This package is considered a duplicate. The official version of this package is found at:https://mrc-ide.r-universe.dev/EpiEstim

Package: EpiEstim 2.1-0

Anne Cori

EpiEstim: EpiEstim: a package to estimate time varying reproduction numbers from epidemic curves

This package provides tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence.

Authors:Anne Cori <[email protected]>

EpiEstim_2.1-0.tar.gz
EpiEstim_2.1-0.zip(r-4.7)EpiEstim_2.1-0.zip(r-4.6)EpiEstim_2.1-0.zip(r-4.5)
EpiEstim_2.1-0.tgz(r-4.6-any)EpiEstim_2.1-0.tgz(r-4.5-any)
EpiEstim_2.1-0.tar.gz(r-4.7-any)EpiEstim_2.1-0.tar.gz(r-4.6-any)
EpiEstim_2.1-0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
EpiEstim/json (API)

# Install 'EpiEstim' in R:

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

Bug tracker:https://github.com/mrc-ide/epiestim/issues

Datasets:

flu_2009_NYC_school - Data on the 2009 H1N1 influenza pandemic in a school in New York city
Flu1918 - Data on the 1918 H1N1 influenza pandemic in Baltimore.
Flu2009 - Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
Measles1861 - Data on the 1861 measles epidemic in Hagelloch, Germany.
MockRotavirus - Mock data on a rotavirus epidemic.
SARS2003 - Data on the 2003 SARS epidemic in Hong Kong.
Smallpox1972 - Data on the 1972 smallpox epidemic in Kosovo

On CRAN:

11.41 score 104 stars 7 packages 1.3k scripts 1.2k downloads 60 mentions 13 exports 81 dependencies

Last updated from:df0d3b8fe4 (on release). Checks:7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	NOTE	185
source / vignettes	OK	237
linux-release-x86_64	NOTE	207
macos-release-arm64	NOTE	154
macos-oldrel-arm64	NOTE	125
windows-devel	NOTE	131
windows-release	NOTE	165
windows-oldrel	NOTE	127
wasm-release	OK	151

Exports:check_cdt_samples_convergence coarse2estim discr_si DiscrSI estimate_R EstimateR init_mcmc_params make_config make_mcmc_control overall_infectivity OverallInfectivity wallinga_teunis WT

Dependencies:askpass aweek base64enc bslib cachem cli coarseDataTools coda cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fitdistrplus fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httr incidence isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack memoise mime openssl otel pillar pkgconfig plotly plyr promises purrr quantreg R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S7 sass scales SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

EpiEstim: a demonstration

Overview | Estimating R on sliding weekly windows, with a parametric serial interval | Estimating R with a non parametric serial interval distribution | Estimating R accounting for uncertainty on the serial interval distribution | Estimating R and the serial interval using data on pairs infector/infected | Changing the time windows for estimation | Different ways of specifying the incidence | Specifying imported cases | EpiEstimApp

Rendered fromdemo.Rmdusingknitr::rmarkdown

Last update: 2018-05-22
Started: 2018-05-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Checking convergence of an MCMC chain by using the Gelman-Rubin algorithm	check_cdt_samples_convergence
Link coarseDataTools and EpiEstim	coarse2estim
Discretized Generation Time Distribution Assuming A Shifted Gamma Distribution	discr_si
Function to ensure compatibility with EpiEstim versions <2.0	DiscrSI
Estimated Instantaneous Reproduction Number	estimate_R
Function to ensure compatibility with EpiEstim versions <2.0	EstimateR
Data on the 2009 H1N1 influenza pandemic in a school in New York city	flu_2009_NYC_school
Data on the 1918 H1N1 influenza pandemic in Baltimore.	Flu1918
Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.	Flu2009
init_mcmc_params Finds clever starting points for the MCMC to be used to estimate the serial interval, e.g. when using option 'si_from_data' in 'estimate_R'	init_mcmc_params
Set and check parameter settings of estimate_R	make_config
make_mcmc_control Creates a list of mcmc control parameters to be used in 'config$mcmc_control', where 'config' is an argument of the 'estimate_R' function. This is used to configure the MCMC chain used to estimate the serial interval within 'estimate_R' (with method "si_from_data").	make_mcmc_control
Data on the 1861 measles epidemic in Hagelloch, Germany.	Measles1861
Mock data on a rotavirus epidemic.	MockRotavirus
Overall Infectivity Due To Previously Infected Individuals	overall_infectivity
Function to ensure compatibility with EpiEstim versions <2.0	OverallInfectivity
Plot outputs of estimate_r	plot.estimate_R
Data on the 2003 SARS epidemic in Hong Kong.	SARS2003
Data on the 1972 smallpox epidemic in Kosovo	Smallpox1972
Estimation of the case reproduction number using the Wallinga and Teunis method	wallinga_teunis
Function to ensure compatibility with EpiEstim versions <2.0	WT