pastis_simple: A simplified interface to the main pastis function.

In pastis: Phylogenetic Assembly with Soft Taxonomic Inferences

Description

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.

Usage

  pastis_simple(pastisData = NULL, base_name,
    paraphyly_constrains = TRUE,
    monophyly_constrains = TRUE, omit_sequences = FALSE)

Arguments

base_name	The base name for all input files may include a leading directory, but should not include a trailing .
pastisData	Input data object of class pastisData
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!

Details

This is a simplified version of pastis_main which assumes that (i) the data are input as a pastisData object (e.g. created with read_input), or (ii) the input files all have the same base (specified by base_name) with diffferent extensions for each file type:

.sequences: the sequence file (FASTA format)

.tree: the constraint tree (Newick format)

.taxa: a list of taxa (see below)

.missingclades: locations of missing clades (see below)

.template: the template for the mrBayes input file (see default_output_template() )

The taxa file consists of a header 'taxon,clade' with each subsequent line containing a taxon,clade pair (separated by a comma)

Each line of the missingclades 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.

The mrBayes input file is written to base_name.nexus.

See Also

pastis_main provides a more flexible interface.

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

Examples

# Generate MrBayes input files with constraints
## Not run: 
data(accipitridaeFullPastis)
pastis_simple(accipitridaeFullPastis, base_name="Accipitridae")

data(accipitridaeBasicPastis)
pastis_simple(accipitridaeBasicPastis, base_name="AccipitridaeBasic")

## End(Not run)

data(pastis_data_1)
pastis_simple(pastis_data_1, base_name="pastis_data_1")
unlink("pastis_data_1.nexus")

data(pastis_data_2)
pastis_simple(pastis_data_2, base_name="pastis_data_2")
unlink("pastis_data_2.nexus")

data(pastis_data_3)
pastis_simple(pastis_data_3, base_name="pastis_data_3")
unlink("pastis_data_3.nexus")

Example output

Loading required package: caper
Loading required package: ape
Loading required package: MASS
Loading required package: mvtnorm

pastis documentation built on May 2, 2019, 7:24 a.m.