{ "_id": "6ae345c7327abcdf868670a0", "Package": "imuGAP", "Title": "Immunity: Geographic and Age-Based Projection", "Version": "0.2.0", "Authors@R": "c(person(\"Carl\", \"Pearson\", email = \"carl.ab.pearson@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0701-7860\")),\nperson(\"Claire Perrin\", \"Smith\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1069-9460\")),\nperson(\"Kelly\", \"Zhen\", email = \"zhen717605@gmail.com\", role = \"ctb\"),\nperson(\"Weston\", \"Voglesonger\", email = \"westonvogle@gmail.com\", role = \"ctb\"),\nperson(\"Joshua\", \"Chen\", email = \"joshuazchen1@gmail.com\", role = \"ctb\"),\nperson(\"Minjae\", \"Kung\", email = \"minjaekung@gmail.com\", role = \"ctb\"))", "Description": "Fits Bayesian hierarchical models of vaccine coverage by\nlocation, birth cohort, and age. Observations of vaccination\nstatus (which may span cohorts, ages, and doses) are used to\nfit a latent survival-style process model that decomposes\ncoverage into a lifetime propensity to vaccinate and a\ntime-varying force of vaccination. Hierarchical spatial\nstructure (e.g., state, county, school) supports partial\npooling via random effects. Models are implemented in 'Stan'\nand fit via 'rstan'. Provides helpers to validate user-supplied\ninput data, and to predict coverage from fitted models.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-US", "Biarch": "true", "SystemRequirements": "GNU make", "Config/Needs/check": "stan-dev/cmdstanr", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://accidda.github.io/imuGAP/,\nhttps://github.com/ACCIDDA/imuGAP", "BugReports": "https://github.com/ACCIDDA/imuGAP/issues", "LazyData": "true", "LazyDataCompression": "xz", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "Config/roxygen2/version": "8.1.0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 12:59:57 UTC", "User": "root" }, "Author": "Carl Pearson [aut, cre] (ORCID:\n), Claire Perrin Smith\n[aut] (ORCID: ), Kelly\nZhen [ctb], Weston Voglesonger [ctb], Joshua Chen [ctb], Minjae\nKung [ctb]", "Maintainer": "Carl Pearson ", "Config/pak/sysreqs": "make", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-02 18:48:18 UTC", "RemoteUrl": "https://github.com/cran/imuGAP", "RemoteRef": "HEAD", "RemoteSha": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "_user": "cran", "_type": "src", "_file": "imuGAP_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/165c67142beb345a92229270751bbfa5a4a77c496468215bb5be01641fedad12", "_filesize": 5142662, "_sha256": "165c67142beb345a92229270751bbfa5a4a77c496468215bb5be01641fedad12", "_expires": "2027-02-06T13:10:28.000Z", "_created": "2026-10-29T12:59:57.000Z", "_published": "2026-10-29T13:10:31.074Z", "_upstream": "https://github.com/cran/imuGAP", "_status": "success", "_maintainer": { "name": "Carl Pearson", "email": "carl.ab.pearson@gmail.com", "login": "pearsonca", "orcid": "0000-0003-0701-7860", "description": "STEM researcher.", "uuid": 1828039 }, "_jobs": [ { "job": 123462982040, "time": 295, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12900101089" }, { "job": 123462981852, "time": 378, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12898798455" }, { "job": 123462981751, "time": 332, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12899712069" }, { "job": 123462981933, "time": 339, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12900060448" }, { "job": 123458793929, "time": 506, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12899565941" }, { "job": 123462981903, "time": 251, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12899696442" }, { "job": 123462982032, "time": 441, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12900006091" }, { "job": 123462981724, "time": 386, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12899622820" }, { "job": 123462981740, "time": 412, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12900295084" }, { "job": 123462982151, "time": 338, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12899656717" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618", "_commit": { "id": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "author": "Carl Pearson ", "committer": "cran-robot ", "message": "version 0.2.0\n", "time": 1788374898 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "BH", "version": ">= 1.90", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.1.2", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.4", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.1.11", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.32", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.32", "role": "LinkingTo" }, { "package": "data.table", "role": "Imports" }, { "package": "flexstanr", "version": ">= 0.2.