Package: coarseDataTools 0.7.2

coarseDataTools: Analysis of Coarsely Observed Data

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. See Reich et al. (2009) <doi:10.1002/sim.3659>, Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.

Authors:Nicholas G. Reich [aut, cre], Justin Lessler [aut], Andrew Azman [aut], Zhian N. Kamvar [ctb], Hugo Gruson [ctb]

coarseDataTools_0.7.2.tar.gz
coarseDataTools_0.7.2.zip(r-4.7)coarseDataTools_0.7.2.zip(r-4.6)coarseDataTools_0.7.2.zip(r-4.5)
coarseDataTools_0.7.2.tgz(r-4.6-any)coarseDataTools_0.7.2.tgz(r-4.5-any)
coarseDataTools_0.7.2.tar.gz(r-4.7-any)coarseDataTools_0.7.2.tar.gz(r-4.6-any)
coarseDataTools_0.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coarseDataTools/json (API)

# Install 'coarseDataTools' in R:

install.packages('coarseDataTools', repos = c('https://nickreich.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nickreich/coarsedatatools/issues

Pkgdown/docs site:https://nickreich.github.io

Datasets:

exp.win.lengths - Exposure window lengths from an influenza outbreak at a NYC school
fluA.inc.per - Coarse incubation period data for influenza A
nycH1N1 - Incubation period data from New York City Public Schools, 2009 H1N1 influenza outbreak
simulated.outbreak.deaths - Simulated case and death reports from a fictional outbreak

On CRAN:

8.17 score 10 stars 8 packages 42 scripts 1.2k downloads 5 mentions 10 exports 10 dependencies

Last updated from:ff02907511. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	130
source / vignettes	OK	201
linux-release-x86_64	OK	138
macos-release-arm64	OK	191
macos-oldrel-arm64	OK	211
windows-devel	OK	102
windows-release	OK	86
windows-oldrel	OK	98
wasm-release	OK	91

Exports:dic.fit dic.fit.mcmc EMforCFR generate.coarse.data get.obs.type logLik loglikhd precision.simulation precision.simulation.coarse precision.simulation.exact

Dependencies:coda lattice MASS Matrix MatrixModels mcmc MCMCpack quantreg SparseM survival

Using outbreak data to estimate the relative case fatality ratio

Introduction to the data | Loading the data and the code | Running an analysis

Rendered fromCFR_vignette.Rmdusingknitr::knitr

Last update: 2023-04-28
Started: 2021-12-07

Help page	Topics
An S4 Class that stores a fitted coarse data object	cd.fit cd.fit-class
An S4 Class that stores a MCMC fit coarse data object	cd.fit.mcmc cd.fit.mcmc-class
Function that calculates dgamma with a offset of 1 (i.e., 1 is equivalent to 0)	dgammaOff1
censored survival data	dic.fit
Fits the distribution to the passed-in data using MCMC as implemented in MCMCpack.	dic.fit.mcmc
A function to estimate the relative case fatality ratio when reporting rates are time-varying and deaths are lagged because of survival time.	EMforCFR
Exposure window lengths from an influenza outbreak at a NYC school	exp.win.lengths
Coarse incubation period data for influenza A	fluA.inc.per
Tries to guess the observation types (SIC, DIC, or exact).	get.obs.type
Get the log-likelihood value of a 'cd.fit' or 'cd.fit.mcmc' object	logLik logLik,cd.fit-method
Negative log likelihood for a dataset of interval-censored data, given a distribution and its parameters.	loglikhd
Does a metropolis hastings for the Erlang distribution	mcmc.erlang
posterior log likelihood function to pass to MCMCpack sampler	mcmcpack.ll
Incubation period data from New York City Public Schools, 2009 H1N1 influenza outbreak	nycH1N1
Function that calculates pgamma with a offset of 1 (i.e., 1 is equivalent to 0)	pgammaOff1
Simulate incubation period analyses with coarse data	generate.coarse.data precision.simulation precision.simulation.coarse precision.simulation.exact
Simulated case and death reports from a fictional outbreak	simulated.outbreak.deaths

Package: coarseDataTools 0.7.2

coarseDataTools: Analysis of Coarsely Observed Data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)