sscaROC {caROC} | R Documentation |
Covariate-adjusted continuous biomarker evaluations for specific population.
Description
Provides evalution for continuous biomarkers at controlled sensitivity/specificity level, or ROC curve in specified sub-population.
Usage
sscaROC(diseaseData, controlData, userFormula, target_covariates,
control_sensitivity = NULL, control_specificity = NULL, mono_resp_method = "ROC",
whichSE = "sample", global_ROC_controlled_by = "sensitivity", nbootstrap = 100,
CI_alpha = 0.95, logit_CI = TRUE, verbose = TRUE)
Arguments
diseaseData |
Data from patients including dependent (biomarker) and independent (covariates) variables. |
controlData |
Data from controls including dependent (biomarker) and independent (covariates) variables. |
userFormula |
A character string to represent the function for covariate adjustment. For example, let Y denote biomarker, Z1 and Z2 denote two covariates. Then userFormula = "Y ~ Z1 + Z2". |
target_covariates |
Covariates of the interested sub-population. It could be a vector, e.g. c(1, 0.5, 0.8), or a matrix, e.g. target_covariates = matrix(c(1, 0.7, 0.9, 1, 0.8, 0.8), 2, 3, byrow = TRUE) |
control_sensitivity |
The level(s) of sensitivity to be controlled at. Could be a scalar (e.g. 0.7) or a numeric vector (e.g. c(0.7, 0.8, 0.9)). |
control_specificity |
The level(s) of specificity to be controlled at. Could be a scalar (e.g. 0.7) or a numeric vector (e.g. c(0.7, 0.8, 0.9)). |
mono_resp_method |
The method used to restore monotonicity of the ROC curve or computed sensitivity/specificity value. It should one from the following: "none", "ROC". "none" is not applying any monotonicity respecting method. "ROC" is to apply ROC-based monotonicity respecting approach. Default value is "ROC". |
whichSE |
The method used to compute standard error. It should be one from the following: "sample", "bootstrap", meaning to calculate the standard error using sample-based approach or bootstrap. Default is "sample". |
global_ROC_controlled_by |
Whether sensitivity/specificity is used to control when computing global ROC. It should one from the following: "sensitivity", "specificity". Default is "sensitivity". |
nbootstrap |
Number of boostrap iterations. Default is 100. |
CI_alpha |
Percentage of confidence interval. Default is 0.95. |
logit_CI |
Whether to apply logit-based confidence interval. Logit-transformed CI has been identified to be more robust near border area. |
verbose |
Whether to print out messages. Default value is true. |
Value
If control_sensitivity or control_specificity is provided, compute covariate-adjusted specificity (sensitivity) at controlled sensitivity (specificity) level.
Estimate |
Covariate-adjusted sensitivity/specificity. |
SE |
Estimated standard error. |
CI |
Estimated confidence intervals. |
If both control_sensitivity and control_specificity are null, compuate covariate-adjusted ROC curve.
sensitivity |
Estimated sensitivity. |
specificity |
Estimated specificity. |
mono_adj |
Monotonicity adjustment method. |
Author(s)
Ziyi.li <zli16@mdanderson.org>
Examples
n1 = n0 = 1000
## generate data
Z_D1 <- rbinom(n1, size = 1, prob = 0.3)
Z_D2 <- rnorm(n1, 0.8, 1)
Z_C1 <- rbinom(n0, size = 1, prob = 0.7)
Z_C2 <- rnorm(n0, 0.8, 1)
Y_C_Z0 <- rnorm(n0, 0.1, 1)
Y_D_Z0 <- rnorm(n1, 1.1, 1)
Y_C_Z1 <- rnorm(n0, 0.2, 1)
Y_D_Z1 <- rnorm(n1, 0.9, 1)
M0 <- Y_C_Z0 * (Z_C1 == 0) + Y_C_Z1 * (Z_C1 == 1) + Z_C2
M1 <- Y_D_Z0 * (Z_D1 == 0) + Y_D_Z1 * (Z_D1 == 1) + 1.5 * Z_D2
diseaseData <- data.frame(M = M1, Z1 = Z_D1, Z2 = Z_D2)
controlData <- data.frame(M = M0, Z1 = Z_C1, Z2 = Z_C2)
userFormula = "M~Z1+Z2"
target_covariates = c(1, 0.7, 0.9)
res <- sscaROC(diseaseData,controlData,
userFormula = userFormula,
control_sensitivity = c(0.2,0.8, 0.9),
target_covariates = target_covariates,
control_specificity = NULL,
mono_resp_method = "none",
whichSE = "sample",nbootstrap = 100,
CI_alpha = 0.95, logit_CI = TRUE)
## bootstrap-based variance estimation
res <- sscaROC(diseaseData,controlData,
userFormula = userFormula,
control_sensitivity = c(0.2,0.8, 0.9),
target_covariates = target_covariates,
control_specificity = NULL,
mono_resp_method = "none",
whichSE = "bootstrap",nbootstrap = 100,
CI_alpha = 0.95, logit_CI = TRUE)
## monotonization by ROC-based
res <- sscaROC(diseaseData,controlData,
userFormula = userFormula,
control_sensitivity = c(0.2,0.8, 0.9),
target_covariates = target_covariates,
control_specificity = NULL,
mono_resp_method = "ROC",
whichSE = "bootstrap",nbootstrap = 100,
CI_alpha = 0.95, logit_CI = TRUE)
## control specificity
res <- sscaROC(diseaseData,controlData,
userFormula = userFormula,
control_sensitivity = NULL,
target_covariates = target_covariates,
control_specificity = c(0.2,0.8, 0.9),
mono_resp_method = "ROC",
whichSE = "bootstrap",nbootstrap = 100,
CI_alpha = 0.95, logit_CI = TRUE)
### get ROC curves
myROC <- sscaROC(diseaseData,
controlData,
userFormula,
target_covariates,
global_ROC_controlled_by = "sensitivity",
mono_resp_method = "none")