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.1.2", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.1.11.2", "role": "Imports" }, { "package": "rstan", "version": ">= 2.32", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.6.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "roxyglobals", "role": "Suggests" }, { "package": "lintr", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "bayesplot", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "pkgload", "role": "Suggests" }, { "package": "thematic", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-26", "n": 1 }, { "week": "2026-36", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-06-22" }, { "name": "0.2.0", "date": "2026-09-02" } ], "_stars": 0, "_contributors": [ { "user": "pearsonca", "count": 2, "uuid": 1828039 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 224, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/imuGAP" }, "_devurl": "https://github.com/accidda/imugap", "_pkgdown": "https://accidda.github.io/imuGAP/", "_searchresults": 12, "_topics": [ "onetbb", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/imuGAP.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/accidda/imugap", "_realowner": "accidda", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-06-22" }, { "version": "0.2.0", "date": "2026-09-08" } ], "_exports": [ "canonicalize_locations", "canonicalize_observations", "canonicalize_populations", "canonicalize_target", "create_observation_populations", "create_target", "extract_imugap", "imugap_options", "sampling", "stan_options" ], "_datasets": [ { "name": "fit_sim", "title": "Example Stan Fit", "object": "fit_sim", "class": [ "imugap_fit" ], "fields": [], "table": false, "tojson": false }, { "name": "fit_sim_1layer", "title": "Example Stan Fit (1 Layer)", "object": "fit_sim_1layer", "class": [ "imugap_fit" ], "fields": [], "table": false, "tojson": false }, { "name": "fit_sim_2layer", "title": "Example Stan Fit (2 Layers)", "object": "fit_sim_2layer", "class": [ "imugap_fit" ], "fields": [], "table": false, "tojson": false }, { "name": "latent_params_sim", "title": "Example Latent Parameter Values", "object": "latent_params_sim", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "locations_sim", "title": "Example Location Data", "object": "locations_sim", "class": [ "data.table", "data.frame" ], "fields": [ "loc_id", "population", "parent_id" ], "rows": 28, "table": true, "tojson": true }, { "name": "observations_sim", "title": "Example Observation Data", "object": "observations_sim", "class": [ "data.table", "data.frame" ], "fields": [ "cohort", "parent_id", "loc_id", "positive", "sample_n", "age_min", "dose", "censored", "age_max", "obs_id", "cohort_min" ], "rows": 841, "table": true, "tojson": true }, { "name": "populations_sim", "title": "Example Population Data", "object": "populations_sim", "class": [ "data.table", "data.frame" ], "fields": [ "obs_id", "loc_id", "cohort", "age", "dose", "weight" ], "rows": 901, "table": true, "tojson": true }, { "name": "predict_sim", "title": "Example Coverage Predictions", "object": "predict_sim", "class": [ "imugap_predict" ], "fields": [], "table": false, "tojson": false }, { "name": "predict_sim_1layer", "title": "Example Coverage Predictions (1 Layer)", "object": "predict_sim_1layer", "class": [ "imugap_predict" ], "fields": [], "table": false, "tojson": false }, { "name": "predict_sim_2layer", "title": "Example Coverage Predictions (2 Layers)", "object": "predict_sim_2layer", "class": [ "imugap_predict" ], "fields": [], "table": false, "tojson": false }, { "name": "target_sim", "title": "Example Prediction Target Populations", "object": "target_sim", "class": [ "data.table", "data.frame" ], "fields": [ "obs_c_id", "loc_id", "age", "cohort", "dose", "weight", "loc_c_id" ], "rows": 1008, "table": true, "tojson": true }, { "name": "target_sim_1layer", "title": "Example Prediction Target Populations (1 Layer)", "object": "target_sim_1layer", "class": [ "data.table", "data.frame" ], "fields": [ "obs_c_id", "loc_id", "age", "cohort", "dose", "weight", "loc_c_id" ], "rows": 36, "table": true, "tojson": true }, { "name": "target_sim_2layer", "title": "Example Prediction Target Populations (2 Layers)", "object": "target_sim_2layer", "class": [ "data.table", "data.frame" ], "fields": [ "obs_c_id", "loc_id", "age", "cohort", "dose", "weight", "loc_c_id" ], "rows": 144, "table": true, "tojson": true } ], "_help": [ { "page": "imuGAP-package", "title": "The 'imuGAP' package.", "topics": [ "imuGAP-package", "imuGAP" ] }, { "page": "as.data.frame.imugap_predict", "title": "Convert coverage predictions to a data.frame", "topics": [ "as.data.frame.imugap_predict" ] }, { "page": "canonicalize", "title": "Canonicalize imuGAP Data Objects", "topics": [ "canonicalize", "canonicalize_locations", "canonicalize_observations", "canonicalize_populations" ] }, { "page": "canonicalize_target", "title": "Canonicalize a target grid against a fit", "topics": [ "canonicalize_target" ] }, { "page": "create_observation_populations", "title": "Create observation populations", "topics": [ "create_observation_populations" ] }, { "page": "create_target", "title": "Construct a target grid for prediction", "topics": [ "create_target" ] }, { "page": "extract_imugap", "title": "Custom imuGAP fit extraction", "topics": [ "extract_imugap" ] }, { "page": "fit_sim", "title": "Example Stan Fit", "topics": [ "fit_sim" ] }, { "page": "fit_sim_1layer", "title": "Example Stan Fit (1 Layer)", "topics": [ "fit_sim_1layer" ] }, { "page": "fit_sim_2layer", "title": "Example Stan Fit (2 Layers)", "topics": [ "fit_sim_2layer" ] }, { "page": "imugap_options", "title": "imuGAP Model Options", "topics": [ "imugap_options" ] }, { "page": "latent_params_sim", "title": "Example Latent Parameter Values", "topics": [ "latent_params_sim" ] }, { "page": "locations_sim", "title": "Example Location Data", "topics": [ "locations_sim" ] }, { "page": "observations_sim", "title": "Example Observation Data", "topics": [ "observations_sim" ] }, { "page": "populations_sim", "title": "Example Population Data", "topics": [ "populations_sim" ] }, { "page": "predict_sim", "title": "Example Coverage Predictions", "topics": [ "predict_sim" ] }, { "page": "predict_sim_1layer", "title": "Example Coverage Predictions (1 Layer)", "topics": [ "predict_sim_1layer" ] }, { "page": "predict_sim_2layer", "title": "Example Coverage Predictions (2 Layers)", "topics": [ "predict_sim_2layer" ] }, { "page": "predict.imugap_fit", "title": "Predict coverage probabilities", "topics": [ "predict.imugap_fit" ] }, { "page": "sampling", "title": "Immunity: Geographic & Age-based Projection, 'imuGAP'", "topics": [ "sampling" ] }, { "page": "subset.imugap_predict", "title": "Subset coverage predictions", "topics": [ "subset.imugap_predict" ] }, { "page": "summary.imugap_predict", "title": "Summarize coverage predictions", "topics": [ "summary.imugap_predict" ] }, { "page": "target_sim", "title": "Example Prediction Target Populations", "topics": [ "target_sim" ] }, { "page": "target_sim_1layer", "title": "Example Prediction Target Populations (1 Layer)", "topics": [ "target_sim_1layer" ] }, { "page": "target_sim_2layer", "title": "Example Prediction Target Populations (2 Layers)", "topics": [ "target_sim_2layer" ] } ], "_pkglogo": "https://github.com/cran/imuGAP/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cran/imuGAP/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "cpp11", "data.table", "desc", "distributional", "farver", "flexstanr", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lifecycle", "loo", "magrittr", "matrixStats", "numDeriv", "otel", "parallelly", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "S7", "scales", "StanHeaders", "tensorA", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libtbb", "package": "libtbb12", "headers": "libtbb-dev", "source": "onetbb", "version": "2022.3.0-2", "name": "onetbb", "homepage": "https://uxlfoundation.github.io/oneTBB/", "description": "parallelism