The npROCRegression package"

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

This document explains the usage of the npROCRegression package. The package allows the user to apply in practice the nonparametric induced and direct ROC regression approaches presented in @MX11a and @MX11b respectively.

R functions to estimate induced nonparametric ROC regression models

The main R function is INPROCreg() which estimates the covariate-specific ROC curve in the presence of a one-dimensional continuous covariate based on the induced nonparametric ROC regression approach presented in @MX11a, and creates an object of class INPROCreg. A brief summary of this class can be obtained by using the functions print.INPROCreg() and summary.INPROCreg(). Finally, the function plot.INPROCreg() provides automatically several plots of interest. A brief description of these functions is shown in the following Table.

Function | Description ------------------- |-------------------------------------------------------------------------------------------- INPROCreg | Fits an induced nonparametric ROC regression model for a continuous covariate. controlINPROCreg | Function used to set several parameters controlling the ROC regression fitting process. print.INPROCreg | Default print method for objects fitted with INPROCreg(). summary.INPROCreg | Produces a summary of an INPROCreg object. plot.INPROCreg | Plots (a) the estimated regression and variance functions in both the healthy and diseased populations, (b) the covariate-specific ROC curve and AUC, (c) the covariate-adjusted ROC curve (AROC); and, optionally, (d) the Youden Index (YI) or the value for which the TPF and the TNF coincides (EQ); and/or (e) the optimal thresholds based on these criteria (TH)).

INPROCreg() function

The function INPROCreg() estimates the covariate-specific ROC curve in the presence of a one-dimensional continuous covariate based on the induced nonparametric ROC regression approach presented in @MX11a. As a result, this function returns an object of class INPROCreg. The following Table shows a description of the arguments of this function.

Argument | Description -------- | ---------------------------------------------------------------------------------------------------------- marker | A character string with the name of the diagnostic test variable. covariate | A character string with the name of the continuous covariate. group | A character string with the name of the variable that distinguishes healthy from diseased individuals. tag.healthy | The value codifying the healthy individuals in the variable group. data | Data frame representing the data and containing all needed variables. ci.fit | A logical value. If TRUE, confidence intervals are computed. test | A logical value. If TRUE, the bootstrap-based test for detecting covariate effect is performed. accuracy | A character vector indicating if the Youden index ("YI"), the value for which the TPF and the TNF coincides ("EQ"), and/or optimal threshold ("TH") based on these two criteria should be computed. accuracy.cal| A character string indicating if the accuracy measures (argument accuracy) should be calculated based on the covariate-specific ROC curve ("ROC") or on the covariate-adjusted ROC curve ("AROC"). newdata | A data frame containing the values of the covariate at which predictions are required control | Output of the controlINROCreg() function. weights | An optional vector of "prior weights" to be used in the fitting process.

Usage is as follows:

INPROCreg (marker, covariate, group, tag.healthy, data, ci.fit=FALSE, test=FALSE, accuracy = NULL, accuracy.cal = c("ROC","AROC"), newdata = NULL, control = controlINPROCreg(), weights=NULL)

Through marker and covariate arguments, users indicate the diagnostic test variable and the continuous covariate of interest, respectively. In group and tag.healthy arguments, we have to indicate respectively the name of the variable that distinguishes healthy from diseased individuals, and the value codifying healthy individuals in that variable. The data argument is a data frame representing the data and containing all needed variables. Bootstrap confidence intervals for the regression and variance functions, as well as for several accuracy measures, are obtained by setting the argument ci.fit to TRUE. Argument test should be set to TRUE in order to evaluate the effect of the continuous covariate on the ROC curve by means of the test presented in @MX16. By default, the INPROCreg() function returns the estimated regression and variance functions in both healthy and diseased populations. As far as accuracy measures is concerned, the function provides the estimated covariate-specific ROC curve, the associated covariate-specific AUCs (with the integral being approximated by numerical integration methods), and the covariate-adjusted ROC curve (AROC) [@Janes09]. In addition, it is also possible to obtain the Youden index ("YI"), the value for which the TPF and the TNF coincides ("EQ"); and/or the optimal thresholds ("TH") based on these two criteria (argument accuracy). Both the YI and the EQ values (and thus the optimal threshold) can be calculated based on the covariate-specific ROC curve or the AROC curve (argument accuracy.cal). It should be noted that, when a diagnostic test's discriminatory capacity is not affected by a covariate, this does not necessarily mean that the threshold value for which optimal operational characteristics are attained will not vary with the covariate values. In such cases, the AROC curve should be used to choose the optimal TPF and TNF pairing [see @Janes09 or @MX11a for more details]. An optional data frame containing the values of the covariate at which predictions are required can be specified in argument newdata. If this dataset is not specified, an adequate set of points from the data used in the fit is selected. A finer control of the fitting process can be achieved by the argument control, which should be the output of the function controlINPROCreg(). This function will be described later on.

