Package: o2geosocial 1.1.3

o2geosocial: Reconstruction of Transmission Chains from Surveillance Data

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).

Authors:Alexis Robert [aut, cre, cph], Sebastian Funk [aut], Adam J Kucharski [aut], Thibaut Jombart [ctb]

o2geosocial_1.1.3.tar.gz
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o2geosocial.pdf |o2geosocial.html✨
o2geosocial/json (API)
NEWS

# Install 'o2geosocial' in R:

install.packages('o2geosocial', repos = c('https://alxsrobert.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alxsrobert/o2geosocial/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

toy_outbreak_long - Simulated outbreaks
toy_outbreak_short - Simulated outbreaks

On CRAN:

baysian-inference markov-chain-monte-carlo transmission-chain-reconstruction

5.08 score 8 stars 5 scripts 305 downloads 1 mentions 8 exports 57 dependencies

Last updated 5 months agofrom:1c3c709577. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 21 2024
R-4.5-win-x86_64	OK	Nov 21 2024
R-4.5-linux-x86_64	OK	Nov 21 2024
R-4.4-win-x86_64	OK	Nov 21 2024
R-4.4-mac-x86_64	OK	Nov 21 2024
R-4.4-mac-aarch64	OK	Nov 21 2024
R-4.3-win-x86_64	OK	Nov 21 2024
R-4.3-mac-x86_64	OK	Nov 21 2024
R-4.3-mac-aarch64	OK	Nov 21 2024

Exports:create_config create_param custom_likelihoods custom_moves custom_priors outbreaker outbreaker_data pre_clustering

Dependencies:ape base64enc bslib cachem cli colorspace data.table digest evaluate fansi farver fastmap fontawesome fs geosphere ggplot2 glue gtable highr htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme outbreaker2 pillar pkgconfig R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales sp tibble tinytex utf8 vctrs viridisLite visNetwork withr xfun yaml

o2geosocial

Alexis Robert, Adam Kucharski, Sebastian Funk

Rendered fromo2geosocial.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2020-08-25
Started: 2020-06-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Set and check parameter settings	create_config
Initializes outputs for outbreaker	create_param outbreaker_param outbreaker_store
Customise likelihood functions for o2geosocial	custom_likelihoods print.custom_likelihoods
Customise samplers for outbreaker	custom_moves
Customise priors for outbreaker	custom_priors print.custom_priors
outbreaker: main function for reconstructing disease outbreaks	outbreaker
Process input data for outbreaker	outbreaker_data
Pre cluster cases in groups according using the genotypes and the arbitrary thresholds gamma (spatial) and delta (temporal).	pre_clustering
Basic methods for processing outbreaker results	outbreaker_chains plot.outbreaker_chains print.outbreaker_chains summary.outbreaker_chains
Simulated outbreaks	toy_outbreak_long
Simulated outbreaks	toy_outbreak_short