Rendered from
dobson.Rmdusingknitr::rmarkdownPackage: serodynamics 0.1.0.9006
Samuel Schildhauer
serodynamics: Modeling Longitudinal Antibody Responses to Infection
Implements Bayesian hierarchical models for estimating antibody kinetic parameters from longitudinal serological data. Fits two-phase within-host models capturing antibody rise, peak, and decay following pathogen infection, using 'JAGS' for posterior inference. Designed as the upstream companion to the 'serocalculator' package for end-to-end seroepidemiological analysis. Methods are described in Teunis and colleagues (2016) <doi:10.1016/j.epidem.2016.04.001> and Teunis and van Eijkeren (2020) <doi:10.1002/sim.8578>.
Authors:
serodynamics_0.1.0.9006.tar.gz
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serodynamics_0.1.0.9006.tgz(r-4.6-any)serodynamics_0.1.0.9006.tgz(r-4.5-any)
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serodynamics_0.1.0.9006.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
serodynamics/json (API)
| # Install 'serodynamics' in R: |
| install.packages('serodynamics', repos = c('https://ucd-serg.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ucd-serg/serodynamics/issues
Pkgdown/docs site:https://ucd-serg.github.io
Datasets:
- nepal_sees - SEES Typhoid data
- nepal_sees_jags_output - SEES Typhoid run_serodynamics jags output
Last updated from:1f61718108. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 270 | ||
| source / vignettes | OK | 218 | ||
| linux-release-x86_64 | OK | 325 | ||
| macos-release-arm64 | OK | 264 | ||
| macos-oldrel-arm64 | OK | 197 | ||
| windows-devel | OK | 293 | ||
| windows-release | OK | 307 | ||
| windows-oldrel | OK | 297 | ||
| wasm-release | OK | 175 |
Exports:as_case_dataautoplotexpect_snapshot_dataget_biomarker_levelsget_biomarker_names_varinitsfunctionload_dataplot_densityplot_essplot_predicted_curveplot_rhatplot_tracepostprocess_jags_outputprep_dataprep_priorsrun_modrun_serodynamicsserodynamics_examplesim_case_datasim_n_obssummarize_posterior
Dependencies:andbitbit64clicliprcodacodetoolscpp11crayondigestdoParalleldplyrfarverforcatsforeachgenericsGGallyggmcmcggplot2ggstatsgluegtablehavenhmsisobanditeratorslabelinglabelledlatticelifecyclemagrittrMASSpatchworkpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangrngtoolsrunjagsS7scalesserocalculatorstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert data into 'case_data' | as_case_data |
| Plot case data | autoplot.case_data |
| JAGS chain initialization function | initsfunction |
| load and format data | load_data |
| SEES Typhoid data | nepal_sees |
| SEES Typhoid run_serodynamics jags output | nepal_sees_jags_output |
| Density Plot Diagnostics | plot_density |
| Plot Effective Sample Size Diagnostics | plot_ess |
| Generate Predicted Antibody Response Curves (Median + 95% CI) | plot_predicted_curve |
| Rhat Plot Diagnostics | plot_rhat |
| Trace Plot Diagnostics | plot_trace |
| Postprocess JAGS output | postprocess_jags_output |
| prepare data for JAGs | prep_data |
| Prepare priors | prep_priors |
| Run Jags Model | run_serodynamics |
| Get path to an example file | serodynamics_example |
| Simulate longitudinal case follow-up data from a homogeneous population | sim_case_data |
| Summary Table of Jags Posterior Estimates | summarize_posterior |
