predictNMB (version 0.2.1)

get_thresholds: Gets probability thresholds given predicted probabilities, outcomes and NMB.

Description

Gets probability thresholds given predicted probabilities, outcomes and NMB.

Usage

get_thresholds(predicted, actual, nmb, cutpoint_methods = NULL)

Value

Returns a list.

Arguments

predicted

A vector of predicted probabilities.

actual

A vector of actual outcomes.

nmb

A named vector containing NMB assigned to true positives, true negatives, false positives and false negatives

cutpoint_methods

Which cutpoint method(s) to return. The default (NULL) uses all the inbuilt methods.

Examples

# \donttest{
# get thresholds using default (all inbuilt) cutpoint methods
get_thresholds(
  predicted = runif(1000),
  actual = sample(c(0, 1), size = 1000, replace = TRUE),
  nmb = c("TP" = -3, "TN" = 0, "FP" = -1, "FN" = -4)
)


# get cutpoints using user-defined functions
# These functions must take the \code{predicted} and \code{actual}
# as arguments. They can also take \code{nmb} (named vector containing NMB
# with values for TP, FP, TN, FN).
fx_roc01 <- function(predicted, actual, ...) {
  cutpointr::cutpointr(
    x = predicted, class = actual, method = cutpointr::minimize_metric,
    metric = cutpointr::roc01,
    silent = TRUE
  )[["optimal_cutpoint"]]
}

fx_sum_sens_spec <- function(predicted, actual, ...) {
  cutpointr::cutpointr(
    x = predicted, class = actual, method = cutpointr::maximize_metric,
    metric = cutpointr::sum_sens_spec,
    silent = TRUE
  )[["optimal_cutpoint"]]
}

get_thresholds(
  predicted = runif(1000),
  actual = sample(c(0, 1), size = 1000, replace = TRUE),
  cutpoint_methods = c("fx_roc01", "fx_sum_sens_spec"),
  nmb = c("TP" = -3, "TN" = 0, "FP" = -1, "FN" = -4)
)

# get a combination of cutpoints from both user-defined functions and
# inbuilt methods
get_thresholds(
  predicted = runif(1000),
  actual = sample(c(0, 1), size = 1000, replace = TRUE),
  cutpoint_methods = c(
    "fx_roc01",
    "fx_sum_sens_spec",
    "youden",
    "all",
    "none"
  ),
  nmb = c("TP" = -3, "TN" = 0, "FP" = -1, "FN" = -4)
)
# }