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:
o2geosocial_1.1.3.tar.gz
o2geosocial_1.1.3.zip(r-4.5)o2geosocial_1.1.3.zip(r-4.4)o2geosocial_1.1.3.zip(r-4.3)
o2geosocial_1.1.3.tgz(r-4.5-x86_64)o2geosocial_1.1.3.tgz(r-4.5-arm64)o2geosocial_1.1.3.tgz(r-4.4-x86_64)o2geosocial_1.1.3.tgz(r-4.4-arm64)o2geosocial_1.1.3.tgz(r-4.3-x86_64)o2geosocial_1.1.3.tgz(r-4.3-arm64)
o2geosocial_1.1.3.tar.gz(r-4.5-noble)o2geosocial_1.1.3.tar.gz(r-4.4-noble)
o2geosocial_1.1.3.tgz(r-4.4-emscripten)o2geosocial_1.1.3.tgz(r-4.3-emscripten)
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
- toy_outbreak_long - Simulated outbreaks
- toy_outbreak_short - Simulated outbreaks
baysian-inferencemarkov-chain-monte-carlotransmission-chain-reconstructioncpp
Last updated 9 months agofrom:1c3c709577. Checks:12 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 21 2025 |
| R-4.5-win-x86_64 | OK | Mar 21 2025 |
| R-4.5-mac-x86_64 | OK | Mar 21 2025 |
| R-4.5-mac-aarch64 | OK | Mar 21 2025 |
| R-4.5-linux-x86_64 | OK | Mar 21 2025 |
| R-4.4-win-x86_64 | OK | Mar 21 2025 |
| R-4.4-mac-x86_64 | OK | Mar 21 2025 |
| R-4.4-mac-aarch64 | OK | Mar 21 2025 |
| R-4.4-linux-x86_64 | OK | Mar 21 2025 |
| R-4.3-win-x86_64 | OK | Mar 21 2025 |
| R-4.3-mac-x86_64 | OK | Mar 21 2025 |
| R-4.3-mac-aarch64 | OK | Mar 21 2025 |
Exports:create_configcreate_paramcustom_likelihoodscustom_movescustom_priorsoutbreakeroutbreaker_datapre_clustering
Dependencies:apebase64encbslibcachemclicolorspacedata.tabledigestevaluatefansifarverfastmapfontawesomefsgeosphereggplot2gluegtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeoutbreaker2pillarpkgconfigR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalessptibbletinytexutf8vctrsviridisLitevisNetworkwithrxfunyaml
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 |