We now turn to illustrate the usage of function INPROCreg() by presenting the code used in the analyses discussed in @MX11a and @Pardo14. For confidentiality reasons, we use here a simulated data set that resemble the original data. Specifically, in that papers we aimed at assessing the performance of the body mass index (BMI) for predicting clusters of cardiovascular disease (CVD) risk factors. Diseased subjects were defined as those having two or more CVD risk factors (raised triglycerides, reduced high-density lipoprotein cholesterol, raised blood pressure and raised fasting plasma glucose), following the International Diabetes Federation criteria [@idf06]. It is well known that anthropometric measures behave differently according to both age and gender, and thus it is advisable to incorporate both covariates into the ROC analysis. Since the proposal implemented in the package only admits one continuous covariate, separate analyses were conducted on men and women.

library(npROCRegression)
data(endosim)
summary(endosim)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Analysis for males
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fit.men <- INPROCreg(marker = "bmi", covariate = "age", group = "idf_status", 
                        tag.healthy = 0, 
                        data = subset(endosim, gender == "Men"), 
                        ci.fit = TRUE, test = TRUE, 
                        accuracy = c("EQ","TH"),
                        accuracy.cal="AROC", 
                        control=controlINPROCreg(p=1,kbin=30,step.p=0.01), 
                        newdata = data.frame(age = seq(18,85,l=50)))

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Analysis for females
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fit.women <- INPROCreg(marker = "bmi", covariate = "age", group = "idf_status", 
                        tag.healthy = 0, 
                        data = subset(endosim, gender == "Women"), 
                        ci.fit = TRUE, test = TRUE, 
                        accuracy = c("EQ","TH"),
                        accuracy.cal="ROC", 
                        control=controlINPROCreg(p=1,kbin=30,step.p=0.01), 
                        newdata = data.frame(age = seq(18,85,l=50)))

As a result, the function INPROCreg() provides a list with the following components:

names(fit.men)

where

Component | Description ----------|----------------------------------------------------------------------------------------------------------- call | The matched call. X | The data frame used in the predictions. fpf | Set of false positive fractions at which the covariate-specific ROC curve has been estimated. h | Estimated regression and variance functions in healthy population. d | Estimated regression and variance functions in diseased population. ROC | Estimated covariate-specific ROC curve. AUC | Estimated covariate-specific AUC, and corresponding confidence intervals if required. AROC | Estimated covariate-adjusted ROC curve. YI/EQ | If required, estimated covariate-specific YI (or values at which the true positive fraction (TPF) and the true negative fraction (TNF) coincide), and corresponding bootstrap confidence intervals. TH | If required, estimated optimal threshold values based on either the YI or the criterion of equality of TPF and TNF, and corresponding bootstrap confidence intervals. pvalue | If required, p-value obtained with the test for checking the effect of the continuous covariate on the ROC curve.

