add_starting_trees_to_xml: Make starting trees, insert into beast xml and create ML tree...
In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses
Description
Usage
Arguments
Value
Description
This will generate multiple starting trees by ML & treedater.
Each tree is produced by a different random resolution of polytomies in the ML tree
Sequence names must have sample times included (see prep_tip_labels)
Usage
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add_starting_trees_to_xml(
xmlfn,
fastafn,
plotout = NULL,
regionDemes = c("Il"),
ntres = 1,
ncpu = 4
)
Arguments
xmlfn
File name of beast xml
fastafn
File name of sequence data (needed for ML tree estimation)
plotout
Output file name for ML tree plot. Set NULL to not plot
regionDemes
regions to colour in the output ML tree
ntres
integer how many start trees to produce? a distinct xml is made for each
ncpu
Number of CPUs to use
Value
Some treedater trees. New XMLs are written to disk
emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.
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Description Usage Arguments Value
Description
This will generate multiple starting trees by ML & treedater. Each tree is produced by a different random resolution of polytomies in the ML tree Sequence names must have sample times included (see prep_tip_labels)
Usage
1 2 3 4 5 6 7 8 | add_starting_trees_to_xml(
xmlfn,
fastafn,
plotout = NULL,
regionDemes = c("Il"),
ntres = 1,
ncpu = 4
)
|
Arguments
xmlfn |
File name of beast xml |
fastafn |
File name of sequence data (needed for ML tree estimation) |
plotout |
Output file name for ML tree plot. Set NULL to not plot |
regionDemes |
regions to colour in the output ML tree |
ntres |
integer how many start trees to produce? a distinct xml is made for each |
ncpu |
Number of CPUs to use |
Value
Some treedater trees. New XMLs are 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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