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 80 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	243
linux-devel-x86_64	NOTE	262
source / vignettes	OK	334
linux-release-arm64	NOTE	221
linux-release-x86_64	NOTE	280
macos-release-arm64	NOTE	139
macos-release-x86_64	NOTE	335
macos-oldrel-arm64	NOTE	286
macos-oldrel-x86_64	NOTE	355
windows-devel	NOTE	327
windows-release	NOTE	319
windows-oldrel	NOTE	337
wasm-release	FAIL	161

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 otel 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)