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-4.7-x86_64)outbreaker2_1.1.3.zip(r-4.7-arm64)outbreaker2_1.1.3.zip(r-4.6-x86_64)outbreaker2_1.1.3.zip(r-4.6-arm64)outbreaker2_1.1.3.zip(r-4.5-x86_64)
outbreaker2_1.1.3.tgz(r-4.6-x86_64)outbreaker2_1.1.3.tgz(r-4.6-arm64)outbreaker2_1.1.3.tgz(r-4.5-x86_64)outbreaker2_1.1.3.tgz(r-4.5-arm64)
outbreaker2_1.1.3.tar.gz(r-4.7-arm64)outbreaker2_1.1.3.tar.gz(r-4.7-x86_64)outbreaker2_1.1.3.tar.gz(r-4.6-arm64)outbreaker2_1.1.3.tar.gz(r-4.6-x86_64)
outbreaker2_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
outbreaker2/json (API)

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

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

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

On CRAN:

Conda:

cpp

8.29 score 36 stars 1 packages 118 scripts 426 downloads 7 mentions 11 exports 45 dependencies

Last updated from:672541efe4. Checks:13 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE150
linux-devel-x86_64NOTE182
source / vignettesOK455
linux-release-arm64NOTE195
linux-release-x86_64NOTE181
macos-release-arm64NOTE138
macos-release-x86_64NOTE291
macos-oldrel-arm64NOTE120
macos-oldrel-x86_64NOTE301
windows-devel-arm64NOTE210
windows-devel-x86_64NOTE191
windows-release-arm64NOTE217
windows-release-x86_64NOTE131
windows-oldrel-x86_64NOTE132
wasm-releaseOK145

Exports:bind_to_functioncases_palchains_palcreate_configcreate_paramcustom_likelihoodscustom_movescustom_priorsget_cpp_apioutbreakeroutbreaker_data

Dependencies:apebase64encbslibcachemclicpp11digestevaluatefarverfastmapfontawesomefsggplot2gluegtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrmemoisemimenlmeR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalestinytexvctrsviridisLitevisNetworkwithrxfunyaml

Using custom priors, likelihood, or movements in outbreaker2
Customising priors | Customizing likelihood | A null model | A model using symptom onset only | Customising movements | Movements in outbreaker2 | A (fake) Gibbs sampler for mu | A new movement of ancestries
Rendered fromcustomisation.Rmdusingknitr::rmarkdown

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

Introduction to outbreaker2
Running the analysis with defaults | Analysing the results | Graphics | Using summary | Customising settings and priors
Rendered fromintroduction.Rmdusingknitr::rmarkdown

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

outbreaker2: package overview
Installing the package | Main visible functions of the package | Main internal functions
Rendered fromoverview.Rmdusingknitr::rmarkdown

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

outbreaker2: Rcpp API
List of available functions | Function signatures | Arguments
Rendered fromRcpp_API.Rmdusingknitr::rmarkdown

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

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