Package: outbreaker2 1.1.3

Finlay Campbell

outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.

Authors:Thibaut Jombart [aut], Finlay Campbell [aut, cre], Rich Fitzjohn [aut], Gerry Tonkin-Hill [ctb], Kristjan Eldjarn [ctb], Alexis Robert [ctb]

outbreaker2_1.1.3.tar.gz
outbreaker2_1.1.3.zip(r-4.5)outbreaker2_1.1.3.zip(r-4.4)outbreaker2_1.1.3.zip(r-4.3)
outbreaker2_1.1.3.tgz(r-4.4-x86_64)outbreaker2_1.1.3.tgz(r-4.4-arm64)outbreaker2_1.1.3.tgz(r-4.3-x86_64)outbreaker2_1.1.3.tgz(r-4.3-arm64)
outbreaker2_1.1.3.tar.gz(r-4.5-noble)outbreaker2_1.1.3.tar.gz(r-4.4-noble)
outbreaker2_1.1.3.tgz(r-4.4-emscripten)outbreaker2_1.1.3.tgz(r-4.3-emscripten)
outbreaker2.pdf |outbreaker2.html✨
outbreaker2/json (API)
NEWS

# Install 'outbreaker2' in R:
install.packages('outbreaker2', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/reconhub/outbreaker2/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

8.14 score 30 stars 1 packages 100 scripts 348 downloads 7 mentions 11 exports 53 dependencies

Last updated 28 days agofrom:672541efe4. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 25 2024
R-4.5-win-x86_64NOTESep 25 2024
R-4.5-linux-x86_64NOTESep 25 2024
R-4.4-win-x86_64NOTESep 25 2024
R-4.4-mac-x86_64NOTESep 25 2024
R-4.4-mac-aarch64NOTESep 25 2024
R-4.3-win-x86_64NOTESep 25 2024
R-4.3-mac-x86_64NOTESep 25 2024
R-4.3-mac-aarch64NOTESep 25 2024

Exports:bind_to_functioncases_palchains_palcreate_configcreate_paramcustom_likelihoodscustom_movescustom_priorsget_cpp_apioutbreakeroutbreaker_data

Dependencies:apebase64encbslibcachemclicolorspacedigestevaluatefansifarverfastmapfontawesomefsggplot2gluegtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalestibbletinytexutf8vctrsviridisLitevisNetworkwithrxfunyaml

Introduction to outbreaker2

Thibaut Jombart

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2021-01-12
Started: 2017-01-30

outbreaker2: package overview

Thibaut Jombart

Rendered fromoverview.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2021-01-12
Started: 2017-01-30

outbreaker2: Rcpp API

Thibaut Jombart

Rendered fromRcpp_API.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2021-01-12
Started: 2017-01-30

Using custom priors, likelihood, or movements in outbreaker2

Thibaut Jombart

Rendered fromcustomisation.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2022-07-03
Started: 2017-01-31

Readme and manuals

Help Manual

Help pageTopics
Encloses argument in a function's environmentbind_to_function
Color palettes used in outbreakercases_pal chains_pal outbreaker_palettes
Set and check parameter settings of outbreakercreate_config print.outbreaker_config
Initializes outputs for outbreakercreate_param outbreaker_param outbreaker_store
Customise likelihood functions for outbreakercustom_likelihoods print.custom_likelihoods
Customise samplers for outbreakercustom_moves print.outbreaker_moves
Customise priors for outbreakercustom_priors print.custom_priors
Small simulated outbreakfake_outbreak
Access internal C++ rountines used in outbreaker2get_cpp_api
outbreaker2: main function for reconstructing disease outbreaksoutbreaker
Process input data for outbreakeroutbreaker_data
outbreaker2: a platform for disease outbreak reconstructionoutbreaker_package
Basic methods for processing outbreaker resultsoutbreaker_chains plot.outbreaker_chains print.outbreaker_chains summary.outbreaker_chains
Simulate contact data from a transmission treesim_ctd