Analysis of Coarsely Observed Data


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Documentation for package ‘coarseDataTools’ version 0.6-5

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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)
plot Plots the estimated survival function with an option to plot the posterior draws or bootstraps behind the fit
plot-method Plots the estimated survival function with an option to plot the posterior draws or bootstraps behind the fit
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