{ "_id": "6a1eebfdb401979e73412440", "Package": "vacalibration", "Title": "Calibration of Computer-Coded Verbal Autopsy Algorithm", "Version": "2.2", "Authors@R": "c(person(\"Sandipan\", \"Pramanik\", role = c(\"aut\", \"cre\"),\nemail = \"sandy.pramanik@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7196-155X\")),\nperson(\"Emily\", \"Wilson\", role = \"aut\",\nemail = \"wilsonem@gmail.com\"),\nperson(\"Jacob\", \"Fiksel\", role = \"aut\",\nemail = \"jfiksel@gmail.com\"),\nperson(\"Brian\", \"Gilbert\", role = \"aut\",\nemail = \"bgilbert345@gmail.com\"),\nperson(\"Abhirup\", \"Datta\", role = \"aut\",\nemail = \"abhidatta@jhu.edu\"))", "Maintainer": "Sandipan Pramanik ", "Description": "Calibrates population-level cause-specific mortality\nfractions (CSMFs) that are derived using computer-coded verbal\nautopsy (CCVA) algorithms. Leveraging the data collected in the\nChild Health and Mortality Prevention Surveillance\n(CHAMPS;) project, the package\nstores misclassification matrix estimates of three CCVA\nalgorithms (EAVA, InSilicoVA, and InterVA) and two age groups\n(neonates aged 0-27 days, and children aged 1-59 months) across\ncountries (specific estimates for Bangladesh, Ethiopia, Kenya,\nMali, Mozambique, Sierra Leone, and South Africa, and a\ncombined estimate for all other countries), enabling global\ncalibration. These estimates are obtained using the framework\nproposed in Pramanik et al. (2025;)\nand are analyzed in Pramanik et al.\n(2026;). Given VA-only data for\nan age group, CCVA algorithm, and country, the package utilizes\nthe corresponding misclassification matrix estimate in the\nmodular VA-Calibration framework (Pramanik et\nal.,2025;) and produces calibrated\nestimates of CSMFs. The package also supports ensemble\ncalibration to accommodate multiple algorithms. More generally,\nthis allows calibration of population-level prevalence derived\nfrom single-class predictions of discrete classifiers. For\nthis, users need to provide fixed or uncertainty-quantified\nmisclassification matrices. This work is supported by the\nEunice Kennedy Shriver National Institute of Child Health K99\nNIH Pathway to Independence Award (1K99HD114884-01A1), the Bill\nand Melinda Gates Foundation (INV-034842), and the Johns\nHopkins Data Science and AI Institute.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Config/Needs/compile": "yes", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://github.com/sandy-pramanik/vacalibration", "BugReports": "https://github.com/sandy-pramanik/vacalibration/issues", "Config/pak/sysreqs": "make default-jdk libicu-dev libssl-dev", "Repository": "https://sandy-pramanik.r-universe.dev", "Date/Publication": "2026-03-20 13:54:05 UTC", "RemoteUrl": "https://github.com/sandy-pramanik/vacalibration", "RemoteRef": "HEAD", "RemoteSha": "02645051968bb26ecf9bb335ba39de9bff04a264", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-19 09:39:48 UTC", "User": "root" }, "Author": "Sandipan Pramanik [aut, cre] (ORCID:\n),\nEmily Wilson [aut],\nJacob Fiksel [aut],\nBrian Gilbert [aut],\nAbhirup Datta [aut]", "MD5sum": "d17637a7144d8e1bf051889f42118a64", "_user": "sandy-pramanik", "_type": "src", "_file": "vacalibration_2.2.tar.gz", "_fileid": "17dba78e0953ac5f21805b30f114930a3fedb5408db5f300cafa7017e4d1463f", "_filesize": 2240544, "_sha256": "17dba78e0953ac5f21805b30f114930a3fedb5408db5f300cafa7017e4d1463f", "_created": "2026-05-19T09:39:48.000Z", "_published": "2026-06-02T14:43:09.065Z", "_distro": "noble", "_jobs": [ { "job": 79097692992, "time": 230, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7080062237" }, { "job": 79097692733, "time": 231, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7080062343" }, { "job": 79097692957, "time": 311, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7080072421" }, { "job": 79097693189, "time": 159, "config": 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"message": "Update: new plot function, clean progress output and documentation\n", "time": 1774014845 }, "_maintainer": { "name": "Sandipan Pramanik", "email": "sandy.pramanik@gmail.com", "login": "sandy-pramanik", "orcid": "0000-0002-7196-155X", "description": "Postdoctoral Fellow, Department of Biostatistics", "uuid": 66769914 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "rstan", "role": "Imports" }, { "package": "openVA", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "LaplacesDemon", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sandy-pramanik", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-29", "n": 1 }, { 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