Recurrent Event Data Analysis

Functions that fit gamma frailty model with spline or piecewise constant baseline rate function for recurrent event data, compute and plot parametric mean cumulative function (MCF) from a fitted model as well as nonparametric sample MCF (Nelson-Aalen estimator) are provided. Most functions are S4 methods that produce S4 class objects.


The R package reda provides function fitting gamma frailty model with baseline rate function modeled by regression splines for recurrent event data, as well as functions computing and ploting the mean cumulative funciton from sample (Nelson-Aalen estimator) and the fitted frailty model.

You can install the released version from CRAN.

install.packages("reda")

The latest version of package is under development at GitHub in branch 'dev'. If it is able to pass the building check by Travis CI, you may consider installing it with the help of devtools by

devtools::install_github("wenjie2wang/reda", ref = "dev")

or cloning this reposotory to local and install by makefile as follows:

git clone https://github.com/wenjie2wang/reda.git
cd reda
make install

The R package reda is free software: You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version (at your option). See the GNU General Public License for details.

The R package reda is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

News

reda v0.3.0

  • Added M-spline for modeling baseline rate to function rateReg.

  • Added argument check to function rateReg so that it is possible to skip the data checking step to slightly speed up the model fitting for cleaned data.

  • Added option verbose to argument control of function rateReg to suppress all possible messages.

  • Added variance estimates for sample MCF by Poisson process method, and confidence interval based on the asymptotic normality of MCF itself (in addition to the logarithm of MCF) to function mcf,formula-method.

  • Allowed multiple categorical variables in function mcf,formula-method for the sample MCF for design with multiple factors.

  • Added sample valve-seat dataset from Nelson (1995) for demonstration.

  • Borrowed the power from R package splines2 for piece-wise constant and splines based baseline rate function, and thus boosted the performance of reda in model fitting.

  • Updated object class of fitted model, rateReg.

  • Replaced generic function plotMcf with methods for function plot.

  • Updated data checking procedure for a better performance.

  • Added variable "gender" in sample simulated dataset, simuDat for a better demonstration of sample MCF function.

Minor changes

  • Renamed all slot named boundaryKnots to Boundary.knots for consistency with spline functions.

  • Updated vignettes for demonstration of new features.

  • Added sample citation entry for reda.

reda v0.2.1

  • Updated S4 method plotMcf,sampleMcf: Replaced show_guide with show.legend in function geom_text to incorporate updates in package ggplot2 v1.0.1.

  • Minor updates that clear checking note from CRAN.

reda v0.2.0

  • Implementation of spline baseline rate function.

  • Added function AIC and BIC.

  • Renamed main function name from heart to rateReg and added new argument.

  • Updated object class of fitted model.

  • Replaced sample simulated dataset for demonstration.

reda v0.1.0

  • First version of reda mainly providing function to fit gamma frailty model with piece-wise constant baseline rate function for recurrent event data.

Reference manual

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install.packages("reda")

0.3.1 by Wenjie Wang, 3 months ago


https://github.com/wenjie2wang/reda


Report a bug at https://github.com/wenjie2wang/reda/issues


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


Authors: Wenjie Wang [aut, cre], Haoda Fu [aut], Jun Yan [ctb]


Documentation:   PDF Manual  


Task views: Survival Analysis


GPL (>= 3) license


Imports ggplot2, graphics, grDevices, methods, splines2, stats

Suggests knitr, rmarkdown


See at CRAN