Recurrent Event Data Analysis

Functions for (1) simulating survival and recurrent event data from stochastic process point of view, (2) exploring and modeling recurrent event data through the mean cumulative function (MCF) or also called the Nelson-Aalen estimator of the cumulative hazard rate function, and gamma frailty model with spline rate function, and (3) comparing two-sample recurrent event responses with the pseudo-score tests.


Overview

The R pacakge reda provides functions for

  • simulating survival, recurrent event, and multiple event data from stochastic process point of view;
  • exploring and modeling recurrent event data through the mean cumulative function (MCF) or also called the Nelson-Aalen estimator of the cumulative hazard rate function, and gamma frailty model with spline rate function;
  • comparing two-sample recurrent event responses with the pseudo-score tests.

Installation of CRAN Version

CRAN_Status_Badge Build Status codecov

You can install the released version from CRAN.

install.packages("reda")

Development

Build Status codecov

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 remotes by

if (! require(remotes)) install.packages("remotes")
remotes::install_github("wenjie2wang/reda", ref = "dev")

Getting Started

License

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 0.4.1

Bug fixes

  • Fixed compiling errors when using clang.

reda 0.4.0

New features

  • Added function simEvent and simEventData for simulating survival, recurrent event, and multiple event data from stochastic process point of view.

  • Added function mcfDiff and mcfDiff.test for comparing two-sample MCFs by difference estimates over time and the pseudo-score tests.

  • Added argument origin to function Survr for modeling processes with different time origins.

  • Added variance estimates of sample MCF from bootstrap methods.

Major changes

  • Updated checking rule of argument event of function Survr for modeling sample MCF of cost in addition to number of events.

  • Updated Lawless and Nadaeu (1995) variance estimates in method mcf.formula for sample MCF.

  • Renamed class sampleMcf to mcf.formula, rateRegMcf to mcf.rateReg, baseRateReg to baseRate.rateReg, summaryRateReg to summary.rateReg.

Minor changes

  • Allowed formula Survr(ID, time, event) ~ 1 for modeling baseline rate function using gamma frailty model in function rateReg without specifying any covariate.

Bug fixes

  • Fixed possible label mismatching in plot,mcf.formula (previously plot,sampleMcf) method.

reda 0.3.1

New features

  • Added estimated baseline rate function and its confidence band, and corresponding plot method.

Major changes

  • Updated function baseRate for estimated baseline rate function instead of the estimated coefficients of spline bases.

Bug fixes

  • Fixed function confint by specifying the correct standard error column.

reda 0.3.0

New features

  • 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.

Major changes

  • 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 0.2.1

New features

  • Implementation of spline baseline rate function.

  • Added function AIC and BIC.

Major changes

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

  • Updated object class of fitted model.

  • Replaced sample simulated dataset for demonstration.

Bug fixes

  • 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 0.1.0

New features

  • 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

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

install.packages("reda")

0.4.1 by Wenjie Wang, 6 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 Rcpp, ggplot2, graphics, grDevices, methods, splines2, stats

Suggests knitr, rmarkdown, testthat

Linking to Rcpp, RcppArmadillo


See at CRAN