Find optimal ROC threshold

Source: R/get_optim_roc.R

[Deprecated] This function takes the dataframe output of the sens_spec_roc() function and finds the optimal threshold of sensitivity and specificity by minimizing the distance to the top left corner of the Receiver Operating Characteristic (ROC) curve

get_optim_roc(roc)

Arguments

roc

a dataframe produced by the sens_spec_roc() function containing the Receiver Operating Characteristic (ROC) curve

Value

vector containing optimal thresholds of sensitivity and specificity

See also

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

Author

Shirlee Wohl, John Giles, and Justin Lessler

Examples

# ebola-like pathogen
R <- 1.5
mut_rate <- 1

# use simulated generation distributions
data(genDistSim)
mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])

# get theoretical genetic distance dist based on mutation rate and generation parameters
dists <- as.data.frame(gen_dists(mut_rate = mut_rate,
                                 mean_gens_pdf = mean_gens_pdf,
                                 max_link_gens = 1))

# reshape dataframe for plotting
dists <- reshape2::melt(dists,
                        id.vars = 'dist',
                        variable.name = 'status',
                        value.name = 'prob')

# get sensitivity and specificity using the same paramters
roc_calc <- sens_spec_roc(cutoff = 1:(max(dists$dist)-1),
                          mut_rate = mut_rate,
                          mean_gens_pdf = mean_gens_pdf)
#> Warning: `sens_spec_roc()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `gendist_roc_format()` instead.

# get the optimal value for the ROC plot
optim_point <- get_optim_roc(roc_calc)
#> Warning: `get_optim_roc()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `optim_roc_threshold()` instead.