tests/testthat/_snaps/theoretical_coi.md

In bailey-lab/coiaf: Complexity of Infection Estimation with Allele Frequencies

coi_method argument is restricted

Code
  theoretical_coi(1:5, seq(0, 0.5, 0.1))
Output
  # A tibble: 6 x 6
    coi_1 coi_2 coi_3 coi_4 coi_5 plmaf
    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
  1     0  0     0    0     0       0  
  2     0  0.18  0.27 0.344 0.410   0.1
  3     0  0.32  0.48 0.589 0.672   0.2
  4     0  0.42  0.63 0.752 0.830   0.3
  5     0  0.48  0.72 0.845 0.912   0.4
  6     0  0.5   0.75 0.875 0.938   0.5

Code
  theoretical_coi(1:5, seq(0, 0.5, 0.1), coi_method = "frequency")
Output
  # A tibble: 6 x 6
    coi_1 coi_2   coi_3   coi_4   coi_5 plmaf
    <dbl> <dbl>   <dbl>   <dbl>   <dbl> <dbl>
  1   NaN NaN   NaN     NaN     NaN       0  
  2   NaN   0.5   0.367   0.291   0.244   0.1
  3   NaN   0.5   0.4     0.337   0.297   0.2
  4   NaN   0.5   0.433   0.388   0.359   0.3
  5   NaN   0.5   0.467   0.443   0.427   0.4
  6   NaN   0.5   0.5     0.5     0.5     0.5

`coi_method` must be one of "variant" or "frequency", not "wrong method".

bailey-lab/coiaf documentation built on April 26, 2023, 6:32 p.m.