[Vegan-commits] r2132 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2012-04-17 12:27:02 +0200 (Tue, 17 Apr 2012)
New Revision: 2132

Modified:
   pkg/vegan/R/adipart.R
   pkg/vegan/inst/ChangeLog
Log:
Squashed commit of the following:

commit 3613e7ddc309f6f186600c0761e1cb8cd5930ef9
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Tue Apr 17 13:15:36 2012 +0300

    adipart assumed constant gamma diversity in all simulations

    The default method ("r2dtable") had constant gamma, but some other
    methods gave variable gamma diversities, and this gave biased
    test results.

    If we are interested in beta, the gamma should *not* vary, and setting
    'relative = TRUE' probably makes sense with variable gamma.

commit 46fc8aca0a2eca71545a84d17ab82aa0583f9bf6
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Tue Apr 17 12:52:39 2012 +0300

    indentation of adipart.R

Modified: pkg/vegan/R/adipart.R
===================================================================
--- pkg/vegan/R/adipart.R	2012-04-15 16:52:06 UTC (rev 2131)
+++ pkg/vegan/R/adipart.R	2012-04-17 10:27:02 UTC (rev 2132)
@@ -63,26 +63,27 @@
     index <- match.arg(index)
     weights <- match.arg(weights)
     switch(index,
-        "richness" = {
-            divfun <- function(x) apply(x > 0, 1, sum)},
-        "shannon" = {
-            divfun <- function(x) diversity(x, index = "shannon", MARGIN = 1, base=base)},
-        "simpson" = {
-            divfun <- function(x) diversity(x, index = "simpson", MARGIN = 1)})
-    sumMatr <- sum(lhs)
+           "richness" = {
+               divfun <- function(x) apply(x > 0, 1, sum)},
+           "shannon" = {
+               divfun <- function(x) diversity(x, index = "shannon", MARGIN = 1, base=base)},
+           "simpson" = {
+               divfun <- function(x) diversity(x, index = "simpson", MARGIN = 1)})
 
     ## this is the function passed to oecosimu
     wdivfun <- function(x) {
+        ## matrix sum *can* change in oecosimu (but default is constant sumMatr)
+        sumMatr <- sum(x)
         if (fullgamma) {
             tmp <- lapply(1:(nlevs-1), function(i) t(model.matrix(ftmp[[i]], rhs)) %*% x)
-            tmp[[nlevs]] <- matrix(colSums(lhs), nrow = 1, ncol = ncol(lhs))
+            tmp[[nlevs]] <- matrix(colSums(x), nrow = 1, ncol = ncol(x))
         } else {
             tmp <- lapply(1:nlevs, function(i) t(model.matrix(ftmp[[i]], rhs)) %*% x)
         }
         ## weights will change in oecosimu thus need to be recalculated
         if (weights == "prop")
             wt <- lapply(1:nlevs, function(i) apply(tmp[[i]], 1, function(z) sum(z) / sumMatr))
-            else wt <- lapply(1:nlevs, function(i) rep(1 / NROW(tmp[[i]]), NROW(tmp[[i]])))
+        else wt <- lapply(1:nlevs, function(i) rep(1 / NROW(tmp[[i]]), NROW(tmp[[i]])))
         a <- sapply(1:nlevs, function(i) sum(divfun(tmp[[i]]) * wt[[i]]))
         if (relative)
             a <- a / a[length(a)]
@@ -91,15 +92,15 @@
     }
     if (nsimul > 0) {
         sim <- oecosimu(lhs, wdivfun, method = method, nsimul=nsimul,
-            burnin=burnin, thin=thin)
-        } else {
-            sim <- wdivfun(lhs)
-            tmp <- rep(NA, length(sim))
-            sim <- list(statistic = sim,
-                oecosimu = list(z = tmp, pval = tmp, method = NA, statistic = sim))
-        }
+                        burnin=burnin, thin=thin)
+    } else {
+        sim <- wdivfun(lhs)
+        tmp <- rep(NA, length(sim))
+        sim <- list(statistic = sim,
+                    oecosimu = list(z = tmp, pval = tmp, method = NA, statistic = sim))
+    }
     nam <- c(paste("alpha", 1:(nlevs-1), sep="."), "gamma",
-        paste("beta", 1:(nlevs-1), sep="."))
+             paste("beta", 1:(nlevs-1), sep="."))
     names(sim$statistic) <- attr(sim$oecosimu$statistic, "names") <- nam
     attr(sim, "call") <- match.call()
     attr(sim, "index") <- index

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-04-15 16:52:06 UTC (rev 2131)
+++ pkg/vegan/inst/ChangeLog	2012-04-17 10:27:02 UTC (rev 2132)
@@ -16,6 +16,11 @@
 	was already analysed by Marti Anderson when introducing the
 	method).
 
+	* adipart: permutation tests assumed constant full gamma diversity
+	in all simulations even when the null model could produce variable
+	gamma diversities. The default method ("r2dtable") had constant
+	gamma diversity.
+
 	* anova of prc() objects by "axis", "terms" or "margin" failed due
 	to NAMESPACE issues. Reported as issue #7 by Eduard Szöcs in
 	github.com.