format_xml_gmrf_exogsir: 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
Usage
Arguments
Details
Value
View source: R/xmlformatting.R
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
BETADEFS
DLOGBETADIM
Usage
1
format_xml_gmrf_exogsir(xmlfn, fastafn, treefn, numchange = 3)
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.
numchange
integer number of change points for beta(t)
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.
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Description Usage Arguments Details Value
View source: R/xmlformatting.R
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 BETADEFS DLOGBETADIM
Usage
1 | format_xml_gmrf_exogsir(xmlfn, fastafn, treefn, numchange = 3)
|
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. |
numchange |
integer number of change points for beta(t) |
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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