[Mattice-commits] r32 - in pkg: . R

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

Author: andrew_hipp
Date: 2008-11-17 16:43:47 +0100 (Mon, 17 Nov 2008)
New Revision: 32

Modified:
   pkg/DESCRIPTION
   pkg/R/informationCriterion.R
   pkg/R/treeTraversal.R
Log:
fixed DESCRIPTION

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-11-17 06:33:03 UTC (rev 31)
+++ pkg/DESCRIPTION	2008-11-17 15:43:47 UTC (rev 32)
@@ -4,7 +4,7 @@
 Title: Mapping Transitions in Continuous Character Evolution
 Author: Andrew Hipp <ahipp at mortonarb.org>, with contributions from Marcial Escudero.
 Maintainer: Andrew Hipp <ahipp at mortonarb.org>
-Depends: R (>= 2.8.0), ouch, ape
-Suggests: phylobase
+Depends: ouch (>= 2.4-2), ape
 Description: Tools for an information-theoretic approach to estimating the probability of continuous character transitions on phylogenetic trees. 
+License: GPL
 URL: http://mattice.R-forge.R-project.org
\ No newline at end of file

Modified: pkg/R/informationCriterion.R
===================================================================
--- pkg/R/informationCriterion.R	2008-11-17 06:33:03 UTC (rev 31)
+++ pkg/R/informationCriterion.R	2008-11-17 15:43:47 UTC (rev 32)
@@ -18,9 +18,7 @@
 
 informationCriterion.hansenBatch <- function(hansenBatch) {
 ## call informationCriterion for a 'hansen.batch' object
-## recall that there are a bunch of trees in here... summarize over these
 ## for right now, just returns AIC, AICc, and BIC weights for the trees analyzed in a hansenBatch object
-##       loglik dof sigma.squared theta / alpha
   outdata <- list(length(hansenBatch$hansens))
   N = hansenBatch$N
   for(i in 1:length(outdata)) {

Modified: pkg/R/treeTraversal.R
===================================================================
--- pkg/R/treeTraversal.R	2008-11-17 06:33:03 UTC (rev 31)
+++ pkg/R/treeTraversal.R	2008-11-17 15:43:47 UTC (rev 32)
@@ -13,7 +13,12 @@
 # 4. allPossibleRegimes
 # 5. regimeVectors
 
+# To do:
+# 1. add a monophyly checker to screen out nodes not present on a tree -- 
+#    one way to do this would be to hold the ape trees in memory and use them for plotting and checking monophyly
+# 2. make allPossibleRegimes more efficient when maxNodes < length(nodes)
 
+
 paintBranches <-
 # Paints branches with regimes changing at nodes specified
 # arguments
@@ -71,6 +76,11 @@
       for(i in 1:length(colorsVector)) if(colorsVector[i] == "") colorsVector[i] <- as.character(i) 
   return(colorsVector) }
 
+isMonophyletic <- 
+# returns T or F on whether a group of taxa is monophyletic in an ouch tree
+function(tree, taxa) {
+  }
+
 mrcaOUCH <-
 # Finds most recent common ancestor for a vector of tips by:
 #  1. Creating a vector of ancestral nodes leading to each tip