{ "_id": "6a1ee426b401979e7341104a", "Package": "imprinting", "Type": "Package", "Title": "Calculate Birth Year-Specific Probabilities of Immune Imprinting\nto Influenza", "Version": "0.1.1", "Authors@R": "c(person(given = \"Katelyn\",\nfamily = \"Gostic\",\nrole = c(\"aut\"),\nemail = \"kgostic@uchicago.edu\"),\nperson(given = \"Alex\",\nfamily = \"Byrnes\",\nrole = c(\"ctb\", \"cre\"),\nemail = \"abyrnes@uchicago.edu\"))", "Description": "Reconstruct birth-year specific probabilities of immune\nimprinting to influenza A, using the methods of Gostic et al.\n(2016) . Plot, save, or export the\ncalculated probabilities for use in your own research. By\ndefault, the package calculates subtype-specific imprinting\nprobabilities, but with user-provided frequency data, it is\npossible to calculate probabilities for arbitrary kinds of\nprimary exposure to influenza A, including primary vaccination\nand exposure to specific clades, strains, etc.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Config/testthat/edition": "3", "RoxygenNote": "7.2.2", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://cobeylab.github.io/imprinting/", "BugReports": "https://github.com/cobeylab/imprinting/issues", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://cobeylab.r-universe.dev", "Date/Publication": "2022-12-16 22:29:31 UTC", "RemoteUrl": "https://github.com/cobeylab/imprinting", "RemoteRef": "HEAD", "RemoteSha": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 06:20:47 UTC", "User": "root" }, "Author": "Katelyn Gostic [aut],\nAlex Byrnes [ctb, cre]", "Maintainer": "Alex Byrnes ", "MD5sum": "ac667d88324e2cb659a7f676d2eb6cdb", "_user": "cobeylab", "_type": "src", "_file": "imprinting_0.1.1.tar.gz", "_fileid": "1c9a7b5a4ef587f02f96ecd8a924200e138d91712ddaee154a4f22dc26cecb65", "_filesize": 750080, "_sha256": "1c9a7b5a4ef587f02f96ecd8a924200e138d91712ddaee154a4f22dc26cecb65", "_created": "2026-05-20T06:20:47.000Z", "_published": "2026-06-02T14:09:42.291Z", "_distro": "noble", "_jobs": [ { "job": 79090385134, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7102723798" }, { "job": 79090384547, "time": 170, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7102715578" }, { "job": 79090385190, "time": 139, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7102702144" }, { "job": 79090384793, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7102702064" }, { "job": 79090383097, "time": 206, "config": 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"name": "Alex Byrnes", "email": "abyrnes@uchicago.edu", "login": "alexbyrnes", "twitter": "@alexbyrnes", "description": "", "uuid": 1862924 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.0.9", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "cowplot", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "cobeylab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "ceirr-cmc" ], "_stars": 0, "_contributors": [ { "user": "kgostic", "count": 171, "uuid": 16617016 }, { "user": "alexbyrnes", "count": 106, "uuid": 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"get_WHO_region", "plot_many_country_years", "plot_one_country_year", "show_available_countries", "show_available_regions" ], "_help": [ { "page": "get_country_cocirculation_data", "title": "Get data on the relative circulation of each influenza A subtype", "topics": [ "get_country_cocirculation_data" ] }, { "page": "get_country_inputs_1997_to_present", "title": "Return raw flu surveillance data for a specific country", "topics": [ "get_country_inputs_1997_to_present" ] }, { "page": "get_country_intensity_data", "title": "Get the relative intensity of influenza A circulation", "topics": [ "get_country_intensity_data" ] }, { "page": "get_imprinting_probabilities", "title": "Calculate imprinting probabilities", "topics": [ "get_imprinting_probabilities" ] }, { "page": "get_p_infection_year", "title": "Calculate the probability imprinting occurs n years after birth", "topics": [ "get_p_infection_year" ] }, { "page": "get_regional_inputs_1997_to_present", "title": "Return raw flu surveillance data for a specific WHO region", "topics": [ "get_regional_inputs_1997_to_present" ] }, { "page": "get_template_data", "title": "Get country-independent flu circulation data for 1918-1996", "topics": [ "get_template_data" ] }, { "page": "get_WHO_region", "title": "Look up a country's WHO region", "topics": [ "get_WHO_region" ] }, { "page": "plot_many_country_years", "title": "Plot imprinting probabilities for up to five country-years", "topics": [ "plot_many_country_years" ] }, { "page": "plot_one_country_year", "title": "Plot imprinting probabilities for a single country and year", "topics": [ "plot_one_country_year" ] }, { "page": "show_available_countries", "title": "Show a list of all available countries", "topics": [ "show_available_countries" ] }, { "page": "show_available_regions", "title": "Show all WHO regions", "topics": [ "show_available_regions" ] } ], "_readme": "https://github.com/cobeylab/imprinting/raw/HEAD/README.md", "_rundeps": [ "cli", "cowplot", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "custom-imprinting-types.Rmd", "filename": "custom-imprinting-types.html", "title": "custom-imprinting-types", "engine": "knitr::rmarkdown", "headings": [ "Generate probabilities of imprinting to custom subsets of influenza A viruses", "Input the custom frequencies into get_imprinting_probabilities()" ], "created": "2022-08-25 18:11:07", "modified": "2022-11-17 22:27:04", "commits": 2 }, { "source": "intro-to-imprinting.Rmd", "filename": "intro-to-imprinting.html", "title": "intro-to-imprinting", "engine": "knitr::rmarkdown", "headings": [ "1. Install the imprinting package", "1.1 Install the devtools package", "1.2 Load the devtools package", "1.3 Install the imprinting package from github", "1.4 Load the imprinting package", "2. Use the package to calculate imprinting probabilities", "2.1 Calculate imprinting probabilities for one country and year of observation", "2.2 Why do we specify the observation_year?", "2.2 View a list of the available countries", "2.3 Generate probabilities for many countries and observation years", "3. Plot the outputs", "3.1 Plot the first country-year combination in the output data frame", "Select a specific country and year to plot", "3.2 Plot up to five countires at a time", "4. Explore the underlying data and components of the imprinting probabilities", "Get the probability that an individual imprinted 0, 1, 2, ... 12 years after birth" ], "created": "2022-08-03 22:49:18", "modified": "2022-11-17 22:27:04", "commits": 5 } ], "_score": 4.146128035678238, "_indexed": true, "_nocasepkg": "imprinting", "_universes": [ "cobeylab", "alexbyrnes" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-05-20T06:23:54.000Z", "distro": "noble", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "387374557c3c4350e712254ab2bcb65679dc0f6532ada466189731e083c9c1be", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.6.0", "os": "linux", "version": "0.1.1", "date": "2026-05-20T06:23:19.000Z", "distro": "noble", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "6ecf55756c1f91a5a5e8a6d90bd06f65b127ecfa7916c53782d44af0f94d12c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-05-20T06:22:42.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "074887bb178629281eb4f696ee956683d1fc6cf2d336849106765ef42f4afaf7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.6.0", "os": "mac", "version": "0.1.1", "date": "2026-05-20T06:22:37.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "6c3faf6ee585b7f7baf61665db75546a685e44d6192431ba9bbd16eb8c61aef9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-05-20T06:22:29.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "974fc90860def262adcbb05f966043e53a0966c87360afc07cddbf548262387c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-05-20T06:22:11.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "d02351c25443181613a1cb1c08004686d57a097d0f838849ffd5a5a7dce56bb0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.6.0", "os": "win", "version": "0.1.1", "date": "2026-05-20T06:22:08.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "58a85937e400707cf453510f621d88ea43eb5dbaaa15af74b0ca1fe2916f6baf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-06-02T14:09:17.000Z", "commit": "266f9cdf2f2d95745e6627a64c35eecdc6fe07e3", "fileid": "2f18e14bd10f8790a57a1e2275ec4b6faa0fea4cdc5bbac3c7ee089c69c76e64", "status": "success", "buildurl": "https://github.com/r-universe/cobeylab/actions/runs/26145086766" } ] }