[Caic-commits] r83 - in pkg: . man

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

Author: davidorme
Date: 2008-10-22 13:06:19 +0200 (Wed, 22 Oct 2008)
New Revision: 83

Modified:
   pkg/DESCRIPTION
   pkg/man/pd.calc.Rd
Log:
fixed problem in markup of pd.calc.Rd; updated version to 1.0.4-83

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-10-22 10:33:21 UTC (rev 82)
+++ pkg/DESCRIPTION	2008-10-22 11:06:19 UTC (rev 83)
@@ -1,7 +1,7 @@
 Package: CAIC
 Type: Package
 Title: Comparative Analyses using Independent Contrasts
-Version: 1.0.4-81
+Version: 1.0.4-83
 Date: 2008-10-01
 Author: David Orme, Rob Freckleton, Gavin Thomas
 Maintainer: David Orme <d.orme at imperial.ac.uk>

Modified: pkg/man/pd.calc.Rd
===================================================================
--- pkg/man/pd.calc.Rd	2008-10-22 10:33:21 UTC (rev 82)
+++ pkg/man/pd.calc.Rd	2008-10-22 11:06:19 UTC (rev 83)
@@ -15,7 +15,7 @@
   \item{root.edge}{Logical indicating whether to include the root edge length in calculations, defaulting to FALSE.}
 }
 \details{
-There are five implemented methods. The default is Total Branch Length (TBL), defined as the sum of all the edge lengths in the subtree given by the tip subset. This measure can be partitioned in two ways: Shared Branch Length (SBL) calculates the sum of all edges in the subtree that are shared by more than one tip; Unique Evolutionary History (UEH) calculates the sum of the edge lengths that give rise to only one tip in the subtree. Note that TBL is the sum of SBL and UEH for a particular subtree and that UEH effectively sums the edges that form tips in the _subtree_. The TIP option calculates the sum of the edges leading to the subset tips in the _complete tree_.  Minimum Spanning Tree (MST) calculate the length of the edges for the smallest tree that links the subset tips, excluding any edges below that node. These options are illustrated in the examples below: the red edges are those summed by each method for the tips labeled in bold. 
+There are five implemented methods. The default is Total Branch Length (TBL), defined as the sum of all the edge lengths in the subtree given by the tip subset. This measure can be partitioned in two ways: Shared Branch Length (SBL) calculates the sum of all edges in the subtree that are shared by more than one tip; Unique Evolutionary History (UEH) calculates the sum of the edge lengths that give rise to only one tip in the subtree. Note that TBL is the sum of SBL and UEH for a particular subtree and that UEH effectively sums the edges that form tips in the \strong{subtree}. The TIP option calculates the sum of the edges leading to the subset tips in the \strong{complete tree}.  Minimum Spanning Tree (MST) calculate the length of the edges for the smallest tree that links the subset tips, excluding any edges below that node. These options are illustrated in the examples below: the red edges are those summed by each method for the tips labelled in bold. 
 }
 \value{
   A list giving: