treeOperators

NeighborhoodRearrangement

TipInterchange

These functions provide tools for tree rearrangement to be used as
 operators in a MCMC run.

manip

Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

Emmanuel Paradis

coalescentMCMC

MCMC Algorithms for the Coalescent

treeOperators function

<dl> <dt>phy</dt>
<dd>a tree of class <code>"phylo"</code>.</dd> <dt>n</dt>
<dd>the number of tips in <code>phy</code>.</dd> <dt>THETA</dt>
<dd>The estimate of \(\Theta\) for <code>phy</code> at the
 node 'target'.</dd> <dt>brtimes</dt>
<dd>the branching times of <code>phy</code>.</dd></dl>

Arguments

Author

Trees Operators for Running MCMC — treeOperators

<dl>

 <dt>phy</dt>
<dd>a tree of class <code>"phylo"</code>.</dd>

 <dt>n</dt>
<dd>the number of tips in <code>phy</code>.</dd>

 <dt>THETA</dt>
<dd>The estimate of \(\Theta\) for <code>phy</code> at the
 node 'target'.</dd>

 <dt>brtimes</dt>
<dd>the branching times of <code>phy</code>.</dd>

</dl>

treeOperators: Trees Operators for Running MCMC

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples