pastis (version 0.1-2)

read_input: Called by create_job to read input files

Description

Reads the specified input files and performs some basic consistency checking between the inputs.

Usage

read_input(constraint_tree, taxa_list, missing_clades = NA, sequences = NA, output_template = NA)

Arguments

constraint_tree

A tree with constraints that are forced to be present in all output trees. Either a filename to a nexus file readable by read.tree or a ape phylo object.

taxa_list

A list of all taxa and their clades. Either a data frame with columns "taxa" and "clade" or a filename for a file readable by read.csv with those columns

missing_clades

A file containing missing clades. Each line of the missing clades file consists of the missing clade, the word "include" or "exclude" and a list of the reference clades (all separated by commas). Lines containing "include" specify that a taxon is contained below the MRCA of the reference clades. Lines containing "exclude" specify that the missing clade cannot attach below the MRCA of the reference clades. #'

output_template

The filename for a template for the output nexus file. This file should look like a regular mrBayes input file with special tags replacing content that will be filled by pastis. In particular:

will be replaced by the sequences (and should go below the MATRIX line)

the number of taxa (i.e. "ntax=" must be somewhere in your template)

the number of characters

the constraints will go here

where the summaries will be written, (i.e. "sumt filename= burnin ...." should be in your template)

see default_output_template for an example (which is used by default)

sequences

A file with all the available sequence information in fasta format for details on that format see read.dna in the ape package.

Value

A list with the loaded input