outbreaker2 v1.1.0

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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>.

Readme

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outbreaker2: a framework for reconstructing disease outbreaks

Welcome to the project page of outbreaker2, a Bayesian framework for integrating epidemiological and genetic data to reconstruct transmission trees of densely sampled outbreaks. It re-implements, generalises and replaces the model of outbreaker, and uses a modular approach which enables fine customisation of priors, likelihoods and parameter movements (see customisation vignette).

NOTE: Correction to genetic likelihood

The genetic likelihood of the original outbreaker paper was found to contain a minor mistake in accounting for unobserved generations of infection. As of June 7th 2019, outbreaker2 will use the correct genetic likelihood published here.

The original genetic likelihood was:

The corrected genetic likelihood is:


Installation

To install the stable version from CRAN:

install.packages("outbreaker2")

To install the development version from github (requires Rtools on windows and GSL headers on all platforms):

devtools::install_github("reconhub/outbreaker2")

To add local copies of the vignettes, you will need to specify:

devtools::install_github("reconhub/outbreaker2", build_vignettes = TRUE)

Then, to load the package, use:

library("outbreaker2")


Documentation

outbreaker2 is fully documented on a dedicated website.

It also comes with the following vignettes:

  • introduction: general introduction using a worked example.
  • overview: brief overview of the package's content.
  • customisation: customisation of priors, likelihoods, and movement functions.
  • Rcpp_API: documentation for the Rcpp API.


Contributors

See details of contributions here.

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Maintainer: Finlay Campbell (f.campbell15@imperial.ac.uk)

Functions in outbreaker2

Name Description
bind_to_function Encloses argument in a function's environment
outbreaker outbreaker2: main function for reconstructing disease outbreaks
print.outbreaker_chains Basic methods for processing outbreaker results
sim_ctd Simulate contact data from a transmission tree
chains_pal Color palettes used in outbreaker
create_param Initializes outputs for outbreaker
custom_likelihoods Customise likelihood functions for outbreaker
custom_moves Customise samplers for outbreaker
custom_priors Customise priors for outbreaker
create_config Set and check parameter settings of outbreaker
fake_outbreak Small simulated outbreak
outbreaker_data Process input data for outbreaker
get_cpp_api Access internal C++ rountines used in outbreaker2
outbreaker_package outbreaker2: a platform for disease outbreak reconstruction
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Vignettes of outbreaker2

Name
figs-customisation/f_pi-1.png
figs-customisation/null_net-1.png
figs-customisation/null_net-2.png
figs-customisation/null_trees-1.png
figs-customisation/res_new_move-1.png
figs-customisation/res_new_move-2.png
figs-customisation/res_null_diag-1.png
figs-customisation/res_null_diag-2.png
figs-customisation/res_null_model-1.png
figs-customisation/res_null_model-2.png
figs-customisation/res_null_model-3.png
figs-customisation/res_null_priors-1.png
figs-customisation/res_null_priors-2.png
figs-customisation/res_wt-1.png
figs-customisation/res_wt-2.png
figs-customisation/res_wt-3.png
figs-customisation/run_custom_move_mu-1.png
figs-customisation/run_custom_move_mu-2.png
figs-customisation/run_custom_move_mu-3.png
figs-customisation/traces_custom_priors-1.png
figs-customisation/traces_custom_priors-2.png
figs-customisation/traces_custom_priors-3.png
figs-customisation/traces_custom_priors-4.png
figs-customisation/traces_custom_priors-5.png
figs-customisation/wt_net-1.png
figs-introduction/basic_trace-1.png
figs-introduction/basic_trace_burn-1.png
figs-introduction/config2-1.png
figs-introduction/config2-2.png
figs-introduction/many_plots-1.png
figs-introduction/many_plots-2.png
figs-introduction/many_plots-3.png
figs-introduction/many_plots-4.png
figs-introduction/many_plots-5.png
figs-introduction/traces-1.png
figs-introduction/traces-2.png
figs-introduction/traces-3.png
figs-introduction/traces-4.png
figs-introduction/w-1.png
Rcpp_API.Rmd
customisation.Rmd
introduction.Rmd
overview.Rmd
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Details

Date 2019-06-12
License MIT + file LICENSE
LazyData true
LinkingTo Rcpp
Encoding UTF-8
RoxygenNote 6.1.1
SystemRequirements C++11
VignetteBuilder knitr
NeedsCompilation yes
Packaged 2019-06-13 10:17:09 UTC; fc1915
Repository CRAN
Date/Publication 2019-06-13 15:40:02 UTC

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