library for C++ - runtime files" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "user_specified_layers.Rmd", "filename": "user_specified_layers.html", "title": "Flexible Location Layers in imuGAP", "engine": "knitr::rmarkdown", "headings": [ "Overview", "The Example Location Hierarchy", "2. Fitting the Model", "3. Using the Fits to Predict Coverage", "4. Comparing Different Resolution Fits", "County-Level Coverage Across Data Resolutions", "Force of Vaccination ($\\lambda$) Estimation", "Conclusion" ], "created": "2026-09-02 18:48:18", "modified": "2026-09-02 18:48:18", "commits": 1 }, { "source": "imuGAP.Rmd", "filename": "imuGAP.html", "title": "imuGAP, Immunity: Geographic & Age-based Projection", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Walkthrough of Basic Usage", "1. Preparing and Validating the Input Data", "Location Hierarchy (locations_sim)", "Coverage Observations (observations_sim)", "Observation Metadata (populations_sim)", "Validation Failure Examples", "2. Exploring the Synthetic Dataset and Latent Features", "State-Level Observations & Latent Propensity", "County-Level Observations & Offsets", "School-Level Observations Across Counties", "3. Fitting the Model", "Basis Spline Coefficients ($\\beta_{\\text{bs}}$)", "Hierarchy Layer Variances ($\\sigma$)", "Vaccination Uptake Rates ($\\lambda_{\\text{raw}}$)", "4. Defining a Target for Predictions", "5. Predicting Coverage" ], "created": "2026-06-22 18:31:44", "modified": "2026-09-02 18:48:18", "commits": 2 } ], "_score": 3.3802112417116064, "_indexed": false, "_nocasepkg": "imugap", "_universes": [ "cran" ], "_indexurl": "https://accidda.r-universe.dev/imuGAP", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-10-29T13:04:35.000Z", "distro": "resolute", "arch": "aarch64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/6e658c86d4f8aadff433ad78645238d5e6b71196ec872a6aa1e406a24d82d89c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-10-29T13:05:04.000Z", "distro": "resolute", "arch": "x86_64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/5af7f97452d62bbe66f2c0cdd615dbf9fd0e939df31e1c5a0da87c77bffe3154", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-10-29T13:05:17.000Z", "distro": "resolute", "arch": "aarch64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/5d21c803ab486cd3c6438189d74775006a59f8762b1563c8dc3f13cefe7670c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-10-29T13:05:03.000Z", "distro": "resolute", "arch": "x86_64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/088e47032fca86bca117a9d8093947a33556275ca1b7ea9a3d1e628e974e92b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-10-29T13:05:10.000Z", "arch": "emscripten", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/ee5f5f7b07b33b33ea0ad6c35fe8e22a14213e8227d3dae1f94b43aceb3e55e6", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-10-29T13:06:31.000Z", "arch": "aarch64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/1a1af6a4e5cd532b611a1e443fc806fc3d5989c1ef95e33f6b74fb1fe56562a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-10-29T13:04:03.000Z", "arch": "x86_64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/0a29178d3c86c6b6e9981d48c4cf173d129885101c1be2b216a227cca09a562d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.6.1", "os": "win", "version": "0.2.0", "date": "2026-10-29T13:06:28.000Z", "arch": "aarch64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/f416639cd1ab2c05b00b9471034e891f550c9babf8bf5094232680b66e5190a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" }, { "r": "4.6.1", "os": "win", "version": "0.2.0", "date": "2026-10-29T13:04:12.000Z", "arch": "x86_64", "commit": "850a5c8791ca98450d9bde66dd59bd32b626c31d", "fileid": "https://r2.ropensci.org/342bd580a8be5114e0f49ca38309afbffce053e2758007f3fff253d42746ed39", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40877096618" } ] }