A numerical summary of the results can be obtained by calling up the print.INPROCreg() or INPROCreg() functions, which can be abbreviated by print() and summary():

summary(fit.men)

summary(fit.women)

controlINPROCreg() function

The argument control of the function INPROCreg() can be used to set several parameters controlling the ROC regression fitting process. This argument is the output of the function controlINPROCreg(). This function has the following arguments:

Argument | Description --------------|--------------------------------------------------------------------------------------------------------- step.p | a numeric value, defaulting to 0.02. ROC curves are calculated at a regular sequence of false positive fractions with step.p increment. kbin | an integer value specifying the number of binning knots. By default 30. p | an integer value specifying the order of the local polynomial kernel estimator for the regression functions. By default 1. h | a vector of length 4 specifying the bandwidths to be used for the estimation of the regression and variance functions in healthy population and the regression and variance functions in diseased populations (in this order). By default -1 (selected using cross-validation.). A value of 0 would indicate a linear fit. seed | an integer value specifying the seed for the bootstrap resamples. If NULL it is initialized randomly. nboot | an integer value specifying the number of bootstrap resamples for the construction of the confidence intervals. By default 500. level | a real value specifying the confidence level for the confidence intervals. By default 0.95. resample.m | a character string specifying if bootstrap resampling (for the confidence intervals) should be done with or without regard to the disease status ("coutcome" or "noutcome"). When the resampling method is done conditionally on the disease status, the resampling is based on the residuals of the regression models in healthy and diseased populations. However, when the bootstrap resampling is done without regard to the disease status, a naive bootstrap is used. By default, the resampling is done conditionally on the disease status.

plot.INPROCreg() function

The function plot.INPROCreg() takes as input argument an INPROCreg object, and returns several plots of interest. By default, the function returns the plot of the estimated regression and variance functions in both healthy and diseased populations, the covariate-specific ROC curve and AUC, and the AROC. When required in the call to the INPROCreg(), this plot function also returns the YI or EQ values, and corresponding optimal thresholds.

layout(matrix(c(1,1,2,2,3,3,4,4,5,5,6,6,0,7,7,0),4,4, byrow = TRUE), widths = c(1.75,1.75,1.75,1.75), heights = c(3.5,3.5,3.5,3.5))
plot(fit.men, ask = FALSE)
layout(matrix(c(1,1,2,2,3,3,4,4,5,5,6,6,0,7,7,0),4,4, byrow = TRUE), widths = c(1.75,1.75,1.75,1.75), heights = c(3.5,3.5,3.5,3.5))
plot(fit.women, ask = FALSE)

R functions to estimate direct nonparametric ROC regression models

The main R function is DNPROCreg() which estimates the covariate-specific ROC curve in the presence of multidimensional covariates by means of the ROC-GAM regression model presented in @MX11b. Once the model is fitted, a brief numerical summary can be obtained by using the functions print.DNPROCreg() and summary.DNPROCreg. A plot of the estimated covariate-specific ROC curve and corresponding AUC can be obtained through the function plot.DNPROCreg(). A summary of these functions is shown in the following Table.

Function | Description --------------------|------------------------------------------------------------------------------------------- DNPROCreg | Fits a direct nonparametric ROC regression model for a set of continuous and categorical covariates. controlDNPROCreg | Function used to set several parameters controlling the ROC regression fitting process. print.DNPROCreg | Default print method for objects fitted with DNPROCreg(). summary.DNPROCreg | Produces a summary of a DNPROCreg object. plot.DNPROCreg | Plots the covariate-specific ROC curve and AUC. DNROCregData | Selects an adequate set of points from the original data to be used as a default dataset for obtaining predictions or plots.

DNPROCreg() function

The following Table shows a description of the arguments of the DNPROCreg() function

Argument | Description ----------------|-------------------------------------------------------------------------------------------- marker | A character string with the name of the diagnostic test variable. formula.h | Right-hand formula(s) giving the mean and variance model(s) to be fitted in healthy population. Atomic values are also valid, being recycled. formula.ROC | Right-hand formula giving the ROC regression model to be fitted (ROC-GAM model). group | A character string with the name of the variable that distinguishes healthy from diseased individuals. tag.healthy | The value codifying the healthy individuals in the variable group. data | Data frame representing the data and containing all needed variables. ci.fit | A logical value. If TRUE, confidence intervals are computed. test.partial | A numeric vector containing the covariate components in the ROC-GAM formula to be tested for a possible effect. If NULL, no test is performed. newdata | A data frame containing the values of the covariate at which predictions are required. control | Output of the controlDNROCreg() function. weights | An optional vector of `prior weights' to be used in the fitting process.

