sequences2xml: Convert sequences to BEAST xml data block.

In bioDS/beter: BEAST Templates in R

Convert sequences to BEAST xml data block.

Description

This functions uses an internal mustache template to convert a named vector of sequences into an XML data block for BEAST.

Usage

sequences2xml(sequences, data = list())

Arguments

sequences	parsed from file
data	**optional** other variables, such as specification of datatype

Details

The internal template uses two parameters, an *alignment_id* and a *datatype*. The *alignment_id* identifies this particular alignment block and is important only when multiple input alignments are used during the BEAST analysis. A good practice might be to use a file name of the sequences as an *alignment_id*.

The *datatype* is much more important an tells BEAST what kind of data the alignment represents. The *beter* will try to guess the most common data types: *standard* (binary or discrete states) or *nucleotide* (DNA nucleotides), but if the data is of any other type, the "datatype" must be specified.

Value

BEAST xml data block

Examples

seq = c("A" = "ACTG", "B" = "CTGA", "C" = "TGAC")
sequences2xml(seq)

sequences2xml(seq, data=list("alignment_id" = "seq", "datatype"="nucleotide") )

bioDS/beter documentation built on June 15, 2022, 7:58 a.m.