librtoDNA: Convert simulation objects to DNA sequences or Nexus/Fasta...
In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description Usage Arguments Value Examples

Creates a character string or matrix of nucleotides (C, A, G, T), output to vector, matrix or Nexus file.

1 2	librtoDNA(sampleID, libr, nuc, ref.strain, key, sampletime=NULL, strings = FALSE, filename = NULL, format = "nexus")

`sampleID`	Vector of sample IDs to output.
`libr`	Library object from simulation functions. A list in which each entry represents a unique genotype, and is a vector of mutated nucleotide positions relative to the reference sequence.
`nuc`	Nucleotide database from simulation functions. A list (corresponding to `libr`) in which each entry represents a unique genotype, and is a vector of mutated nucleotides relative to the reference sequence.
`ref.strain`	Reference strain to which the `libr` and `nuc` objects are compared (string of integers in 1,...,4).
`key`	Vector of sample IDs corresponding to the order of `libr`.
`sampletime`	Vector of sample times. If specified, incorporates sample times into genome name in Nexus file.
`strings`	If `TRUE`, returns a character vector, each element containing one genotype. Otherwise, returns a (number of genotypes)x(length of genome) character matrix.
`filename`	File to which sequence data should be written. Output format is Nexus. Not written out if `NULL`.
`format`	File format to be exported (if `filename!=NULL`). Options are `"nexus"` and `"fasta"`.

A character vector or matrix, depending on strings.

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data(withinhost)
G <- librtoDNA(sampleID=withinhost$obs.strain, libr=withinhost$libr, nuc=withinhost$nuc, 
               ref.strain=withinhost$ref.strain, key=withinhost$librstrains, strings=TRUE)