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 |

http://cran.r-project.org/package=coarseDataTools |

**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

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
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