coarseDataTools: A Collection of Functions to Help with Analysis of Coarsely Observed Data
Version 0.6-3

Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package.

Browse man pages Browse package API and functions Browse package files

AuthorNicholas G. Reich <nick@schoolph.umass.edu>, Justin Lessler <jlessler@jhsph.edu>, Andrew Azman <andrewazman@gmail.com>
Date of publication2016-03-12 00:15:41
MaintainerNicholas G. Reich <nick@schoolph.umass.edu>
LicenseGPL (>= 2)
Version0.6-3
URL http://cran.r-project.org/package=coarseDataTools
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("coarseDataTools")

Man pages

cd.fit: An S4 Class that stores a fitted coarse data object
cd.fit.mcmc: An S4 Class that stores a MCMC fit coarse data object
dic.fit: Fits a log-normal, gamma, or Weibull model to doubly interval...
dic.fit.mcmc: Fits the distribution to the passed-in data using MCMC as...
EMforCFR: A function to estimate the relative case fatality ratio when...
exp.win.lengths: Exposure window lengths from an influenza outbreak at a NYC...
fluA.inc.per: Coarse incubation period data for influenza A
get.obs.type: Tries to guess the observation types (SIC, DIC, or exact).
loglikhd: Negative log likelihood for a dataset of interval-censored...
logLik-methods: Get the log-likelihood value of a 'cd.fit' or 'cd.fit.mcmc'...
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,...
plot-methods: Plots the estimated survival function with an option to plot...
precision.simulation: Simulate incubation period analyses with coarse data
simulated.outbreak.deaths: Simulated case and death reports from a fictional outbreak

Functions

EMforCFR Man page Source code
SEM.variance Source code
cd.fit Man page
cd.fit-class Man page
cd.fit.mcmc Man page
cd.fit.mcmc-class Man page
check.data.structure Source code
dic.fit Man page Source code
dic.fit.mcmc Man page Source code
dic.get.boots Source code
dic.getSE Source code
diclik Source code
diclik2 Source code
diclik2.helper1 Source code
diclik2.helper2 Source code
dist.optim.transform Source code
dist.optim.untransform Source code
exactlik Source code
exp.win.lengths Man page
fluA.inc.per Man page
fw1 Source code
fw3 Source code
generate.coarse.data Man page Source code
get.obs.type Man page Source code
lik Source code
logLik Man page
logLik,cd.fit-method Man page
loglikhd Man page Source code
mcmc.erlang Man page Source code
mcmcpack.ll Man page Source code
nycH1N1 Man page
pl.par1 Source code
pl.par2 Source code
plot Man page
plot,cd.fit-method Man page
precision.simulation Man page Source code
precision.simulation.coarse Man page Source code
precision.simulation.exact Man page Source code
run.Estep Source code
run.Mstep Source code
siclik Source code
simulated.outbreak.deaths Man page
single.boot Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/CFR_vignette.pdf
inst/doc/CFR_vignette.Rnw
inst/doc/CFR_vignette.R
NAMESPACE
data
data/fluA.inc.per.rda
data/nycH1N1.rda
data/exp.win.lengths.rda
data/simulated.outbreak.deaths.rda
R
R/dic.fit.R
R/S4stuff.R
R/coarseDataTools-package.R
R/CFR_estimation.R
R/sampleSizeSimulation.R
R/get.obs.type.R
R/dic.fit.mcmc.R
vignettes
vignettes/CFR_vignette.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/fluA.inc.per.Rd
man/plot-methods.Rd
man/nycH1N1.Rd
man/dic.fit.Rd
man/mcmc.erlang.Rd
man/simulated.outbreak.deaths.Rd
man/mcmcpack.ll.Rd
man/cd.fit.mcmc.Rd
man/dic.fit.mcmc.Rd
man/cd.fit.Rd
man/loglikhd.Rd
man/EMforCFR.Rd
man/exp.win.lengths.Rd
man/logLik-methods.Rd
man/precision.simulation.Rd
man/get.obs.type.Rd
coarseDataTools documentation built on May 29, 2017, 8:38 p.m.