[Caic-commits] r90 - in pkg: . man

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

Author: davidorme
Date: 2009-04-22 14:58:45 +0200 (Wed, 22 Apr 2009)
New Revision: 90

Modified:
   pkg/DESCRIPTION
   pkg/man/fusco.test.Rd
   pkg/man/phylo.d.Rd
Log:
Minor syntax corrections in .Rd files (whitespace before brace)

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-04-22 11:17:16 UTC (rev 89)
+++ pkg/DESCRIPTION	2009-04-22 12:58:45 UTC (rev 90)
@@ -1,7 +1,7 @@
 Package: CAIC
 Type: Package
 Title: Comparative Analyses using Independent Contrasts
-Version: 1.0.4-89
+Version: 1.0.4-90
 Date: 2008-10-01
 Author: David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz
 Maintainer: David Orme <d.orme at imperial.ac.uk>

Modified: pkg/man/fusco.test.Rd
===================================================================
--- pkg/man/fusco.test.Rd	2009-04-22 11:17:16 UTC (rev 89)
+++ pkg/man/fusco.test.Rd	2009-04-22 12:58:45 UTC (rev 90)
@@ -44,13 +44,13 @@
   \item{right}{Use right or left open intervals in plotting the distribution and calculating the correction}
   \item{I.prime}{Plot distribution of I' or I.}
   \item{sim.reps}{Number of replicate Markov trees to simulate}
-  \item{sim.CI} {Confidence intervals to calculate on simulated trees}
+  \item{sim.CI}{Confidence intervals to calculate on simulated trees}
   \item{rand.reps}{Number of randomizations}
-  \item{rand.CI} {Confidence intervals to use on randomizations}
+  \item{rand.CI}{Confidence intervals to use on randomizations}
   \item{nTips}{Number of tips in simulated tree}
   \item{nSpecies}{Number of species on simulated tree}
   \item{plot}{If changed to FALSE, then the plot method does not plot the frequency histogram. Because the method invisibly returns a table of histogram bins along with the observed and corrected frequencies, this isn't as dim an option as it sounds.}
-  \item{...} {Further arguments to generic methods}
+  \item{...}{Further arguments to generic methods}
 }
 \details{
 I is calculated only at bifurcating nodes giving rise to more than 3 tips (or more than 3 species at the tips): nodes with three or fewer descendants have no variation in I and are not informative in assessing imbalance. The expected distribution of the nodal imbalance values between 0 and 1 is theoretically uniform under a Markov null model. However, the range of possible I values at a node is constrained by the number of descendent species. For example, for a node with 8 species, only the values 0, 0.33, 0.66, 1 are possible, corresponding to 4:4, 5:3, 6:2 and 7:1 splits (Fusco and Cronk, 1995). As node size increases, this departure from a uniform distribution decreases. The plot method incorporates a correction, described by Fusco and Cronk (1995), that uses the distribution of all possible splits at each node to characterize and correct for the departure from uniformity.

Modified: pkg/man/phylo.d.Rd
===================================================================
--- pkg/man/phylo.d.Rd	2009-04-22 11:17:16 UTC (rev 89)
+++ pkg/man/phylo.d.Rd	2009-04-22 12:58:45 UTC (rev 90)
@@ -33,12 +33,12 @@
 }
 \value{
 Returns an object of class 'phylo.d', which is a list of the following:
-\item{DEstimate} {The estimated D value}
-\item{Pval1} {A p value, giving the result of testing whether D is significantly different from one}
-\item{Pval0} {A p value, giving the result of testing whether D is significantly different from zero}
-\item{Parameters} {A list of the Observed, MeanRandom and MeanBrownian sums of sister-clade differences}
-\item{Permutations} {A list with elements random and brownian, containing the sums of sister-clade differences from random permutations and simulations of Brownian evolution under a threshold model}
-\item{NodalVals} {A list with elements observed, random and brownian, containing the nodal values estimated for the observed trait (as a numeric with names that correspond to node numbers in the phylo object) and those estimated in the permutations (as dataframes with a column for each node, named e.g. X17 for node 17)}
+\item{DEstimate}{The estimated D value}
+\item{Pval1}{A p value, giving the result of testing whether D is significantly different from one}
+\item{Pval0}{A p value, giving the result of testing whether D is significantly different from zero}
+\item{Parameters}{A list of the Observed, MeanRandom and MeanBrownian sums of sister-clade differences}
+\item{Permutations}{A list with elements random and brownian, containing the sums of sister-clade differences from random permutations and simulations of Brownian evolution under a threshold model}
+\item{NodalVals}{A list with elements observed, random and brownian, containing the nodal values estimated for the observed trait (as a numeric with names that correspond to node numbers in the phylo object) and those estimated in the permutations (as dataframes with a column for each node, named e.g. X17 for node 17)}
 \item{binvar}{The binary variable used}
 \item{phyName}{The name of the phylogeny object used}
 \item{dsName}{The name of the dataframe used}