Compute Agreement Between Alternative Species Delimitation Partitions

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, sorted = TRUE)

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. doi:10.1093/sysbio/syw002

Arguments

delim: Output from delim_join.
sorted: If output should be sorted by match ratio values. Default to TRUE.

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-locmin       19      21      17        0.85
#>  2 bgmyc-gmyc        18      21      15        0.77
#>  3 abgd-bgmyc        19      18      14        0.76
#>  4 bgmyc-ptp         18      17      13        0.74
#>  5 abgd-ptp          19      17      13        0.72
#>  6 asap-ptp          14      17      11        0.71
#>  7 gmyc-locmin       21      21      15        0.71
#>  8 gmyc-ptp          21      17      13        0.68
#>  9 asap-morph        14      16      10        0.67
#> 10 bgmyc-locmin      18      21      13        0.67
#> # ℹ 18 more rows