Package: outbreaker2 1.1.4

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_1.1.4.tar.gz
outbreaker2_1.1.4.zip(r-4.7)outbreaker2_1.1.4.zip(r-4.6)outbreaker2_1.1.4.zip(r-4.5)
outbreaker2_1.1.4.tgz(r-4.6-x86_64)outbreaker2_1.1.4.tgz(r-4.6-arm64)outbreaker2_1.1.4.tgz(r-4.5-x86_64)outbreaker2_1.1.4.tgz(r-4.5-arm64)
outbreaker2_1.1.4.tar.gz(r-4.7-arm64)outbreaker2_1.1.4.tar.gz(r-4.7-x86_64)outbreaker2_1.1.4.tar.gz(r-4.6-arm64)outbreaker2_1.1.4.tar.gz(r-4.6-x86_64)
outbreaker2_1.1.4.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://finlaycampbell.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On CRAN:

Conda:

cpp

8.01 score 1 packages 110 scripts 450 downloads 7 mentions 11 exports 45 dependencies

Last updated from:69f5b23202. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK168
linux-devel-x86_64OK172
source / vignettesOK484
linux-release-arm64OK159
linux-release-x86_64OK179
macos-release-arm64OK217
macos-release-x86_64OK388
macos-oldrel-arm64OK188
macos-oldrel-x86_64OK408
windows-develOK137
windows-releaseOK170
windows-oldrelOK147
wasm-releaseOK131

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