A collection of functions to help with analysis of coarse infectious disease data


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Documentation for package ‘coarseDataTools’ version 0.3

Help Pages

dic.fit Fitting log-normal models to doubly interval-censored data
dic.getSE Calculates the standard errors for estimates from dic.fit() using the delta method.
diclik Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
diclik2 Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
diclik2.helper1 Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
diclik2.helper2 Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
EMforCFR A function to estimate the relative case fatality ratio when reporting rates are time-varying and deaths are lagged because of survival time.
exactlik Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
fluA.inc.per Coarse incubation period data for influenza A
fw1 Functions to calculate the product of the density and the likelihood weight functions.
fw3 Functions to calculate the product of the density and the likelihood weight functions.
fwFuncs Functions to calculate the product of the density and the likelihood weight functions.
lik Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
LikelihoodFuncs Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
loglik General likelihood function used in the maximization performed in dic.fit().
pl.mu Profile likelihood helper functions used by dic.fit().
pl.sigma Profile likelihood helper functions used by dic.fit().
ProfileLiks Profile likelihood helper functions used by dic.fit().
run.Estep The expectation step for a specialized EM algorithm
run.Mstep The maximization step for a specialized EM algorithm
SEM.variance Implementation of the Supplemented EM algorithm
siclik Functions to calculate the likelihood for a given, possibly coarse, survival-time observation.
simulated.outbreak.deaths Simulated case and death reports from a fictional outbreak