[Vegan-commits] r1107 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-01-07 12:27:20 +0100 (Thu, 07 Jan 2010)
New Revision: 1107

Modified:
   pkg/vegan/R/fieller.MOStest.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/MOStest.Rd
Log:
removed doubled adjustment for overdispersion in fieller.MOStest

Modified: pkg/vegan/R/fieller.MOStest.R
===================================================================
--- pkg/vegan/R/fieller.MOStest.R	2010-01-07 09:16:30 UTC (rev 1106)
+++ pkg/vegan/R/fieller.MOStest.R	2010-01-07 11:27:20 UTC (rev 1107)
@@ -2,18 +2,18 @@
     function (object, level = 0.95) 
 {
     smodel <- summary(object$mod)
+    ## overdispersion included in cov.scaled
     var <- smodel$cov.scaled
     fam <- family(object$mod)
-    od <- smodel$dispersion
     k <- coef(object$mod)
     b2 <- -2 * k[3]
     u <- -k[2]/2/k[3]
     alpha <- (1-level)/2
     limits <- numeric(2)
     names(limits) <- paste(round(100*(c(alpha, 1-alpha)), 1), "%") 
-    wvar <- var[2,2] * od
-    uvar <- 4 * var[3,3] * od
-    vvar <- -2 * var[2,3] * od
+    wvar <- var[2,2] 
+    uvar <- 4 * var[3,3] 
+    vvar <- -2 * var[2,3]
     z <- qnorm(1 - alpha)
     g <- z^2 * uvar/b2^2
     if (g >= 1) {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-01-07 09:16:30 UTC (rev 1106)
+++ pkg/vegan/inst/ChangeLog	2010-01-07 11:27:20 UTC (rev 1107)
@@ -12,6 +12,11 @@
 	* betadisper: 'type = "median"' is now the default type of
 	analysis.
 
+	* fieller.MOStest: removed erroneous multiplication of variances
+	by overdispersion, because this was already done in cov.scaled,
+	and therefore was doubled and gave much too wide (up to Infinite)
+	limits. 
+
 Version 1.16-34 (closed January 2, 2009) -- (codename: Lucia)
 
 	* twostagechao: deleted, because question regarding the

Modified: pkg/vegan/man/MOStest.Rd
===================================================================
--- pkg/vegan/man/MOStest.Rd	2010-01-07 09:16:30 UTC (rev 1106)
+++ pkg/vegan/man/MOStest.Rd	2010-01-07 11:27:20 UTC (rev 1107)
@@ -163,9 +163,8 @@
 mod
 plot(mod)
 par(op)
-## Infinite confidence limits (NA)
+## Confidence Limits
 fieller.MOStest(mod)
-## Finite limits with the profile
 confint(mod)
 plot(profile(mod))
 }