Risk Model Decision Analysis

Provides tools to evaluate the value of using a risk prediction instrument to decide treatment or intervention (versus no treatment or intervention). Given one or more risk prediction instruments (risk models) that estimate the probability of a binary outcome, rmda provides functions to estimate and display decision curves and other figures that help assess the population impact of using a risk model for clinical decision making. Here, "population" refers to the relevant patient population. Decision curves display estimates of the (standardized) net benefit over a range of probability thresholds used to categorize observations as 'high risk'. The curves help evaluate a treatment policy that recommends treatment for patients who are estimated to be 'high risk' by comparing the population impact of a risk-based policy to "treat all" and "treat none" intervention policies. Curves can be estimated using data from a prospective cohort. In addition, rmda can estimate decision curves using data from a case-control study if an estimate of the population outcome prevalence is available. Version 1.4 of the package provides an alternative framing of the decision problem for situations where treatment is the standard-of-care and a risk model might be used to recommend that low-risk patients (i.e., patients below some risk threshold) opt out of treatment. Confidence intervals calculated using the bootstrap can be computed and displayed. A wrapper function to calculate cross-validated curves using k-fold cross-validation is also provided.


The package rmda (risk model decision analysis) provides tools to evaluate the value of using a risk prediction instrument to decide treatment or intervention (versus no treatment or intervention). Given one or more risk prediction instruments (risk models) that estimate the probability of a binary outcome, rmda provides functions to estimate and display decision curves and other figures that help assess the population impact of using a risk model for clinical decision making. Here, “population” refers to the relevant patient population.

Decision curves display estimates of the (standardized) net benefit over a range of probability thresholds used to categorize observations as 'high risk.' The curves help evaluate a treatment policy that recommends treatment for patients who are estimated to be ‘high risk’ by comparing the population impact of a risk-based policy to “treat all” and “treat none” intervention policies. Curves can be estimated using data from a prospective cohort. In addition, rmda can estimate decision curves using data from a case-control study if an estimate of the population outcome prevalence is available. Version 1.5 of the package provides an alternative framing of the decision problem for situations where treatment is the standard-of-care and a risk model might be used to recommend that low-risk patients (i.e., patients below some risk threshold) opt out of treatment.

Confidence intervals calculated using the bootstrap can be computed and displayed. A wrapper function to calculate cross-validated curves using k-fold cross-validation is also provided.

Key functions are:

  • decision_curve: Estimate (standardized) net benefit curves with bootstrap confidence intervals.

  • plot_decision_curve: Plot a decision curve or multiple curves.

  • plot_clinical_impact and plot_roc_components: Alternative plots for the output of decision_curve showing measures of clinical impact or the components of the ROC curve (true/false positive rates) across a range of risk thresholds. See help files or tutorial for more info.

  • cv_decision_curve: Calculate k-fold cross-validated estimates of a decision curve and its components.

Installation

The easiest way to get the package is directly from CRAN:

install.packages("rmda")

or install the package directly from github using devtools.

## install.packages("devtools")
library(devtools)
install_github("mdbrown/rmda")

You may also download the current version of the package here:

https://github.com/mdbrown/rmda/releases

navigate to the source package and use

install.packages("../rmda_1.5.tar.gz", 
                  repos = NULL, 
                  type = "source")

Tutorial

Click here for a tutorial to get you started.

News

rmda v 1.6

  • update default y-axis limits for sNB plots to show positive values only.
  • print a message warning of bias due to overfitting when the same data is used to fit and evaluate a model using decision_curve.
  • fix a bug where CI's for the policy of treating 'None' were not plotted or printed using summary when policy = "opt-out".

rmda v 1.5

  • Update the cost:benefit axes labels for decision curves generated for an 'opt-out' treatment policy so that the definition of costs and benefits are consistent for opt-out vs. opt-in policies.

rmda v1.4

*Package has changed names to rmda (risk model data analysis).

v 1.4

  • Version 1.4 of the package provides an alternative framing of the decision problem for situations where treatment is the standard-of-care and a risk model might be used in order for low-risk patients (i.e., patients below some risk threshold) to opt out of treatment. This is implemented in the package with the addition of the 'policy' argument to function decision_curve.

v 1.3

  • fixed bug in the inputs for createFolds for cv_decision_curve.

  • allowed for multiple curves to be plotted together when one curve has CI’s and the other doesn’t

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("rmda")

1.6 by Marshall Brown, a year ago


http://mdbrown.github.io/rmda/, https://github.com/mdbrown/rmda


Browse source code at https://github.com/cran/rmda


Authors: Marshall Brown


Documentation:   PDF Manual  


GPL-2 license


Imports reshape, pander, MASS, caret


See at CRAN