[Mattice-commits] r106 - pkg/man

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

Author: andrew_hipp
Date: 2008-12-22 23:23:50 +0100 (Mon, 22 Dec 2008)
New Revision: 106

Modified:
   pkg/man/carex.Rd
   pkg/man/ouSim.Rd
   pkg/man/paintBranches.Rd
   pkg/man/regimeVectors.Rd
Log:
cleaned up code vs. pkg formatting

Modified: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd	2008-12-22 18:04:32 UTC (rev 105)
+++ pkg/man/carex.Rd	2008-12-22 22:23:50 UTC (rev 106)
@@ -18,7 +18,7 @@
 \details{
   \item{phylogeny}{
   Phylogeny (\code{tree}) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using penalized likelihood
-  in \code{ape}, and then the tree was pruned down to only those taxa for which chromosome counts were available.
+  in \pkg{ape}, and then the tree was pruned down to only those taxa for which chromosome counts were available.
   }
   \item{chromosome counts}{
   Chromosome counts (\code{dat}) were averaged by population, and the means log-transformed for analysis.

Modified: pkg/man/ouSim.Rd
===================================================================
--- pkg/man/ouSim.Rd	2008-12-22 18:04:32 UTC (rev 105)
+++ pkg/man/ouSim.Rd	2008-12-22 22:23:50 UTC (rev 106)
@@ -19,10 +19,10 @@
 \details{
   A call to \code{ouSim} detects the class of \code{object} and behaves as follows:
   \item{phylo}{
-    With an \code{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
+    With an \pkg{ape}-style tree, all parameters of the model are specified by branch. Most flexibility, least convenience.
     }
   \item{ouchtree}{
-    With an \code{ouch}-style (S4) tree, again, all parameters of the model are specified by branch. 
+    With an \pkg{ouch}-style (S4) tree, again, all parameters of the model are specified by branch. 
     Somewhat less flexibility than \code{ouSim.phylo} but all the pain. Typically just called by the next two methods.
     }
   \item{browntree}{

Modified: pkg/man/paintBranches.Rd
===================================================================
--- pkg/man/paintBranches.Rd	2008-12-22 18:04:32 UTC (rev 105)
+++ pkg/man/paintBranches.Rd	2008-12-22 22:23:50 UTC (rev 106)
@@ -10,7 +10,7 @@
 }
 \arguments{
   \item{tree}{
-   An S4 ouchtree object, generated using \code{ape2ouch} or \code{ouchtree}. 
+   An S4 \code{ouchtree} object, generated using \code{ape2ouch} or \code{ouchtree}. 
    Old-style ouch trees (data frames) will not work but can be translated using \code{ouchtree}.
    }
   \item{regimeShiftNodes}{
@@ -33,5 +33,5 @@
   The regime is formated to input directly into \code{hansen}
 }
 \seealso{
-  \code{\link{regimeVectors}}, \code{\link{isMonophyletic}}, \code{\link{nodeDescendents}}, \code{\link{mrcaOUCH}}
+  \code{\link{regimeVectors}}, \code{\link{isMonophyletic}}
 }

Modified: pkg/man/regimeVectors.Rd
===================================================================
--- pkg/man/regimeVectors.Rd	2008-12-22 18:04:32 UTC (rev 105)
+++ pkg/man/regimeVectors.Rd	2008-12-22 22:23:50 UTC (rev 106)
@@ -10,7 +10,7 @@
 }
 \arguments{
 \item{ouchTrees}{
-  A list of S4 ouchtree objects
+  A list of S4 \code{ouchtree} objects
   }
 \item{cladeMembersList}{
   A list of taxa defining nodes.