Package: imuGAP 0.1.0
Carl Pearson
imuGAP: Immunity: Geographic and Age-Based Projection
Fits Bayesian hierarchical models of vaccine coverage by location, birth cohort, and age. Observations of vaccination status (which may span cohorts, ages, and doses) are used to fit a latent survival-style process model that decomposes coverage into a lifetime propensity to vaccinate and a time-varying force of vaccination. Hierarchical spatial structure (e.g., state, county, school) supports partial pooling via random effects. Models are implemented in 'Stan' and fit via 'rstan'. Provides helpers to validate user-supplied input data, and to predict coverage from fitted models.
Authors:
imuGAP_0.1.0.tar.gz
imuGAP_0.1.0.tar.gz(r-4.7-arm64)imuGAP_0.1.0.tar.gz(r-4.7-x86_64)imuGAP_0.1.0.tar.gz(r-4.6-arm64)imuGAP_0.1.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
imuGAP/json (API)
NEWS
| # Install 'imuGAP' in R: |
| install.packages('imuGAP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/accidda/imugap/issues
Pkgdown/docs site:https://accidda.github.io
- fit_sim - Example Stan Fit
- latent_params_sim - Example Latent Parameter Values
- locations_sim - Example Location Data
- observations_sim - Example Observation Data
- populations_sim - Example Population Data
- predict_sim - Example Coverage Predictions
- target_sim - Example Prediction Target Populations
Last updated from:c6cd0c9883. Checks:5 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 282 | ||
| linux-devel-x86_64 | OK | 267 | ||
| source / vignettes | OK | 375 | ||
| linux-release-arm64 | OK | 297 | ||
| linux-release-x86_64 | OK | 289 | ||
| wasm-release | FAIL | 168 |
Exports:canonicalize_locationscanonicalize_observationscanonicalize_populationscreate_targetextract_imugapimugap_optionssamplingstan_options
Dependencies:abindbackportsBHcallrcheckmateclicpp11data.tabledescdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'imuGAP' package. | imuGAP-package imuGAP |
| Convert coverage predictions to a data.frame | as.data.frame.imugap_predict |
| Canonicalize imuGAP Data Objects | canonicalize canonicalize_locations canonicalize_observations canonicalize_populations |
| Create target population for prediction | create_target |
| Custom imuGAP fit extraction | extract_imugap |
| Example Stan Fit | fit_sim |
| imuGAP Model Options | imugap_options |
| Example Latent Parameter Values | latent_params_sim |
| Example Location Data | locations_sim |
| Example Observation Data | observations_sim |
| Example Population Data | populations_sim |
| Example Coverage Predictions | predict_sim |
| Predict coverage probabilities | predict.imugap_fit |
| Immunity: Geographic & Age-based Projection, 'imuGAP' | sampling |
| Stan Sampler Options | stan_options |
| Subset coverage predictions | subset.imugap_predict |
| Summarize coverage predictions | summary.imugap_predict |
| Example Prediction Target Populations | target_sim |
