format_xml0: Generates a runnable XML by inserting sequence data, a...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

The names of the sequence data and trees must match and must be in the standard form for inferring tip dates. The XML skeleton must have these entries to be overwritten: SEQUENCES START_TREE DATE_TRAIT SEIJR_START SUSC_SIZE

Usage

format_xml0(xmlfn, fastafn, treefn, start = 2020.085, susc_size = NULL)

Arguments

xmlfn	The file name of the XML skeleton
fastafn	The file name of the sequence data in fasta format
treefn	The file name of the newick format starting trees.
start	The numeric date when the model dynamics (SEIJR) will initiate
susc_size	The initial number of susceptible, replaces SUSC_SIZE in xml, also sets scale for exponential size prior; supported in seijr0.1.3_skeleton.xml

Details

A XML file will be generated for each starting tree provided

Value

Character string of runnable xml. Individual XMLs for each starting tree will be written to disk

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.