Usage is as follows:

DNPROCreg(marker, formula.h=~1, formula.ROC=~1, group, tag.healthy, data, ci.fit=FALSE, test.partial=NULL, newdata=NULL, control=controlDNPROCreg(), weights=NULL)

The diagnostic test variable is indicated by the argument marker. The nonparametric location-scale regression model for the healthy population is specified by formula.h. This argument should be a vector (of length $2$) of right-hand formulas (atomic values are also valid, because they are recycled). The first right-hand formula is the model for the conditional mean function, and the second one is the model for the (logarithm) of the conditional variance function. These formulas are similar to that used for the glm() function, except that nonparametric functions can be added to the additive predictor by means of function s(). For instance, specification ~ x1 + s(x2) would assume a linear effect of x1 and a nonparametric effect of x2. Categorical variables (factors) can be also incorporated, as well as factor-by-curve interaction terms. For example, to include the interaction between age and gender we need to specify ~ gender + s(age) + s(age, by = gender). Note that, for identifiability purposes, the "main" effects of the continuous and categorical covariates need to be included into the formula. All these considerations also apply to the argument formula.ROC, where the ROC-GAM regression model is specified. The name of the variable that distinguishes healthy from diseased individuals is specified in argument group, and in tag.healthy the value codifying the healthy individuals in this variable. The data argument is a data frame representing the data and containing all needed variables. Pointwise bootstrap confidence intervals for each component of the additive predictor of the ROC-GAM, as well as the covariate-specific AUCs (with the integral being approximated by numerical integration methods), are obtained by setting the argument ci.fit to TRUE. The components of the ROC-GAM to be tested for their possible effect are indicated in test.partial. In this argument, we pass the position of the components as specified in the formula.ROC argument. An optional data frame containing the covariate values at which predictions are required can be specified in argument newdata. If missing, an adequate set of points from the dataset used in the fit is selected. To that end, the function DNPROCregdata() is used. Argument control allows to modify some default parameters that control the fitting process, and should be the output of the function controlDNPROCreg(). This function will be described later on.

To illustrate the usage of this function, we now analyse the endocrine data presented above and discussed in @MX11b. For the sake of illustration, in the following we will show only the statistical analysis conducted with the Body Mass Index (BMI). Since it is well established that anthropometric measures perform differently according to gender, the age-by-gender interaction was included in both the location-scale regression model for healthy population and the ROC-GAM.

library(npROCRegression)
data(endosim)

fit.endo <- DNPROCreg(marker = "bmi", formula.h = "~ gender + s(age) + s(age, by = gender)", 
                formula.ROC = "~ gender + s(age) + s(age, by = gender)", 
                group = "idf_status", 
                tag.healthy = 0, 
                data = endosim, 
                control = list(card.P=50, kbin=30, step.p=0.02),
                ci.fit = TRUE, test.partial = 3)

As a result, the function DNPROCreg() provides a list with the following components:

names(fit.endo)

where

Component | Description ------------|-------------------------------------------------------------------------------------------- call | The matched call. model | Data frame containing all variables and observations used in the fitting process. fpf | Set of false positive fractions at which the covariate-specific ROC curve has been estimated. newdata | Data frame containing the values of the covariates at which the covariate-specific ROC curve has been estimated. pfunctions | Matrices containing the estimates of each component of the additive predictor of the ROC-GAM. One matrix contains the effects of the covariates, the other the effect of the FPF. Confidence intervals are returned if required). coefficients| Vector of parametric coefficient of the fitted ROC-GAM. ROC | Estimated covariate-specific ROC curve. AUC | Estimated covariate-specific AUC, and corresponding confidence intervals if required. pvalue | If required, p-values are obtained - with two different bootstrap-based tests [@MX16] - for each model term indicated in argument test.partial (T2: $L_{2}$-based test; and T1: $L_{1}$-based test).

