cut_perf: Cutoff Performance Evaluation

In BioPred: An R Package for Biomarkers Analysis in Precision Medicine

Cutoff Performance Evaluation

Description

This function evaluates the performance of a predictive model at a selected cutoff point.

Usage

cut_perf(
  yvar,
  censorvar = NULL,
  xvar,
  cutoff,
  dir,
  xvars.adj = NULL,
  data,
  type,
  yvar.display = yvar,
  xvar.display = xvar
)

Arguments

yvar	Response variable name.
censorvar	Censoring variable name (0-censored, 1-event).
xvar	Biomarker name.
cutoff	Selected cutoff value.
dir	Direction for desired subgroup (">", ">=", "<", "<=").
xvars.adj	Other covariates to adjust when evaluating the performance.
data	Data frame containing the variables.
type	Type of analysis: "c" for continuous, "s" for survival, and "b" for binary.
yvar.display	Display name of response variable.
xvar.display	Display name of biomarker variable.

Value

A list containing various performance metrics and optionally, plots.

Examples

# Load a sample dataset
data <- data.frame(
  survival_time = rexp(100, rate = 0.1),  # survival time
  status = sample(c(0, 1), 100, replace = TRUE),  # censoring status
  biomarker = rnorm(100, mean = 0, sd = 1),  # biomarker levels
  covariate1 = rnorm(100, mean = 50, sd = 10)  # an additional covariate
)
# Perform cutoff performance evaluation for continuous outcome
data$continuous_outcome <- rnorm(100, mean = 10, sd = 5)
cut_perf(
  yvar = "continuous_outcome",
  xvar = "biomarker",
  cutoff = 0.5,
  dir = ">=",
  data = data,
  type = "c",
  yvar.display = "Continuous Outcome",
  xvar.display = "Biomarker Level"
)

# Perform cutoff performance evaluation for binary outcome
data$binary_outcome <- sample(c(0, 1), 100, replace = TRUE)
cut_perf(
  yvar = "binary_outcome",
  xvar = "biomarker",
  cutoff = 0,
  dir = "<=",
  data = data,
  type = "b",
  yvar.display = "Binary Outcome",
  xvar.display = "Biomarker Level"
)

BioPred documentation built on Nov. 4, 2024, 9:06 a.m.