Package: jointlyr 0.0.1

Sangeeta Bhatia

jointlyr: Joint estimation of initial incidence and reproduction number

Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.

Authors:Sangeeta Bhatia [aut, cre], Pierre Nouvellet [aut], Anne Cori [aut], Jack Wardle [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
jointlyr/json (API)

# Install 'jointlyr' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

2.00 score 1 scripts 1 exports 79 dependencies

Last updated from:614603f6c5 (on master). Checks:11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-arm64	NOTE	249
linux-devel-x86_64	NOTE	267
source / vignettes	OK	317
linux-release-arm64	NOTE	240
linux-release-x86_64	NOTE	225
macos-release-arm64	NOTE	146
macos-release-x86_64	NOTE	430
macos-oldrel-arm64	NOTE	125
macos-oldrel-x86_64	NOTE	424
windows-devel	NOTE	280
windows-release	NOTE	265
windows-oldrel	NOTE	274
wasm-release	FAIL	178

Exports:jointly_estimate

Dependencies:abind aweek backports BH callr checkmate cli coarseDataTools coda cpp11 data.table desc distcrete distributional dplyr EpiEstim epitrix farver fastymd fitdistrplus generics ggplot2 glue grates gridExtra gtable incidence incidence2 inline isoband labeling lattice lifecycle loo magrittr MASS Matrix MatrixModels matrixStats mcmc MCMCpack numDeriv patchwork pillar pkgbuild pkgconfig plyr posterior processx ps purrr quantreg QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel reshape2 rlang rstan rstantools S7 scales sodium SparseM StanHeaders stringi stringr survival tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr ympes

Set up data | Incidence | Serial Interval Distribution

Rendered fromusing-jointlyr.Rmdusingknitr::rmarkdown

Last update: 2021-03-04
Started: 2021-03-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'jointlyr' package.	jointlyr-package jointlyr
Jointly estimate I0 and Rt	jointly_estimate

Usage by other packages (reverse dependencies)