version 1.1-3

ChangeLog

@@ -1,3 +1,20 @@
+			CHANGES IN OUTBREAKER VERSION 1.1-3
+
+BUG FIXES
+	o fixed a bug due to the odd conversion of long numbers into
+	characters by read.table - handling specific errors with R 3.1.0
+	on some Mac versions.
+
+
+
+			CHANGES IN OUTBREAKER VERSION 1.1-2
+
+BUG FIXES
+	o fixed a bug due to the odd conversion of long numbers into
+	characters by read.table.
+
+
+
 			CHANGES IN OUTBREAKER VERSION 1.1-1
 NEW FEATURES
 	o added an argument max.kappa which allows to limit the number of

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: outbreaker
-Version: 1.1-2
-Date: 2014/04/28
+Version: 1.1-3
+Date: 2014/05/08
 Title: Bayesian reconstruction of disease outbreaks by combining
         epidemiologic and genomic data
 Author: Thibaut Jombart <t.jombart@imperial.ac.uk>, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil Ferguson
@@ -11,7 +11,7 @@ Imports: utils, ape, igraph, adegenet, parallel
 URL: http://sites.google.com/site/therepiproject/r-pac/outbreaker
 Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.
 License: GPL (>= 2)
-Packaged: 2014-04-28 16:03:50 UTC; thibaut
+Packaged: 2014-05-08 05:44:19 UTC; thibaut
 NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2014-04-28 19:47:01
+Date/Publication: 2014-05-08 08:02:08

MD5

@@ -1,7 +1,7 @@
-58c588de81db556a2ccf5fb55fadf9a8 *ChangeLog
-4ba24d5b98f19769aed503c9e1850514 *DESCRIPTION
+6f7601de240d16818c58279443234e82 *ChangeLog
+0afe399fe818cbf347093bab4ed0587b *DESCRIPTION
 b1c3a9ccc2b95d7b57297d94b2386013 *NAMESPACE
-9a0e35cba236939ec9ce5bda030d8fcd *R/interface.R
+5a4911c7c93d8f013f5b4d50f177664f *R/interface.R
 c0d0d9160caaf41e22f0265b788c7e00 *R/mutationRates.R
 9a32af7fc041e4b0647256cd3b1c0d78 *R/plot.R
 7c5f7e13c48e36773a0bf21ccf150540 *R/reproRate.R
@@ -11,7 +11,7 @@ dc26678070da5a3942b779aa0670d4f3 *R/selectChains.R
 92d8aa7bf09017257369dcfdf00a82cb *R/zzz.R
 72b5047fee7ef404647d8c939b9ec91b *configure
 a6d485ade20b5042ab8459e99f45c895 *configure.ac
-999579b31cc165da3ac161c33966957e *data/fakeOutbreak.RData
+6c78ac58c5fe4b01507d3c0e248d9e73 *data/fakeOutbreak.RData
 2cb344c2133da976ccf7ab341e81353b *inst/CITATION
 0d5cd8ac8f915095773450ce55e2f669 *man/Rstat.Rd
 c774351eefcfdd1193bc820ceb2efd8c *man/fakeOutbreak.Rd

R/interface.R

@@ -267,13 +267,8 @@ outbreaker <- function(dna=NULL, dates, idx.dna=NULL,
 
     ## BUILD OUTPUT ##
     ## read table
-    chains <- read.table(res.file.name, header=TRUE)
-
-    ## force numeric class for post, like, prior
-    ## (weird behaviour of read.table in some R versions)
-    chains$post <- as.numeric(chains$post)
-    chains$like <- as.numeric(chains$like)
-    chains$prior <- as.numeric(chains$prior)
+    chains <- read.table(res.file.name, header=TRUE, stringsAsFactors=FALSE,
+                         colClasses=c("integer", rep("numeric",7+n.ind*2)))
 
     chains$run <- rep(1, nrow(chains))
     call <- match.call()
@@ -414,13 +409,6 @@ outbreaker.parallel <- function(n.runs, parallel=require("parallel"), n.cores=NU
     res$n.runs <- n.runs
     res$call <- match.call()
 
-    ## force numeric class for post, like, prior
-    ## (weird behaviour of read.table in some R versions)
-    res$chains$post <- as.numeric(res$chains$post)
-    res$chains$like <- as.numeric(res$chains$like)
-    res$chains$prior <- as.numeric(res$chains$prior)
-
-
     ## RETURN RESULTS ##
     return(res)
 } # end outbreaker.parallel