R/writeSimpleSumtNexus.R

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

# write simple sumt

# The standard MrBayes output format for summary trees is difficult to read into and depict in R with support values at nodes. 
# This script creates a NEXUS file with a MrBayes block that would load the output of existing MrBayes analyses, 
# then run the 'sumt' command with the correct formatting for use in R, thus quickly generating all desired summary trees in the correct format.


writeSimpleSumtNexus <- function(directory,origNexus = NULL,outputNexus = NULL){
	#
	# The standard MrBayes output format for summary trees is difficult to read into and depict in R with support values at nodes. 
	# This script creates a NEXUS file with a MrBayes block that would load the output of existing MrBayes analyses, 
	# then run the 'sumt' command with the correct formatting for use in R, thus quickly generating all desired summary trees in the correct format.
	#
	#change to dir for MB files
	#setwd(directory)
	#get files
	files <- list.files(directory)
	paths <- paste0(directory,"//",files)
	#get tree files
	treeFiles <- files[grep(x = files,pattern = "run..t")]  
	#get the unique identifiers
	inputs <- sort(unique(sub(".run..t","",treeFiles)))
	#get the nexus files
	inputs <- sort(unique(sub(".tree.","",inputs)))
	#
	# this should catch partitioned unlinked analyses 
	# (with more than one tree) as separate instances
	# for calculating consensus trees as the rest of the nexus file is read...
	#
	#now start constructing sumt lines
	bayesBlock <- "#NEXUS"
	for(i in (1:length(inputs))){
		if(is.null(origNexus)){
			origNex <- scan(inputs[i],what = "character",sep = "\n",blank.lines.skip = FALSE)
		}else{
			origNex <- scan(origNexus,what = "character",sep = "\n",blank.lines.skip = FALSE)
			}
		cropNex <- origNex[2:grep(origNex,pattern = "mcmcp")[1]]
		#remove log line
		cropNex <- cropNex[-grep(cropNex,pattern = "log start")]
		sumtLine <- paste0("sumt filename = ",inputs[i]," outputname = ",
			paste0(inputs[i],".simple")," conformat = simple;")
		bayesBlock <- c(bayesBlock,cropNex,sumtLine,"","end;","")
		}
	#remove log line
	cropNex <- cropNex[-grep(cropNex,pattern = "log start")]
	#now generate lines for all inputs
	for(i in 1:length(inputs)){
		sumtLine <- paste0("sumt filename = ",inputs[i]," outputname = ",
			paste0(inputs[i],".simple")," conformat = simple;")
		bayesBlock <- c(bayesBlock,cropNex,sumtLine,"","end;","")
		}
	if(!is.null(outputNexus)){
		write(bayesBlock,file = outputNexus)
	}else{
		return(bayesBlock)
		}
	}