version 1.2

ChangeLog

@@ -1,3 +1,51 @@
+11-10-2010: 1.2 released 
+	* added memory handler so that memory allocated in C is no longer
+	  lost due to function interrupt (or failure to explicitly free it)
+	* added support for alternate lineage-specific models within
+	  the tree model object
+	* added support for codon models (HKY_CODON, REV_CODON, SSREV_CODON),
+	  also codon.clean.msa function
+	* to support lineage-specific models, added support for labels in
+	  phylogenetic trees which are denoted by the pound sign ie,
+	  "((human #primate, chimp #primate)#primate, mouse)"
+	* many changes to phyloFit; allow lineage-specific models, arbitrary
+	  parameter boundaries, hold specified boundaries constant.  Some
+	  of the default options are now different from command-line phyloFit.
+	* added plot.msa and as.track.msa functions which plot alignment; only
+	  currently works if alignment fits in the plotting window.  Also
+	  added coord.range.msa function to support this.
+	* added plot.rate.matrix (and plot.tm and plot.altmodel.tm)
+	* added set.rate.matrix.tm and get.rate.matrix.params.tm which set 
+	  a rate matrix based on substitution model parameters, or get the 
+	  substitution model parameters describing a rate matrix, respectively.
+	* added summary.tree function which returns a data frame with various
+	  information about each branch
+	* fixed bug in split.by.feature.msa in which offset of resulting msas
+	  was one higher than it should have been
+	* changed several function names to increase consistency in naming 
+	  conventions:
+	    addUTRs.feat -> add.UTRs.feat
+	    addIntrons.feat -> add.introns.feat
+	    addSignals.feat -> add.signals.feat
+	    fixStartStop.feat -> fix.start.stop.feat
+	    validFormatStr.msa -> is.format.msa
+	    isSubstMod.tm -> is.subst.mod.tm
+	    branchlen.tree -> branchlength.tree
+	    wig.track -> as.track.wig
+	    feat.track -> as.track.feat
+	    gene.track -> as.track.feat(is.gene=TRUE)
+	* added pairwise.diff.msa function which returns pairwise differences
+	  per site between pairs of sequences in an alignment
+	* fixed some minor bugs in documentation (multiple notes in functions,
+	  help("[.msa") not working previously)
+	* Switched order of arguments in write.feat to (feature, file) for 
+	  consistency with all other write functions.
+	* added functions postprob.msa, expected.subs.msa, and 
+	  total.expected.subs.msa
+	* allow ref.idx argument in phyloP to refer to features object
+	* removed region.bounds argument from coverage.feat; now requires at 
+	  least one features object have not=FALSE
+
 2010-09-17: 1.1 released
 	* updated DESCRIPTION
 	* updates to Makevars and configure.ac to resolve error compiling 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rphast
-Version: 1.1
-Date: 2009-12-14
-Title: RPHAST: R interface to PHAST
+Version: 1.2
+Date: 2010-11-01
+Title: R interface to PHAST software for comparative genomics
 Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
 Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
 Description: RPHAST is an R interface to the PHAST pacakge
@@ -13,15 +13,16 @@ Description: RPHAST is an R interface to the PHAST pacakge
         phylogenetic hidden Markov models.  It can also perform many
         basic operations on multiple sequence alignments and
         phylogenetic trees.
-License: GPL (>= 2)
+License: BSD
 URL: http://compgen.bscb.cornell.edu/rphast
 Copyright: The code in src/pcre is Copyright (c) 1997-2010 University
         of Cambridge.  All other code is Copyright (c) 2002-2010
         University of California, Cornell University.
+Depends: stats
 Suggests: ape, seqLogo
 Collate: 'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R'
-        'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R' 'treeModel.R'
-        'trees.R'
-Packaged: 2010-09-20 18:59:43 UTC; melissa
+        'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R' 'rphast.R'
+        'treeModel.R' 'trees.R'
+Packaged: 2010-11-10 16:54:07 UTC; melissa
 Repository: CRAN
-Date/Publication: 2010-09-21 08:15:27
+Date/Publication: 2010-11-11 12:40:48

