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Compute Agreement Between Alternative Species Delimitation Partitions

Source: R/match_ratio.R
match_ratio.Rd

match_ratio() uses the Match Ratio statistic of Ahrens et al. (2014) to compute agreement between all pairs of species delimitation partitions in delim_join output.

Usage

match_ratio(delim)

Source

Ahrens D., Fujisawa T., Krammer H. J., Eberle J., Fabrizi S., Vogler A. P. 2016. Rarity and Incomplete Sampling in DNA-Based Species Delimitation. Systematic Biology 65 (3): 478-494.

Arguments

delim

Output from delim_join.

Value

an object of class tbl_df.

Details

match_ratio() iterates between all species delimitation partitions in delim_join output and returns a tbl_df containing the following columns:

  • pairs pairs of species delimitation methods analyzed.

  • delim_1 number of species partitions in method 1.

  • delim_2 number of species partitions in method 2.

  • n_match number of identical species partitions in methods 1 and 2.

  • match_ratio match ratio statistic, where 0 indicates no agreement between pairs of species delimitation partitions and 1 indicates complete agreement between them.

Author

Pedro S. Bittencourt

Examples


# estimate match ratio statistics
match_ratio(geophagus_delims)
#> # A tibble: 28 × 5
#>    pairs       delim_1 delim_2 n_match match_ratio
#>    <chr>         <int>   <int>   <int>       <dbl>
#>  1 abgd-asap        19      14      10        0.61
#>  2 abgd-bgmyc       19      18      14        0.76
#>  3 abgd-gmyc        19      21      12        0.6 
#>  4 abgd-locmin      19      21      17        0.85
#>  5 abgd-morph       19      16       9        0.51
#>  6 abgd-mptp        19      11       5        0.33
#>  7 abgd-ptp         19      17      13        0.72
#>  8 asap-bgmyc       14      18      10        0.62
#>  9 asap-gmyc        14      21       9        0.51
#> 10 asap-locmin      14      21       8        0.46
#> # ℹ 18 more rows