Calculate sequence-based diversity and divergence — calc_div_metrics • wavess

See vignette('analyze_output') for more details.

Usage

calc_div_metrics(aln, founder, gen)

Arguments

aln: DNA alignment in ape::DNAbin format
founder: Name of the founder sequence in the alignment
gen: Vector that indicates the generation of each sequence in the alignment, assumed to be in the same order as the alignment

Value

tibble including mean sequence-based diversity and divergence for each generation

Examples

# This example is somewhat contrived, but it shows how it works.
calc_div_metrics(
  hxb2_cons_founder,
  "B.FR.83.HXB2_LAI_IIIB_BRU.K03455",
  c(1, 2, 2)
)
#> # A tibble: 2 × 3
#>     gen diversity divergence
#>   <dbl>     <dbl>      <dbl>
#> 1     1  NaN          0     
#> 2     2    0.0660     0.0542