[Analogue-commits] r178 - in pkg: . R inst man

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

Author: gsimpson
Date: 2010-06-28 19:25:39 +0200 (Mon, 28 Jun 2010)
New Revision: 178

Added:
   pkg/R/chooseTaxa.R
   pkg/man/chooseTaxa.Rd
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
Log:
add function chooseTaxa and document, bump package version

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-06-23 20:53:54 UTC (rev 177)
+++ pkg/DESCRIPTION	2010-06-28 17:25:39 UTC (rev 178)
@@ -1,9 +1,9 @@
 Package: analogue
 Type: Package
 Title: Analogue and weighted averaging methods for palaeoecology
-Version: 0.6-24
+Version: 0.6-25
 Date: $Date$
-Depends: R (>= 2.5.0), stats, graphics, vegan, lattice, grid, MASS
+Depends: R (>= 2.5.0), stats, graphics, vegan, lattice, grid, MASS, princurve
 Author: Gavin L. Simpson, Jari Oksanen
 Maintainer: Gavin L. Simpson <gavin.simpson at ucl.ac.uk>
 Description: Fits Modern Analogue Technique and Weighted Averaging transfer 

Added: pkg/R/chooseTaxa.R
===================================================================
--- pkg/R/chooseTaxa.R	                        (rev 0)
+++ pkg/R/chooseTaxa.R	2010-06-28 17:25:39 UTC (rev 178)
@@ -0,0 +1,18 @@
+chooseTaxa <- function(object, ...) {
+    UseMethod("chooseTaxa")
+}
+
+chooseTaxa.default <- function(object, n.occ = 1, max.abun = 0,
+                               type = c("AND","OR"), ...) {
+    if(missing(type))
+        type <- "AND"
+    type <- match.arg(type)
+    occ.want <- colSums(object > 0) >= n.occ
+    abun.want <- apply(object, 2, max) >= max.abun
+    want <- if(isTRUE(all.equal(type, "AND"))) {
+        occ.want & abun.want
+    } else {
+        occ.want & abun.want
+    }
+    return(object[,want])
+}

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2010-06-23 20:53:54 UTC (rev 177)
+++ pkg/inst/ChangeLog	2010-06-28 17:25:39 UTC (rev 178)
@@ -1,5 +1,11 @@
 analogue Change Log
 
+Version 0.6-25
+
+	* chooseTaxa: new function to select species on basis of number
+	of occurrences and maximum abundance. Function is an S3 generic
+	with a default method.
+
 Version 0.6-24
 
 	* Dependencies: package now depends on package 'grid'.

Added: pkg/man/chooseTaxa.Rd
===================================================================
--- pkg/man/chooseTaxa.Rd	                        (rev 0)
+++ pkg/man/chooseTaxa.Rd	2010-06-28 17:25:39 UTC (rev 178)
@@ -0,0 +1,57 @@
+\name{chooseTaxa}
+\alias{chooseTaxa}
+\alias{chooseTaxa.default}
+\title{Select taxa (variables) on basis of maximum abundance attained
+  and number of occurrences}
+\description{
+  Select taxa (variables) from an object on the basis of one or both of
+  maximum abundance and number of occurrences greater than user-specified
+  values. This is a simple utility function to encapsulate this common
+  task in filtering palaeoecological data sets.
+}
+\usage{
+chooseTaxa(object, \dots)
+
+\method{chooseTaxa}{default}(object, n.occ = 1, max.abun = 0,
+           type = c("AND","OR"), \dots)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{object}{an R object for which a suitable method exists. The
+    default method assumes a matrix-like object such as a data
+    frame or a numeric matrix.}
+  \item{n.occ}{numeric; number of occurrences representing the lower
+    limit for selection. A taxon is included in the returned subset if
+    it is present a total of \code{n.occ} times or more. See argument
+    \code{type} for a modifier which might exclude the taxon even if it
+    would be included on the basis of \code{n.occ}.}
+  \item{max.abun}{numeric; maximum abundance representing the lower
+    limit for selection. A taxon is included in the returned subset if
+    it attains abundance equal to or greater than \code{max.abun} in one
+    or more sample. See argument \code{type} for a modifier which might
+    exclude the taxon even if it would be included on the basis
+    of \code{max.abun}.}
+  \item{type}{character; one of \code{"AND"} or \code{"OR"}, controlling
+    how the criteria \code{n.occ} and \code{max.abun} are combined to
+    generate a subset of the variables in \code{object}.}
+  \item{\dots}{arguments passed on to subsequent methods.}
+}
+%\details{
+%}
+\value{
+  Returns the supplied data frame or matrix with a subset of columns
+  (taxa) that meet the criteria chosen.
+}
+%\references{
+%}
+\author{Gavin L. Simpson}
+%\seealso{
+%}
+\examples{
+data(ImbrieKipp)
+IK2 <- chooseTaxa(ImbrieKipp, n.occ = 5)
+dim(ImbrieKipp)
+dim(IK2)
+}
+\keyword{methods}
+\keyword{multivariate}