{
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  "Package": "nhanesR",
  "Type": "Package",
  "Title": "Download, Parse, and Analyze NHANES Data with Mortality Linkage",
  "Version": "0.1.7",
  "Authors@R": "person(\"David\", \"Winsemius\", email = \"dwinsemius@comcast.net\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Provides tools for downloading and organizing National\nHealth and Nutrition Examination Survey (NHANES) public-use\ndata files and the National Center for Health Statistics (NCHS)\nPublic-Use Linked Mortality Files (LMF). Supports structured\nlocal caching, codebook access, survey-aware merging, and\npreparation of survival analysis datasets using NHANES-National\nDeath Index (NDI) linked mortality data (follow-up through\nDecember 31, 2019). NHANES methodology is described at\n<https://wwwn.cdc.gov/nchs/nhanes/Default.aspx>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
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  "URL": "https://dwinsemius.github.io/nhanesR/,\nhttps://github.com/dwinsemius/nhanesR",
  "BugReports": "https://github.com/dwinsemius/nhanesR/issues",
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  "Repository": "https://dwinsemius.r-universe.dev",
  "Date/Publication": "2026-10-03 04:30:09 UTC",
  "RemoteUrl": "https://github.com/dwinsemius/nhanesr",
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  "Author": "David Winsemius [aut, cre]",
  "Maintainer": "David Winsemius <dwinsemius@comcast.net>",
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    "author": "David Winsemius <dwinsemius@comcast.net>",
    "committer": "David Winsemius <dwinsemius@comcast.net>",
    "message": "Rebuild pkgdown site: NHANES III column-selection functions\n\nNew reference pages for nhanes3_files, nhanes3_download, nhanes3_layout and nhanes3_read,\nthe new reference section, the updated package page, NHANES III article, news, search index\nand sitemap. Two pages whose only differences were temp-folder names and download timings\nin their example output were left as committed.\n\nCo-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>\n",
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    "email": "dwinsemius@comcast.net",
    "login": "dwinsemius",
    "description": "Retired. Former Medical director for Heritage Labs (since acquired by CRL) and for several life insurance companies. Prev. Asst Professor of Family Med, UCONN",
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      "date": "2026-07-17"
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      "date": "2026-08-25"
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  "_exports": [
    "mortality_tabulation",
    "NH_describe",
    "NH_label",
    "nhanes_cache_dir",
    "nhanes_cycles",
    "nhanes_download",
    "nhanes_download_analyte",
    "nhanes_followup_summary",
    "nhanes_harmonize",
    "nhanes_lmf_cycles",
    "nhanes_manifest",
    "nhanes_merge",
    "nhanes_mortality_download",
    "nhanes_mortality_link",
    "nhanes_mortality_parse",
    "nhanes_search_variables",
    "nhanes_stack",
    "nhanes_survival_prep",
    "nhanes_ucod_labels",
    "nhanes_variable_map",
    "nhanes3_download",
    "nhanes3_files",
    "nhanes3_layout",
    "nhanes3_read",
    "nhis_data_years",
    "nhis_download",
    "nhis_lmf_years",
    "nhis_mortality_download",
    "nhis_mortality_link",
    "nhis_mortality_parse",
    "svycph_fuse",
    "svycph_set_basehaz",
    "tabulation_grid",
    "weighted_basehaz"
  ],
  "_help": [
    {
      "page": "mortality_tabulation",
      "title": "Tabulate deaths, person-years and crude mortality rates",
      "topics": [
        "mortality_tabulation"
      ]
    },
    {
      "page": "NH_describe",
      "title": "NHANES-annotated variable descriptions",
      "topics": [
        "NH_describe"
      ]
    },
    {
      "page": "NH_label",
      "title": "Attach CDC variable descriptions as Hmisc-style labels",
      "topics": [
        "NH_label"
      ]
    },
    {
      "page": "nhanes_cache_dir",
      "title": "Get or set the nhanesR local cache directory",
      "topics": [
        "nhanes_cache_dir"
      ]
    },
    {
      "page": "nhanes_cycles",
      "title": "List available NHANES cycles",
      "topics": [
        "nhanes_cycles"
      ]
    },
    {
      "page": "nhanes_download",
      "title": "Download and cache NHANES XPT data files",
      "topics": [
        "nhanes_download"
      ]
    },
    {
      "page": "nhanes_download_analyte",
      "title": "Download NHANES files for an analyte using the CDC variable catalog",
      "topics": [
        "nhanes_download_analyte"
      ]
    },
    {
      "page": "nhanes_followup_summary",
      "title": "Summarize mortality follow-up by cycle",
      "topics": [
        "nhanes_followup_summary"
      ]
    },
    {
      "page": "nhanes_harmonize",
      "title": "Harmonize variable names across NHANES cycles and stack into one data frame",
      "topics": [
        "nhanes_harmonize"
      ]
    },
    {
      "page": "nhanes_lmf_cycles",
      "title": "List NHANES cycles with a public-use LMF",
      "topics": [
        "nhanes_lmf_cycles"
      ]
    },
    {
