[Picante-commits] r98 - branches/gsoc/man

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

Author: mrhelmus
Date: 2008-06-11 09:45:28 +0200 (Wed, 11 Jun 2008)
New Revision: 98

Modified:
   branches/gsoc/man/psd.Rd
   branches/gsoc/man/specaccum.psr.Rd
Log:
Cleaned up documentation... perhaps ready to be merged into the trunk...

Modified: branches/gsoc/man/psd.Rd
===================================================================
--- branches/gsoc/man/psd.Rd	2008-06-11 07:25:05 UTC (rev 97)
+++ branches/gsoc/man/psd.Rd	2008-06-11 07:45:28 UTC (rev 98)
@@ -28,7 +28,7 @@
  shared by all species in a community. The expected value of PSV is statistically independent of species richness, is one when all species in a sample
  are unrelated (i.e., a star phylogeny) and approaches zero as species become more related. PSV is directly related to mean phylogenetic distance. The 
  expected variance around PSV for any sample of a particular species richness can be approximated. 
- To address how individual species contribute to the mean PSV of a data set, the function psv.spp gives signed proportions of the total deviation 
+ To address how individual species contribute to the mean PSV of a data set, the function \code{psv.spp} gives signed proportions of the total deviation 
  from the mean PSV that occurs when all species are removed from the data set one at a time. The absolute values of these \dQuote{species effects} 
  tend to positively correlate with species prevalence. 
  \cr

Modified: branches/gsoc/man/specaccum.psr.Rd
===================================================================
--- branches/gsoc/man/specaccum.psr.Rd	2008-06-11 07:25:05 UTC (rev 97)
+++ branches/gsoc/man/specaccum.psr.Rd	2008-06-11 07:45:28 UTC (rev 98)
@@ -1,31 +1,31 @@
-\name{specaccum.PSR}
-\alias{specaccum.PSR}
+\name{specaccum.psr}
+\alias{specaccum.psr}
 
 \title{ Phylogenetic Species Richness Sample-Based Rarefaction Curve }
 \description{
   Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples.
 }
 \usage{
-specaccum.PSR(samp, tree, permutations = 100, method = "random", ...)
+specaccum.psr(samp, tree, permutations = 100, method = "random", ...)
 }
 
 \arguments{
   \item{samp}{ Community data matrix }
   \item{tree}{ A phylo tree object or a phylogenetic covariance matrix}
-  \item{permutations}{ Number of permutations with method \enc{method= "random"}{typewriter} }
-  \item{method}{ Species accumulation method, currently only \enc{"random"}{typewriter} is supported which adds samples in random order. }
+  \item{permutations}{ Number of permutations with method \code{method= "random"} }
+  \item{method}{ Species accumulation method, currently only \code{"random"} is supported which adds samples in random order. }
   \item{\dots}{ Other parameters to functions }
 }
 
 \value{
-The function returns an object of class \enc{"specaccum"}{typewriter} with items:
+The function returns an object of class \code{"specaccum"} with items:
 
 \item{call}{ Function call. }
 \item{method}{ Accumulator method. }
-\item{sites}{ Number of sites/samples. For \enc{method = "rarefaction"}{typewriter} this is the average number of sites corresponding to a certain number of individuals.}
-\item{richness}{ The phylogenetic species richness corresponding to number of sites/samples. With \enc{method = "collector"}{typewriter} this is the observed phylogenetic species richness, for other methods the average or expected phylogenetic species richness. }
-\item{sd}{ The standard deviation of phylogenetic apecies accumulation curve (or its standard error). This is NULL in \enc{method = "collector"}{typewriter}, and it is estimated from permutations in \enc{method = "random"}{typewriter}, and from analytic equations in other methods. }
-\item{perm}{ Permutation results with \enc{method = "random"}{typewriter} and NULL in other cases. Each column in perm holds one permutation. }
+\item{sites}{ Number of sites/samples. }
+\item{richness}{ The mean phylogenetic species richness corresponding to number of sites/samples. }
+\item{sd}{ The standard deviation of phylogenetic apecies accumulation curve (or its standard error) estimated from permutations in \code{method = "random"}. }
+\item{perm}{ Permutation results with \code{method = "random"} and NULL in other cases. Each column in perm holds one permutation. }
 }
 
 \references{ Gotelli N.J. & Colwell R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391\cr