pastis_main: Phylogenetic Assembly with Soft Taxonomic Inferences
In pastis: Phylogenetic Assembly with Soft Taxonomic Inferences

Description Usage Arguments Details Value See Also Examples

This function assimilates sequences, taxonomic information and tree constraints into a mrBayes file. This permits the construction of trees that are compatible with all of these sources of tdata and contain all known taxa.

  pastis_main(pastisData = NULL, constraint_tree,
    taxa_list, missing_clades = NA, sequences = NA,
    output_template = NA, output_file = "output.nex",
    paraphyly_constrains = TRUE,
    monophyly_constrains = TRUE, omit_sequences = FALSE)

`pastisData`	Input data object of class pastisData
`output_file`	The filename for the mrBayes output file (will be overwritten if it exists)
`paraphyly_constrains`	If TRUE, missing clades are prevented from entering paraphyletic clades.
`monophyly_constrains`	If TRUE, missing clades are precented from entering monophyletic clades.
`omit_sequences`	If set to TRUE the sequence file (if any) will be ignored. This is useful for testing the constraints created by pastis as mrBayes runs much quicker without sequence data!
`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. #'
`sequences`	A file with all the available sequence information in fasta format for details on that format see read.dna in the ape package.
`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: <sequences> will be replaced by the sequences (and should go below the MATRIX line) <ntax> the number of taxa (i.e. "ntax=<ntax>" must be somewhere in your template) <nchar> the number of characters <constraints> the constraints will go here <outputfile> where the summaries will be written, (i.e. `"sumt filename=<outputfile> burnin ...."` should be in your template) see default_output_template for an example (which is used by default)

This is the main function in pastis which assimilates sequences, taxonomic information and tree constraints and creates a mrBayes input file. This input file contains the tree structure specified by constraint_tree with missing taxa in taxa_list and missing clades in missing_clades added and placed loosely in the tree using the constraint logic outlined in Thomas et al. MEE (in review) and Jetz et al. (2012 Nature, 491, 444-448).

See read_input for a description of the required format of the input files. At a minimum the constraining input tree and taxa list must be provided.

In addition to the input checks conducted by read_input this function also checks for compatibility between the missing genus constraints and constraint tree.

PASTIS: Phylogenetic Assembly with Soft Taxonomic InferenceS?

 A bright motmot was
  acting quite rowdy- weaving and squawking quite loudly
  "Pastis is delise" he burped with a sneese "but why is
  everything suddenly cloudy?"

– Arne Mooers

NULL

pastis_simple provides a simplified interface to pastis_main.

read_input describes the required file formats

default_output_template provides an example of the output template (also the default)

## Not run: 
# Generate MrBayes input files with constraints
data(accipitridaeFullPastis)
pastis_main(accipitridaeFullPastis, output_file="Accipitridae.nexus")

data(accipitridaeBasicPastis)
pastis_main(accipitridaeBasicPastis, output_file="AccipitridaeBasic.nexus")

## End(Not run)

data(pastis_data_1)
pastis_main(pastis_data_1, output_file="pastis_data_1")
unlink("pastis_data_1.nexus")

data(pastis_data_2)
pastis_main(pastis_data_2, output_file="pastis_data_2")
unlink("pastis_data_2.nexus")

data(pastis_data_3)
pastis_main(pastis_data_3, output_file="pastis_data_3")
unlink("pastis_data_3.nexus")