[Vegan-commits] r2144 - in pkg/vegan: R inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 23 21:12:10 CEST 2012
Author: psolymos
Date: 2012-04-23 21:12:10 +0200 (Mon, 23 Apr 2012)
New Revision: 2144
Modified:
pkg/vegan/R/hiersimu.default.R
pkg/vegan/R/hiersimu.formula.R
pkg/vegan/R/multipart.default.R
pkg/vegan/R/multipart.formula.R
pkg/vegan/inst/ChangeLog
Log:
multipart ad hiersimu follow adipart (constant gamma fix)
Modified: pkg/vegan/R/hiersimu.default.R
===================================================================
--- pkg/vegan/R/hiersimu.default.R 2012-04-23 17:29:12 UTC (rev 2143)
+++ pkg/vegan/R/hiersimu.default.R 2012-04-23 19:12:10 UTC (rev 2144)
@@ -66,7 +66,7 @@
evalFUN <- function(x) {
if (fullgamma && !drop.highest) {
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)
}
Modified: pkg/vegan/R/hiersimu.formula.R
===================================================================
--- pkg/vegan/R/hiersimu.formula.R 2012-04-23 17:29:12 UTC (rev 2143)
+++ pkg/vegan/R/hiersimu.formula.R 2012-04-23 19:12:10 UTC (rev 2144)
@@ -69,7 +69,7 @@
evalFUN <- function(x) {
if (fullgamma && !drop.highest) {
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)
}
Modified: pkg/vegan/R/multipart.default.R
===================================================================
--- pkg/vegan/R/multipart.default.R 2012-04-23 17:29:12 UTC (rev 2143)
+++ pkg/vegan/R/multipart.default.R 2012-04-23 19:12:10 UTC (rev 2144)
@@ -78,7 +78,7 @@
wdivfun <- function(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)
}
@@ -94,7 +94,7 @@
wdivfun <- function(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)
}
Modified: pkg/vegan/R/multipart.formula.R
===================================================================
--- pkg/vegan/R/multipart.formula.R 2012-04-23 17:29:12 UTC (rev 2143)
+++ pkg/vegan/R/multipart.formula.R 2012-04-23 19:12:10 UTC (rev 2144)
@@ -82,7 +82,7 @@
wdivfun <- function(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)
}
@@ -98,7 +98,7 @@
wdivfun <- function(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)
}
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2012-04-23 17:29:12 UTC (rev 2143)
+++ pkg/vegan/inst/ChangeLog 2012-04-23 19:12:10 UTC (rev 2144)
@@ -4,24 +4,29 @@
Version 2.1-14 (opened March 9, 2012)
- * adipart, multipart, hiersimu: these are now generic functions
- with default and formula methods. The formula method is
- identical to the previous function, the default method
- can take two matrices as input, but the second argument
- describing the hierarchy can be missing. In this case
- a trivial two-level hierarchy will be assumed (each row
- is a seperate group, all rows are in same group).
+ * multipart and hiersimu: 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.
- * scoverage: new function for sample coverage based
- correction for calculation of relative frequencies in count
- community matrices (Good 1953, Biometrika 40, 237--264).
+ * adipart, multipart, hiersimu: these are now generic functions
+ with default and formula methods. The formula method is
+ identical to the previous function, the default method
+ can take two matrices as input, but the second argument
+ describing the hierarchy can be missing. In this case
+ a trivial two-level hierarchy will be assumed (each row
+ is a seperate group, all rows are in same group).
- * clamtest: wrongly used frequencies instead of the counts
- when calculating sample coverage to test x < coverage.limit.
- No detectable differences were produced when rerunning
- examples from Chazdon et al. 2011 (Ecology, 92, 1332--1343)
- and vegan help page.
+ * scoverage: new function for sample coverage based
+ correction for calculation of relative frequencies in count
+ community matrices (Good 1953, Biometrika 40, 237--264).
+ * clamtest: wrongly used frequencies instead of the counts
+ when calculating sample coverage to test x < coverage.limit.
+ No detectable differences were produced when rerunning
+ examples from Chazdon et al. 2011 (Ecology, 92, 1332--1343)
+ and vegan help page.
+
* Opened a new version with the CRAN release of vegan 2.0-3 on
March 3, 2012.
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