As before, a numerical summary of the results can be obtained by calling up the print() and summary() functions:

summary(fit.endo)

controlDNPROCreg() function

The argument control of the function DNPROCreg() can be used to set several parameters controlling the ROC regression fitting process. This argument is the output of the function controlDNPROCreg(). This function has the following arguments:

Argument | Description ------------|-------------------------------------------------------------------------------------------- step.p | a numeric value, defaulting to 0.02. ROC curves are calculated at a regular sequence of false positive fractions with step.p increment. kbin | an integer value specifying the number of binning knots. By default 30. card.P | an integer value specifying the cardinality of the set of false positive fractions used in the estimation process. By default 50. p | an integer value specifying the order of the local polynomial kernel estimator. By default 1. seed | an integer value specifying the seed for the bootstrap resamples. If NULL it is initialized randomly. nboot | an integer value specifying the number of bootstrap resamples for the construction of the confidence intervals. By default 500. level | a real value specifying the confidence level for the confidence intervals. By default 0.95. resample.m| a character string specifying if bootstrap resampling (for the confidence intervals) should be done with or without regard to the disease status ("coutcome" or "noutcome"). In both cases, a naive bootstrap is used. By default, the resampling is done conditionally on the disease status. link | a character string specifying the link function ("probit", "logit" or "cloglog"). By default the link is the probit function.

plot.DNPROCreg() function

The function plot.DNPROCreg() takes as input argument an `DNPROCreg' object, and returns the plots of the covariate-specific ROC curve and AUC.

layout(matrix(c(1,3,2,4),2,2, byrow = FALSE), widths = c(3.5,3.5), heights = c(3.5,3.5))
plot(fit.endo, ask = FALSE)

The function plot.DNPROCreg() does not plot the partial effects of the covariates on the ROC curve. However, these plots can be obtained from the element pfunctions of the DNPROCreg object.

names(fit.endo$pfunctions)
names(fit.endo$pfunctions$covariates)
names(fit.endo$pfunctions$fpf)

layout(matrix(c(1,3,2,4),2,2, byrow = FALSE), widths = c(3.5,3.5), heights = c(3.5,3.5))
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Main effect of age
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sel.row <- fit.endo$newdata$gender == "Women" # Same effect for both genders
plot(fit.endo$newdata$age[sel.row],fit.endo$pfunctions$covariates[sel.row, "s(age)"], xlab="age", ylab="s(age)", type="l", main = "Main effect of age", ylim=c(-1,1))
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age)ul"], lty=2)
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age)ll"], lty=2)
abline(h = 0, col="grey")

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Effect of age: deviation for males
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sel.row <- fit.endo$newdata$gender == "Women"
plot(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)"], xlab="age", ylab = "s(age, by=gender)", type = "l", main = " Age effect: Deviation for males", ylim = c(-1.2, 0.8))
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)ul"], lty=2)
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)ll"], lty=2)
abline(h = 0, col="grey")

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Effect of age: deviation for females
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
sel.row <- fit.endo$newdata$gender == "Men"
plot(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)"], xlab="age", ylab = "s(age, by=gender)", type = "l", main = " Age effect: Deviation for females", ylim = c(-0.8, 1.2))
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)ul"], lty=2)
lines(fit.endo$newdata$age[sel.row], fit.endo$pfunctions$covariates[sel.row, "s(age, by = gender)ll"], lty=2)
abline(h = 0, col="grey")

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Effect of FPF
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
plot(fit.endo$fpf, fit.endo$pfunctions$fpf[,1], xlab = "fpf", ylab = "s(fpf)", main = "False positive fraction", type="l")
lines(fit.endo$fpf, fit.endo$pfunctions$fpf[,2], lty=2)
lines(fit.endo$fpf, fit.endo$pfunctions$fpf[,3], lty=2)
abline(h = 0, col="grey")


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npROCRegression documentation built on May 2, 2019, 5:17 a.m.