Package: linelistBayes 1.0

linelistBayes: Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches

Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.

Authors:Chad Milando [aut, cre], Tenglong Li [ctb], Laura White [ctb]

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linelistBayes.pdf |linelistBayes.html✨
linelistBayes/json (API)

# Install 'linelistBayes' in R:

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

Bug tracker:https://github.com/cmilando/linelistbayes/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

out_list_demo - Sample datasets
sample_cases - Sample datasets
sample_dates - Sample datasets
sample_location - Sample datasets
sample_onset_dates - Sample datasets
sample_report_dates - Sample datasets

On CRAN:

5.08 score 4 stars 2 scripts 443 downloads 18 exports 23 dependencies

Last updated 6 months agofrom:85ac016db4. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	OK	Oct 31 2024
R-4.5-linux-x86_64	OK	Oct 31 2024
R-4.4-win-x86_64	OK	Oct 31 2024
R-4.4-mac-x86_64	OK	Oct 31 2024
R-4.4-mac-aarch64	OK	Oct 31 2024
R-4.3-win-x86_64	OK	Oct 31 2024
R-4.3-mac-x86_64	OK	Oct 31 2024
R-4.3-mac-aarch64	OK	Oct 31 2024

Exports:backnow_cm convert_to_linelist create_caseCounts create_linelist dnb dummy findmiss get_mu_vec getr lambda logLikNB plot.backnow plot.caseCounts pnb prop rnb run_backnow si

Dependencies:cli coda cpp11 dplyr fansi generics glue lattice lifecycle lubridate magrittr pillar pkgconfig R6 Rcpp RcppArmadillo rlang tibble tidyselect timechange utf8 vctrs withr

linelistBayes: an introduction

Rendered fromIntro.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-05-02
Started: 2024-04-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get Bayesian Back-calculation Estimates and Model Diagnostics	backnow_cm
Convert Case Counts to a Line List	convert_to_linelist
Create a Case Counts Data Frame	create_caseCounts
Create a Line List from Report and Onset Dates	create_linelist
Calculate Log-Probability Density for Negative Binomial Distribution	dnb
Generate Dummy Variables Matrix for Weeks and Weekends	dummy
Locate Missing Values in a Numeric Vector	findmiss
Calculate Exponential of Linear Combinations	get_mu_vec
Calculate Time-Varying Reproduction Number R(t)	getr
Calculate Lambda Values for Poisson Distribution Mean	lambda
Compute Log-Likelihood for a Right-Truncated Negative Binomial Model	logLikNB
Plot Estimates or Reproduction Numbers	plot.backnow
Plot Case Counts Over Time	plot.caseCounts
Compute Cumulative Distribution Function for Negative Binomial Distribution	pnb
Calculate Proportions of Event Counts Within a Specified Time Range	prop
Generate Random Samples from a Negative Binomial Distribution	rnb
Run Back Calculation and Estimate Reproduction Numbers	run_backnow
Sample datasets	out_list_demo sample_cases sample_dates sample_location sample_onset_dates sample_report_dates
Calculate Serial Interval Distribution for COVID-19	si