Calculate sensitivity and specificity

Source: R/sens_spec_calc.R

[Deprecated] Function to calculate the sensitivity and specificity of a genetic distance cutoff given an underlying mutation rate and mean number of generations between cases

sens_spec_calc(
  cutoff,
  mut_rate,
  mean_gens_pdf,
  max_link_gens = 1,
  max_gens = NULL,
  max_dist = NULL
)

Arguments

cutoff

the maximum genetic distance at which to consider cases linked

mut_rate

mean number of mutations per generation, assumed to be Poisson distributed

mean_gens_pdf

the density distribution of the mean number of generations between cases; the index of this vector is assumed to be the discrete distance between cases

max_link_gens

the maximum generations of separation for linked pairs

max_gens

the maximum number of generations to consider, if NULL (default) value set to the highest number of generations in mean_gens_pdf with a non-zero probability

max_dist

the maximum distance to calculate, if NULL (default) value set to max_gens * 99.9th percentile of mut_rate Poisson distribution

Value

a data frame with the sensitivity and specificity for a particular genetic distance cutoff

See also

Other mutrate_functions: gen_dists(), get_optim_roc(), sens_spec_roc()

Author

Shirlee Wohl and Justin Lessler

Examples

# calculate the sensitivity and specificity for a specific genetic distance threshold of 2 mutations
sens_spec_calc(cutoff=2,
               mut_rate=1,
               mean_gens_pdf=c(0.02,0.08,0.15,0.75),
               max_link_gens=1)
#> Warning: `sens_spec_calc()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `gendist_sensspec_cutoff()` instead.
#>      cutoff sensitivity specificity
#> [1,]      2   0.7357589   0.8662894

# calculate the sensitivity and specificity for a a range of genetic distance thresholds
sens_spec_calc(cutoff=1:10,
               mut_rate=1,
               mean_gens_pdf=c(0.02,0.08,0.15,0.75),
               max_link_gens=1)
#>       cutoff sensitivity specificity
#>  [1,]      1   0.3678794 0.967314682
#>  [2,]      2   0.7357589 0.866289434
#>  [3,]      3   0.9196986 0.697765199
#>  [4,]      4   0.9810118 0.499227295
#>  [5,]      5   0.9963402 0.316627604
#>  [6,]      6   0.9994058 0.178637743
#>  [7,]      7   0.9999168 0.090198436
#>  [8,]      8   0.9999898 0.041044514
#>  [9,]      9   0.9999989 0.016951040
#> [10,]     10   0.9999999 0.006396198