[Vegan-commits] r2830 - in pkg/vegan: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 10 12:03:26 CET 2014
Author: jarioksa
Date: 2014-01-10 12:03:26 +0100 (Fri, 10 Jan 2014)
New Revision: 2830
Modified:
pkg/vegan/R/treedist.R
pkg/vegan/R/treedive.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/treedive.Rd
Log:
default now match.force=TRUE and treedive can be silenced
Modified: pkg/vegan/R/treedist.R
===================================================================
--- pkg/vegan/R/treedist.R 2014-01-08 09:33:40 UTC (rev 2829)
+++ pkg/vegan/R/treedist.R 2014-01-10 11:03:26 UTC (rev 2830)
@@ -1,5 +1,5 @@
`treedist` <-
- function(x, tree, relative = TRUE, match.force = FALSE, ...)
+ function(x, tree, relative = TRUE, match.force = TRUE, ...)
{
n <- nrow(x)
ABJ <- matrix(0, n , n)
Modified: pkg/vegan/R/treedive.R
===================================================================
--- pkg/vegan/R/treedive.R 2014-01-08 09:33:40 UTC (rev 2829)
+++ pkg/vegan/R/treedive.R 2014-01-10 11:03:26 UTC (rev 2830)
@@ -1,17 +1,17 @@
`treedive` <-
- function(comm, tree, match.force = FALSE)
+ function(comm, tree, match.force = TRUE, verbose = TRUE)
{
if (!inherits(tree, c("hclust", "spantree")))
stop("'clus' must be an 'hclust' or 'spantree' result object")
m <- as.matrix(cophenetic(tree))
## Check tree/comm match by names
if (match.force || ncol(comm) != ncol(m)) {
- if (match.force)
+ if (match.force && verbose)
message("Forced matching of 'tree' labels and 'comm' names")
- else
+ else if (verbose)
message("Dimensions do not match between 'comm' and 'tree'")
fnd <- colnames(comm) %in% tree$labels
- if (!all(fnd)) {
+ if (!all(fnd) && verbose) {
warning("not all names of 'comm' found in 'tree'")
comm <- comm[, fnd]
}
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2014-01-08 09:33:40 UTC (rev 2829)
+++ pkg/vegan/inst/ChangeLog 2014-01-10 11:03:26 UTC (rev 2830)
@@ -20,6 +20,10 @@
with three points was reported by Paul Bacquet (Louvain,
Belgium).
+ * treedive, treedist: default is now match.force = TRUE, and
+ treedive() gained new argument 'verbose' to turn of most messages
+ -- which is practical in oecosimu().
+
* BCI: names checked after http://www.theplantlist.org, but kept
the old (alphabetic) order of species. The changes are: Abarema
macradenium -> A. macradenia, Apeiba aspera -> A. glabra,
Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd 2014-01-08 09:33:40 UTC (rev 2829)
+++ pkg/vegan/man/treedive.Rd 2014-01-10 11:03:26 UTC (rev 2830)
@@ -3,7 +3,7 @@
\alias{treeheight}
\alias{treedist}
-\title{ Functional Diversity and Community Distances from Species Trees}
+\title{Functional Diversity and Community Distances from Species Trees}
\description{ Functional diversity is defined as the total branch
length in a trait dendrogram connecting all species, but excluding
@@ -12,9 +12,9 @@
combining two sites. }
\usage{
-treedive(comm, tree, match.force = FALSE)
+treedive(comm, tree, match.force = TRUE, verbose = TRUE)
treeheight(tree)
-treedist(x, tree, relative = TRUE, match.force = FALSE, ...)
+treedist(x, tree, relative = TRUE, match.force = TRUE, ...)
}
\arguments{
@@ -26,6 +26,7 @@
matching only happens when dimensions differ (with a warning or
message). The order of data must match to the order in \code{tree}
if matching by names is not done.}
+ \item{verbose}{Print diagnostic messages and warnings.}
\item{relative}{Use distances relative to the height of combined tree.}
\item{\dots}{Other arguments passed to functions (ignored).}
}
@@ -35,7 +36,8 @@
dendrogram that can be coerced to a correct type using
\code{\link{as.hclust}}. When applied to a clustering of species
traits, this is a measure of functional diversity (Petchey and Gaston
- 2002, 2006).
+ 2002, 2006), and when applied to phylogenetic trees this is
+ phylogenetic diversity.
Function \code{treedive} finds the \code{treeheight} for each site
(row) of a community matrix. The function uses a subset of
@@ -45,7 +47,7 @@
calculating \code{\link{cophenetic}} distances from the input
dendrogram, then reconstructing the dendrogram for the subset of the
cophenetic distance matrix for species occurring in each
- site. Diversity is 0 for one spcies, and \code{NA} for empty
+ site. Diversity is 0 for one species, and \code{NA} for empty
communities.
Function \code{treedist} finds the dissimilarities among
@@ -64,15 +66,17 @@
index attains its maximum value \eqn{2}. The dissimilarity is zero
from a combined zero-height tree.
- The functions need a dendrogram of species traits as an input. If
- species traits contain \code{\link{factor}} or \code{\link{ordered}}
- factor variables, it is recommended to use Gower distances for mixed
- data (function \code{\link[cluster]{daisy}} in package \pkg{cluster}),
- and usually the recommended clustering method is UPGMA
- (\code{method = "average"} in function \code{\link{hclust}})
- (Podani and Schmera 2006).
+ The functions need a dendrogram of species traits or phylogenies as an
+ input. If species traits contain \code{\link{factor}} or
+ \code{\link{ordered}} factor variables, it is recommended to use Gower
+ distances for mixed data (function \code{\link[cluster]{daisy}} in
+ package \pkg{cluster}), and usually the recommended clustering method
+ is UPGMA (\code{method = "average"} in function \code{\link{hclust}})
+ (Podani and Schmera 2006). Phylogenetic trees can be changed into
+ dendrograms using \code{\link[ape]{as.hclust.phylo}} (package
+ \pkg{ape})
- It is possible to analyse the non-randomness of functional diversity
+ It is possible to analyse the non-randomness of tree diversity
using \code{\link{oecosimu}}. This needs specifying an adequate Null
model, and the results will change with this choice.
}
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