| Type: | Package |
| Title: | Detect Population Structure Within Phylogenetic Trees |
| Version: | 0.1.0 |
| Date: | 2020-01-20 |
| Author: | Erik Volz |
| Maintainer: | Erik Volz <erik.volz@gmail.com> |
| Description: | Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns. The methods are described in Volz, E., Wiuf, C., Grad, Y., Frost, S., Dennis, A., & Didelot, X. (2020) <doi:10.1093/sysbio/syaa009>. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Suggests: | ggtree,ggplot2,knitr |
| Imports: | ape (≥ 5.0) |
| LinkingTo: | Rcpp |
| VignetteBuilder: | knitr |
| RoxygenNote: | 6.1.0 |
| NeedsCompilation: | yes |
| Packaged: | 2020-02-06 13:41:39 UTC; erikvolz |
| Repository: | CRAN |
| Date/Publication: | 2020-02-17 15:20:02 UTC |
treestructure: Detect Population Structure Within Phylogenetic Trees
Description
Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns. The methods are described in Volz, E., Wiuf, C., Grad, Y., Frost, S., Dennis, A., & Didelot, X. (2020) <doi:10.1093/sysbio/syaa009>.
Details
Methods for detecting structure in phylogenies. Includes the *trestruct* function for partitioning a tree and methods for printing and plotting trees with structure. Refer to the vignettes for common usage.
References
Erik Volz, Carsten Wiuf, Yonatan Grad, Simon Frost, Ann Dennis, Xavier Didelot, "Identification of hidden population structure in time-scaled phylogenies", bioRxiv 704528
Plot TreeStructure tree with cluster and partition variables
Description
Plot TreeStructure tree with cluster and partition variables
Usage
## S3 method for class 'TreeStructure'
plot(x, use_ggtree = TRUE, ...)
Arguments
x |
A TreeStructure object |
use_ggtree |
Toggle ggtree or ape plotting behaviour |
... |
Additional arguments passed to ggtree or ape::plot.phylo |
Detect cryptic population structure in time trees
Description
Detect cryptic population structure in time trees
Usage
trestruct(tre, minCladeSize = 25, minOverlap = -Inf, nsim = 1000,
level = 0.01, ncpu = 1, verbosity = 1, debugLevel = 0)
Arguments
tre |
A tree of type ape::phylo. Must be rooted and binary. |
minCladeSize |
All clusters within parititon must have at least this many tips. |
minOverlap |
Threshold time overlap required to find splits in a clade |
nsim |
Number of simulations for computing null distribution of test statistics |
level |
Significance level for finding new split within a set of tips |
ncpu |
If >1 will compute statistics in parallel using multiple CPUs |
verbosity |
If > 0 will print information about progress of the algorithm |
debugLevel |
If > 0 will produce additional data in return value |
Details
Estimates a partition of a time-scaled tree by contrasting coalescent patterns. The algorithm is premised on a Kingman coalescent null hypothesis and a test statistic is formulated based on the rank sum of node times in the tree.
Value
A TreeStructure object which includes cluster and partitition assignment for each tip of the tree.
References
E.M. Volz, Wiuf, C., Grad, Y., Frost, S., Dennis, A., Didelot, X.D. (2020) Identification of hidden population structure in time-scaled phylogenies.
Author(s)
Erik M Volz <erik.volz@gmail.com>
Examples
tree <- ape::rcoal(50)
struct <- trestruct( tree )