sscaROC {caROC} | R Documentation |

Provides evalution for continuous biomarkers at controlled sensitivity/specificity level, or ROC curve in specified sub-population.

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)

`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. |

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. |

Ziyi.li <zli16@mdanderson.org>

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")

[Package *caROC* version 0.1.5 Index]