PredictABEL: Assessment of Risk Prediction Models

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PredictABEL includes functions to assess the performance of risk models. The package contains functions for the various measures that are used in empirical studies, including univariate and multivariate odds ratios (OR) of the predictors, the c-statistic (or area under the receiver operating characteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Also included are functions to create plots, such as risk distributions, ROC curves, calibration plot, discrimination box plot and predictiveness curves. In addition to functions to assess the performance of risk models, the package includes functions to obtain weighted and unweighted risk scores as well as predicted risks using logistic regression analysis. These logistic regression functions are specifically written for models that include genetic variables, but they can also be applied to models that are based on non-genetic risk factors only. Finally, the package includes function to construct a simulated dataset with genotypes, genetic risks, and disease status for a hypothetical population, which is used for the evaluation of genetic risk models.

Author
Suman Kundu, Yurii S. Aulchenko, A. Cecile J.W. Janssens
Date of publication
2014-12-21 17:55:30
Maintainer
Suman Kundu <suman_math@yahoo.com>
License
GPL (>= 2)
Version
1.2-2
URLs

View on CRAN

Man pages

ExampleData
A hypothetical dataset that is used to demonstrate all...
ExampleModels
An example code to construct a risk model using logistic...
fitLogRegModel
Function to fit a logistic regression model.
ORmultivariate
Function to obtain multivariate odds ratios from a logistic...
ORunivariate
Function to compute univariate ORs for genetic predictors.
plotCalibration
Function for calibration plot and Hosmer-Lemeshow goodness of...
plotDiscriminationBox
Function for box plots of predicted risks separately for...
plotPredictivenessCurve
Function for predictiveness curve.
plotPriorPosteriorRisk
Function to plot posterior risks against prior risks.
plotRiskDistribution
Function to plot histogram of risks separated for individuals...
plotRiskscorePredrisk
Function to plot predicted risks against risk scores.
plotROC
Function for a receiver operating characteristic curve (ROC)...
PredictABEL-package
An R package for the analysis of (genetic) risk prediction...
predRisk
Function to compute predicted risks for all individuals in...
reclassification
Function for reclassification table and statistics.
riskScore
Function to compute genetic risk scores.
simulatedDataset
Function to construct a simulated dataset containing...

Files in this package

PredictABEL
PredictABEL/NAMESPACE
PredictABEL/NEWS
PredictABEL/data
PredictABEL/data/ExampleData.RData
PredictABEL/R
PredictABEL/R/PredictABEL.R
PredictABEL/MD5
PredictABEL/DESCRIPTION
PredictABEL/man
PredictABEL/man/simulatedDataset.Rd
PredictABEL/man/ORmultivariate.Rd
PredictABEL/man/plotDiscriminationBox.Rd
PredictABEL/man/fitLogRegModel.Rd
PredictABEL/man/plotPriorPosteriorRisk.Rd
PredictABEL/man/plotCalibration.Rd
PredictABEL/man/ExampleData.Rd
PredictABEL/man/plotRiskscorePredrisk.Rd
PredictABEL/man/riskScore.Rd
PredictABEL/man/plotROC.Rd
PredictABEL/man/plotPredictivenessCurve.Rd
PredictABEL/man/ExampleModels.Rd
PredictABEL/man/plotRiskDistribution.Rd
PredictABEL/man/predRisk.Rd
PredictABEL/man/ORunivariate.Rd
PredictABEL/man/reclassification.Rd
PredictABEL/man/PredictABEL-package.Rd