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.
Arguments
- gmyc_res
Output from gmyc().
- delimname
Character. String to rename the delimitation method in the table. Default to 'gmyc'.
Value
An object of class tbl_df.
Details
gmyc() optimizes genetic clusters, and spec.list() clusters
samples into species partitions from the result. gmyc_tbl() turns these results
into a tibble which matches the output from bgmyc_tbl and locmin_tbl.
Examples
# \donttest{
# run GMYC
gmyc_res <- try( gmyc(ape::as.phylo(geophagus_beast)) )
# create a tibble
gmyc_df <- try( gmyc_tbl(gmyc_res) )
# check
try(gmyc_df)
#> # A tibble: 137 × 2
#> labels gmyc
#> <chr> <int>
#> 1 GU701784.1 1
#> 2 GU701785.1 1
#> 3 MH780911.1 1
#> 4 OR732927.1 1
#> 5 JN988869.1 1
#> 6 OR732928.1 1
#> 7 MZ504387.1 2
#> 8 MZ504388.1 2
#> 9 MZ504369.1 2
#> 10 MZ504390.1 2
#> # ℹ 127 more rows
# }