NAMESPACE

@@ -26,10 +26,10 @@ export(hist.feat)
 export(overlap.feat)
 export(inverse.feat)
 export(coverage.feat)
-export(addUTRs.feat)
-export(addIntrons.feat)
-export(addSignals.feat)
-export(fixStartStop.feat)
+export(add.UTRs.feat)
+export(add.introns.feat)
+export(add.signals.feat)
+export(fix.start.stop.feat)
 export(rbind.feat)
 export(split.feat)
 export(sort.feat)
@@ -50,14 +50,17 @@ export(is.msa)
 useDynLib(rphast)
 export(msa)
 export(ncol.msa)
+S3method(ncol, msa)
 S3method(dim, msa)
 export(dim.msa)
 export(ninf.msa)
 export(nrow.msa)
-export(validFormatStr.msa)
+S3method(nrow, msa)
+export(is.format.msa)
 export(offset.msa)
 export(alphabet.msa)
 export(is.ordered.msa)
+S3method(is.ordered, msa)
 export(names.msa)
 S3method(names, msa)
 export(from.pointer.msa)
@@ -70,21 +73,31 @@ export(print.msa)
 S3method(print, msa)
 export(read.msa)
 export(complement)
-export(reverse.complement)
-S3method(sub, msa)
+export(reverse.complement.msa)
 export(sub.msa)
 export(strip.gaps.msa)
 S3method("[", msa)
 export("[.msa")
+export(postprob.msa)
+export(expected.subs.msa)
+export(total.expected.subs.msa)
 export(likelihood.msa)
 export(simulate.msa)
+importFrom(stats, simulate)
+S3method(simulate, msa)
 S3method(sample, msa)
 export(sample.msa)
 export(get4d.msa)
 export(extract.feature.msa)
 export(concat.msa)
 export(split.by.feature.msa)
 export(informative.regions.msa)
+export(codon.clean.msa)
+export(state.freq.msa)
+export(base.freq.msa)
+export(gc.content.msa)
+export(pairwise.diff.msa)
+export(plot.msa)
 export(phastCons)
 export(phyloFit)
 export(phyloP)
@@ -94,9 +107,9 @@ export(is.track)
 export(range.track)
 export(smooth.wig)
 export(plot.track)
-export(wig.track)
-export(feat.track)
-export(gene.track)
+export(as.track.wig)
+export(as.track.msa)
+export(as.track.feat)
 export(is.tm)
 export(read.tm)
 export(write.tm)
@@ -106,16 +119,29 @@ export(as.list.tm)
 S3method(as.list, tm)
 export(print.tm)
 S3method(print, tm)
-export(isSubstMod.tm)
+export(is.subst.mod.tm)
 export(subst.mods)
 export(tm)
+export(bgc.sel.factor)
+export(apply.bgc.sel)
+export(unapply.bgc.sel)
+export(add.alt.mod)
+export(set.rate.matrix.tm)
+export(get.rate.matrix.params.tm)
+export(plot.rate.matrix)
+export(plot.tm)
+export(plot.altmodel.tm)
 export(fix.semicolon.tree)
 export(read.newick.tree)
 export(numnodes.tree)
-export(branchlen.tree)
+export(numleaf.tree)
+export(branchlength.tree)
 export(depth.tree)
 export(prune.tree)
 export(name.ancestors)
 export(subtree)
 export(rescale.tree)
 export(rename.tree)
+export(label.branches)
+export(label.subtree)
+export(summary.tree)

R/checkArgs.R

@@ -7,6 +7,7 @@
 # arg is NULL and null.OK==FALSE
 # length(arg) < min.length or length(arg) > max.length
 ##' @export
+##' @nord
 check.arg <- function(arg, argname="argument", class=NULL,
                      null.OK=TRUE, min.length=1L, max.length=1L) {
   if (is.null(arg)) {