# Analysis of Coarsely Observed Data

## Documentation for package ‘coarseDataTools’ version 0.7.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cd.fit | An S4 Class that stores a fitted coarse data object
cd.fit-class | An S4 Class that stores a fitted coarse data object
cd.fit.mcmc | An S4 Class that stores a MCMC fit coarse data object
cd.fit.mcmc-class | An S4 Class that stores a MCMC fit coarse data object
dgammaOff1 | Function that calculates dgamma with a offset of 1 (i.e., 1 is equivalent to 0)
dic.fit | censored survival data
dic.fit.mcmc | Fits the distribution to the passed-in data using MCMC as implemented in MCMCpack.
EMforCFR | A function to estimate the relative case fatality ratio when reporting rates are time-varying and deaths are lagged because of survival time.
exp.win.lengths | Exposure window lengths from an influenza outbreak at a NYC school
fluA.inc.per | Coarse incubation period data for influenza A
generate.coarse.data | Simulate incubation period analyses with coarse data
get.obs.type | Tries to guess the observation types (SIC, DIC, or exact).
logLik | Get the log-likelihood value of a 'cd.fit' or 'cd.fit.mcmc' object
logLik-method | Get the log-likelihood value of a 'cd.fit' or 'cd.fit.mcmc' object
loglikhd | Negative log likelihood for a dataset of interval-censored data, given a distribution and its parameters.
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, 2009 H1N1 influenza outbreak
pgammaOff1 | Function that calculates pgamma with a offset of 1 (i.e., 1 is equivalent to 0)
precision.simulation | Simulate incubation period analyses with coarse data
precision.simulation.coarse | Simulate incubation period analyses with coarse data
precision.simulation.exact | Simulate incubation period analyses with coarse data
simulated.outbreak.deaths | Simulated case and death reports from a fictional outbreak