coarseDataTools: A Collection of Functions to Help with Analysis of Coarsely Observed Data

Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package.

Author
Nicholas G. Reich <nick@schoolph.umass.edu>, Justin Lessler <jlessler@jhsph.edu>, Andrew Azman <andrewazman@gmail.com>
Date of publication
2016-03-12 00:15:41
Maintainer
Nicholas G. Reich <nick@schoolph.umass.edu>
License
GPL (>= 2)
Version
0.6-3
URLs

View on CRAN

Man pages

cd.fit
An S4 Class that stores a fitted coarse data object
cd.fit.mcmc
An S4 Class that stores a MCMC fit coarse data object
dic.fit
Fits a log-normal, gamma, or Weibull model to doubly interval...
dic.fit.mcmc
Fits the distribution to the passed-in data using MCMC as...
EMforCFR
A function to estimate the relative case fatality ratio when...
exp.win.lengths
Exposure window lengths from an influenza outbreak at a NYC...
fluA.inc.per
Coarse incubation period data for influenza A
get.obs.type
Tries to guess the observation types (SIC, DIC, or exact).
loglikhd
Negative log likelihood for a dataset of interval-censored...
logLik-methods
Get the log-likelihood value of a 'cd.fit' or 'cd.fit.mcmc'...
mcmc.erlang
Does a metropolis hastings for the Erlang distribution
mcmcpack.ll
posterior log likelihood function to pass to MCMCpack sampler
nycH1N1
Incubation period data from New York City Public Schools,...
plot-methods
Plots the estimated survival function with an option to plot...
precision.simulation
Simulate incubation period analyses with coarse data
simulated.outbreak.deaths
Simulated case and death reports from a fictional outbreak

Files in this package

coarseDataTools
coarseDataTools/inst
coarseDataTools/inst/CITATION
coarseDataTools/inst/doc
coarseDataTools/inst/doc/CFR_vignette.pdf
coarseDataTools/inst/doc/CFR_vignette.Rnw
coarseDataTools/inst/doc/CFR_vignette.R
coarseDataTools/NAMESPACE
coarseDataTools/data
coarseDataTools/data/fluA.inc.per.rda
coarseDataTools/data/nycH1N1.rda
coarseDataTools/data/exp.win.lengths.rda
coarseDataTools/data/simulated.outbreak.deaths.rda
coarseDataTools/R
coarseDataTools/R/dic.fit.R
coarseDataTools/R/S4stuff.R
coarseDataTools/R/coarseDataTools-package.R
coarseDataTools/R/CFR_estimation.R
coarseDataTools/R/sampleSizeSimulation.R
coarseDataTools/R/get.obs.type.R
coarseDataTools/R/dic.fit.mcmc.R
coarseDataTools/vignettes
coarseDataTools/vignettes/CFR_vignette.Rnw
coarseDataTools/README.md
coarseDataTools/MD5
coarseDataTools/build
coarseDataTools/build/vignette.rds
coarseDataTools/DESCRIPTION
coarseDataTools/ChangeLog
coarseDataTools/man
coarseDataTools/man/fluA.inc.per.Rd
coarseDataTools/man/plot-methods.Rd
coarseDataTools/man/nycH1N1.Rd
coarseDataTools/man/dic.fit.Rd
coarseDataTools/man/mcmc.erlang.Rd
coarseDataTools/man/simulated.outbreak.deaths.Rd
coarseDataTools/man/mcmcpack.ll.Rd
coarseDataTools/man/cd.fit.mcmc.Rd
coarseDataTools/man/dic.fit.mcmc.Rd
coarseDataTools/man/cd.fit.Rd
coarseDataTools/man/loglikhd.Rd
coarseDataTools/man/EMforCFR.Rd
coarseDataTools/man/exp.win.lengths.Rd
coarseDataTools/man/logLik-methods.Rd
coarseDataTools/man/precision.simulation.Rd
coarseDataTools/man/get.obs.type.Rd