Function reference • coarseDataTools

All functions

EMforCFR(): A function to estimate the relative case fatality ratio when reporting rates are time-varying and deaths are lagged because of survival time.

cd.fit cd.fit-class: An S4 Class that stores a fitted coarse data object

cd.fit.mcmc 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.

exp.win.lengths: Exposure window lengths from an influenza outbreak at a NYC school

fluA.inc.per: Coarse incubation period data for influenza A

get.obs.type(): Tries to guess the observation types (SIC, DIC, or exact).

logLik(<cd.fit>): 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() precision.simulation.exact() precision.simulation.coarse() generate.coarse.data(): Simulate incubation period analyses with coarse data

simulated.outbreak.deaths: Simulated case and death reports from a fictional outbreak