Function reference

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

cd.fit
cd.fitclass
 An S4 Class that stores a fitted coarse data object

cd.fit.mcmc
cd.fit.mcmcclass
 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 passedin 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 loglikelihood value of a
cd.fit
orcd.fit.mcmc
object

loglikhd()
 Negative log likelihood for a dataset of intervalcensored 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