
+	* anova.ccalist: removed. Revisions were 1273, 1274, 1276. Could
+	not make this work consistently with other anova models, except
+	with 'model = "direct"'. The function would also chage the API so
+	that "..." come as the second argument breaking partial matching
+	of other arguments. 
 	
 Version 1.18-11 (closed September 17, 2010)