Abstract | Introduction | Implementation | Overall structure | Likelihood and priors | Genotype | Conditional report ratio | Time | Space | Age | Overall likelihood | Tree proposals | Tutorial | Part one: First models and outputs | Run the models with `outbreaker()' | Model evaluation | Interpretation of the results | Part two: Modify the likelihoods, priors and movements lists: the Stouffer's rank module | Conclusion
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-4.7)o2geosocial_1.1.3.zip(r-4.6)o2geosocial_1.1.3.zip(r-4.5)
o2geosocial_1.1.3.tgz(r-4.6-x86_64)o2geosocial_1.1.3.tgz(r-4.6-arm64)o2geosocial_1.1.3.tgz(r-4.5-x86_64)o2geosocial_1.1.3.tgz(r-4.5-arm64)
o2geosocial_1.1.3.tar.gz(r-4.7-arm64)o2geosocial_1.1.3.tar.gz(r-4.7-x86_64)o2geosocial_1.1.3.tar.gz(r-4.6-arm64)o2geosocial_1.1.3.tar.gz(r-4.6-x86_64)
o2geosocial_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
o2geosocial/json (API)
| # 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
Datasets:
- toy_outbreak_long - Simulated outbreaks
- toy_outbreak_short - Simulated outbreaks
baysian-inferencemarkov-chain-monte-carlotransmission-chain-reconstructioncpp
Last updated from:1c3c709577. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 173 | ||
| linux-devel-x86_64 | OK | 187 | ||
| source / vignettes | OK | 367 | ||
| linux-release-arm64 | OK | 179 | ||
| linux-release-x86_64 | OK | 164 | ||
| macos-release-arm64 | OK | 153 | ||
| macos-release-x86_64 | OK | 331 | ||
| macos-oldrel-arm64 | OK | 169 | ||
| macos-oldrel-x86_64 | OK | 367 | ||
| windows-devel | OK | 155 | ||
| windows-release | OK | 142 | ||
| windows-oldrel | OK | 155 | ||
| wasm-release | OK | 130 |
Exports:create_configcreate_paramcustom_likelihoodscustom_movescustom_priorsoutbreakeroutbreaker_datapre_clustering
Dependencies:apebase64encbslibcachemclicpp11data.tabledigestevaluatefarverfastmapfontawesomefsgeosphereggplot2gluegtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrmemoisemimenlmeoutbreaker2R6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalestinytexvctrsviridisLitevisNetworkwithrxfunyaml
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 |
