[Picante-commits] r160 - branches/gsoc/man

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

Author: mrhelmus
Date: 2008-08-13 05:32:59 +0200 (Wed, 13 Aug 2008)
New Revision: 160

Modified:
   branches/gsoc/man/pblm.Rd
   branches/gsoc/man/randomizeSample.Rd
Log:
Made some edits to allow the gsoc branch to be merged with the main branch

Modified: branches/gsoc/man/pblm.Rd
===================================================================
--- branches/gsoc/man/pblm.Rd	2008-08-12 02:28:15 UTC (rev 159)
+++ branches/gsoc/man/pblm.Rd	2008-08-13 03:32:59 UTC (rev 160)
@@ -47,12 +47,14 @@
   \item{CI.boot}{ 95 percent CIs for all parameters }
   \item{variates}{ matrix of model variates (can be used for plotting) }
   \item{residuals}{ matrix of residuals from the three models (full, star and base) }
+  \item{predicted}{ predicted associations }
   \item{bootvalues}{ matrix of parameters estimated from the \code{nreps} bootstrap replicated data sets used to calculate CIs }
-  \item{cors.1}{ correlations among predicted and observed associations for species of tree1, \code{NA} if \code{predict.originals=FALSE} }
-  \item{cors.2}{ correlations among predicted and observed associations for species of tree2,  \code{NA} if \code{predict.originals=FALSE} }
-  \item{pred.novels1}{ predicted associations for the novel speices of tree1 }
-  \item{pred.novels2}{ predicted associations for the novel speices of tree2 }
-}
+  \item{phylocovs}{ phylogenetic covariance matricies scaled by the estimated \code{d1} and \code{d2} }
+  \item{cors.1}{ correlations among predicted and observed associations for species of \code{tree1}, \code{NA} if \code{predict.originals=FALSE} }
+  \item{cors.2}{ correlations among predicted and observed associations for species of \code{tree2},  \code{NA} if \code{predict.originals=FALSE} }
+  \item{pred.novels1}{ predicted associations for the novel speices of \code{tree1} }
+  \item{pred.novels2}{ predicted associations for the novel speices of \code{tree2} }
+}      
 
 
 

Modified: branches/gsoc/man/randomizeSample.Rd
===================================================================
--- branches/gsoc/man/randomizeSample.Rd	2008-08-12 02:28:15 UTC (rev 159)
+++ branches/gsoc/man/randomizeSample.Rd	2008-08-13 03:32:59 UTC (rev 160)
@@ -18,6 +18,7 @@
     \item{trialswap}{Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) by drawing species from sample pool with probability weighted by occurrence frequency (maintains both species occurrence frequency and sample species richness)}
   }
   \item{lang}{run code in C or R? C is faster.} 
+  \item{it}{ number of independent or trial-swaps to perform }
 }
 \value{
   Randomized community data matrix