estimatetree: estimate a tree
In JamesStimson/transnp: Transmission inference using SNP data
Description
Usage
Arguments
Value
Examples
Description
estimate a tree
Usage
1
estimatetree(aln, maxit = 10000, optNni = TRUE, bf = basefreqs, ...)
Arguments
aln
Alignment in DNAbin format
maxit
Max number of iterations in optimisation
optNni
(TRUE) optimise the topology of the tree
...
further parameters for optim.pml
Value
tree object of type phylo
Examples
1
2
test=estimatetree(aln)
myModel <- setDatesFromFile(myModel, datefile)
JamesStimson/transnp documentation built on May 30, 2019, 3:51 p.m.
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Description Usage Arguments Value Examples
Description
estimate a tree
Usage
1 | estimatetree(aln, maxit = 10000, optNni = TRUE, bf = basefreqs, ...)
|
Arguments
aln |
Alignment in DNAbin format |
maxit |
Max number of iterations in optimisation |
optNni |
(TRUE) optimise the topology of the tree |
... |
further parameters for optim.pml |
Value
tree object of type phylo
Examples
1 2 | test=estimatetree(aln)
myModel <- setDatesFromFile(myModel, datefile)
|
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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