gmyc_tbl: Turns GMYC Results Into a Tibble

In delimtools: Helper Functions for Species Delimitation Analysis

Turns GMYC Results Into a Tibble

Description

gmyc_tbl() processes output from gmyc into an object of class tbl_df.

Usage

gmyc_tbl(gmyc_res, delimname = "gmyc")

Arguments

gmyc_res	Output from gmyc.
delimname	Character. String to rename the delimitation method in the table. Default to 'gmyc'.

Details

splits package uses gmyc to optimize genetic clusters and spec.list to cluster samples into species partitions. gmyc_tbl() turns these results into a tibble which matches the output from bgmyc_tbl and locmin_tbl.

Value

An object of class tbl_df.

Author(s)

Thomas Ezard, Tomochika Fujisawa, Tim Barraclough.

Source

Pons J., Barraclough T. G., Gomez-Zurita J., Cardoso A., Duran D. P., Hazell S., Kamoun S., Sumlin W. D., Vogler A. P. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology. 55:595-609.

Monaghan M. T., Wild R., Elliot M., Fujisawa T., Balke M., Inward D. J. G., Lees D. C., Ranaivosolo R., Eggleton P., Barraclough T. G., Vogler A. P. 2009. Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology. 58:298-311.

Fujisawa T., Barraclough T. G. 2013. Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets. Systematic Biology. 62(5):707–724.

Examples

# run GMYC
gmyc_res <- splits::gmyc(ape::as.phylo(geophagus_beast))

# create a tibble
gmyc_df <- gmyc_tbl(gmyc_res)

# check
gmyc_df

delimtools documentation built on April 3, 2025, 9:28 p.m.