Simplified code, progress on ropensci/software-review#209

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(beast2out.read.trees)
 export(calc_act)
 export(calc_act_r)
 export(calc_ess)
@@ -20,7 +19,6 @@ export(parse_beast_output_files)
 export(parse_beast_posterior)
 export(parse_beast_state_operators)
 export(parse_beast_trees)
-export(parse_beast_trees_impl_2)
 export(remove_burn_in)
 export(remove_burn_ins)
 importFrom(Rcpp,sourceCpp)

R/parse_beast_trees.R

@@ -19,7 +19,7 @@ parse_beast_trees <- function(
   }
 
   trees <- tryCatch({
-      parse_beast_trees_impl_2(filename)
+      ape::read.nexus(filename)
     },
     error = function(cond) {
       stop("invalid file")
@@ -32,69 +32,3 @@ parse_beast_trees <- function(
   class(trees) <- "multiPhylo"
   trees
 }
-
-#' Parses a BEAST2 .trees output file
-#' @param filename name of the BEAST2 .trees output file
-#' @return the phylogenies in the posterior
-#' @export
-#' @examples
-#'   trees_filename <- get_tracerer_path("beast2_example_output.trees")
-#'   posterior <- parse_beast_trees(trees_filename)
-#'   testit::assert(is_trees_posterior(posterior))
-#' @author Richel J.C. Bilderbeek
-#' @noRd
-parse_beast_trees_impl_2 <- function(
-  filename
-) {
-	ape::read.nexus(filename)
-}
-
-
-#' Extract a list of phylogenies from a BEAST2 posterior file
-#' @param file name of the BEAST2 posterior filename, usually ends with '.trees'
-#' @param opt.rescale.edge.length Rescaling factor of the phylogenies,
-#'   a value of 1.0 denotes that the original edge lengths are maintained
-#' @param opt.burnin how many phylogenies to discard, an value of will keep all trees
-#' @return a list of phylogenies of type 'phylo'
-#' @examples
-#'   trees_file <- "vignettes/example.trees"
-#'   testit::assert(file.exists(trees_file))
-#'   posterior <- beast2out.read.trees(trees_file)
-#'   testit::assert(length(posterior) == 10)
-#'   testit::assert(class(posterior[[1]]) == "phylo")
-#' @export
-#' @author Oliver Ratmann
-#' @noRd
-beast2out.read.trees <- function(
-  file,
-  opt.rescale.edge.length= 1.,
-  opt.burnin=0
-)
-{
-	tmp			<- readLines(file, n=2e3, warn = FALSE)
-	tmp			<- which( grepl('#NEXUS', tmp) )
-	if(length(tmp)>1)
-	{
-		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', tail(tmp,1)))
-		cmd		<- paste('sed -i".bak" 1,',tail(tmp,1)-1,'d ', file, sep='')
-		system(cmd)
-		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
-		system(cmd)
-		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
-		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
-		file.remove(cmd)
-	}
-	mph			<- ape::read.nexus(file)
-	#	remove burn in
-	tmp			<- regexpr('[0-9]+',names(mph))
-	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
-	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
-	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
-	mph.it		<- mph.it[ mph.it > opt.burnin ]
-	names(mph)	<- paste('STATE_',mph.it,sep='')
-	#	rescale edge lengths
-	if(opt.rescale.edge.length!=1.)
-		for(j in seq_along(mph))
-			mph[[j]]$edge.length	<- mph[[j]]$edge.length * opt.rescale.edge.length
-	mph
-}