mrbayes.prset

Set prior distributions for <code>mrbayes</code>.

Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.

Martin R. Smith

Interfaces to Phylogenetic Software in R

Christoph Heibl

Natalie Cusimano

Franz-Sebastian Krah

mrbayes.prset function

<dl> <dt>...</dt>
<dd>arguments in <code>tag = value</code> form, or a list of tagged values. The tags must come from the names of prior distribution parameters described in the ‘Prior Distribution Parameters’ section.</dd></dl>

Arguments

<dl>
 <dt>traitiopr</dt>
<dd></dd> <dt>revmatpr</dt>
<dd></dd> <dt>aamodelpr</dt>
<dd></dd> <dt>aarevmatpr</dt>
<dd></dd> <dt>omegapr</dt>
<dd></dd> <dt>ny98omega1pr</dt>
<dd></dd> <dt>ny98omega3pr</dt>
<dd></dd> <dt>m3omegapr</dt>
<dd></dd> <dt>codoncatfreqs</dt>
<dd></dd> <dt>statefreqpr</dt>
<dd></dd> <dt>shapepr</dt>
<dd></dd> <dt>ratecorrpr</dt>
<dd></dd> <dt>pinvarpr</dt>
<dd></dd> <dt>covswitchpr</dt>
<dd></dd> <dt>symdirihyperpr</dt>
<dd></dd> <dt>topologypr</dt>
<dd></dd> <dt>brlenspr</dt>
<dd></dd> <dt>clockvarpr</dt>
<dd></dd> <dt>igrvarpr</dt>
<dd></dd> 
</dl>

Prior Distribution Parameters

Author

Set Priors for MrBayes — mrbayes.prset

<dl>

 <dt>...</dt>
<dd>arguments in <code>tag = value</code> form, or a list of tagged values. The tags must come from the names of prior distribution parameters described in the ‘Prior Distribution Parameters’ section.</dd>

</dl>

<dl>
 <dt>traitiopr</dt>
<dd></dd>

 <dt>revmatpr</dt>
<dd></dd>

 <dt>aamodelpr</dt>
<dd></dd>

 <dt>aarevmatpr</dt>
<dd></dd>

 <dt>omegapr</dt>
<dd></dd>

 <dt>ny98omega1pr</dt>
<dd></dd>

 <dt>ny98omega3pr</dt>
<dd></dd>

 <dt>m3omegapr</dt>
<dd></dd>

 <dt>codoncatfreqs</dt>
<dd></dd>

 <dt>statefreqpr</dt>
<dd></dd>

 <dt>shapepr</dt>
<dd></dd>

 <dt>ratecorrpr</dt>
<dd></dd>

 <dt>pinvarpr</dt>
<dd></dd>

 <dt>covswitchpr</dt>
<dd></dd>

 <dt>symdirihyperpr</dt>
<dd></dd>

 <dt>topologypr</dt>
<dd></dd>

 <dt>brlenspr</dt>
<dd></dd>

 <dt>clockvarpr</dt>
<dd></dd>

 <dt>igrvarpr</dt>
<dd></dd>

 
</dl>

mrbayes.prset: Set Priors for MrBayes

Description

Usage

Value

Arguments

Prior Distribution Parameters

Author

References

See Also

Examples