      "page": "nhanes_manifest",
      "title": "List available files for a NHANES cycle and component",
      "topics": [
        "nhanes_manifest"
      ]
    },
    {
      "page": "nhanes_merge",
      "title": "Merge NHANES component data frames by SEQN",
      "topics": [
        "nhanes_merge"
      ]
    },
    {
      "page": "nhanes_mortality_download",
      "title": "Download NHANES Public-Use Linked Mortality Files",
      "topics": [
        "nhanes_mortality_download"
      ]
    },
    {
      "page": "nhanes_mortality_link",
      "title": "Link mortality data onto an NHANES analytic dataset",
      "topics": [
        "nhanes_mortality_link"
      ]
    },
    {
      "page": "nhanes_mortality_parse",
      "title": "Parse NHANES Linked Mortality Files into data frames",
      "topics": [
        "nhanes_mortality_parse"
      ]
    },
    {
      "page": "nhanes_search_variables",
      "title": "Search NHANES variables by keyword",
      "topics": [
        "nhanes_search_variables"
      ]
    },
    {
      "page": "nhanes_stack",
      "title": "Stack NHANES data across multiple cycles",
      "topics": [
        "nhanes_stack"
      ]
    },
    {
      "page": "nhanes_survival_prep",
      "title": "Prepare an NHANES-LMF dataset for survival analysis",
      "topics": [
        "nhanes_survival_prep"
      ]
    },
    {
      "page": "nhanes_ucod_labels",
      "title": "Lookup table for UCOD_LEADING cause-of-death codes",
      "topics": [
        "nhanes_ucod_labels"
      ]
    },
    {
      "page": "nhanes_variable_map",
      "title": "Build a per-cycle variable map for an analyte",
      "topics": [
        "nhanes_variable_map"
      ]
    },
    {
      "page": "nhanes3_download",
      "title": "Download NHANES III files into the nhanesR cache",
      "topics": [
        "nhanes3_download"
      ]
    },
    {
      "page": "nhanes3_files",
      "title": "List the NHANES III data files and their CDC addresses",
      "topics": [
        "nhanes3_files"
      ]
    },
    {
      "page": "nhanes3_layout",
      "title": "The variables in an NHANES III file: names, labels and column positions",
      "topics": [
        "nhanes3_layout"
      ]
    },
    {
      "page": "nhanes3_read",
      "title": "Read chosen columns of an NHANES III file",
      "topics": [
        "nhanes3_read"
      ]
    },
    {
      "page": "nhis_data_years",
      "title": "List NHIS survey years with Household/Person data available",
      "topics": [
        "nhis_data_years"
      ]
    },
    {
      "page": "nhis_download",
      "title": "Download and parse an NHIS Household or Person file",
      "topics": [
        "nhis_download"
      ]
    },
    {
      "page": "nhis_lmf_years",
      "title": "List NHIS survey years with a public-use LMF",
      "topics": [
        "nhis_lmf_years"
      ]
    },
    {
      "page": "nhis_mortality_download",
      "title": "Download NHIS Public-Use Linked Mortality Files",
      "topics": [
        "nhis_mortality_download"
      ]
    },
    {
      "page": "nhis_mortality_link",
      "title": "Link NHIS mortality data onto an NHIS analytic dataset",
      "topics": [
        "nhis_mortality_link"
      ]
    },
    {
      "page": "nhis_mortality_parse",
      "title": "Parse NHIS Linked Mortality Files into data frames",
      "topics": [
        "nhis_mortality_parse"
      ]
    },
    {
      "page": "svycph_fuse",
      "title": "Fuse svycoxph and cph objects for rms ecosystem compatibility",
      "topics": [
        "svycph_fuse"
      ]
    },
    {
      "page": "svycph_set_basehaz",
      "title": "Substitute weighted baseline hazard into a fused cph object",
      "topics": [
        "svycph_set_basehaz"
      ]
    },
    {
      "page": "tabulation_grid",
      "title": "Pivot a mortality tabulation into a two-way grid",
      "topics": [
        "tabulation_grid"
      ]
    },
    {
      "page": "weighted_basehaz",
      "title": "Compute survey-weighted cumulative baseline hazard with variance",
      "topics": [
        "weighted_basehaz"
      ]
    }
  ],
  "_readme": "https://github.com/dwinsemius/nhanesr/raw/HEAD/README.md",
  "_rundeps": [
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    "bit",
    "bit64",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
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    "forcats",
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  "_vignettes": [
    {
      "source": "survival-framework-comparison.Rmd",
      "filename": "survival-framework-comparison.html",
      "title": "Comparing Survival Frameworks: Cox, Piecewise Exponential, and mgcv-Poisson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivation",
        "Key references",
        "Notation",
        "Cox: the partial-likelihood contribution",
        "Piecewise exponential: the Poisson-trick contribution",
        "Profiling out $\\alpha_k$ recovers Cox",
        "mgcv-Poisson (PAMM): the same contribution, a penalized $\\alpha_k$",
        "Side-by-side comparison",
        "Design weights: why the effect on β differs from the effect on marginal means",
        "The marginal case: weighted mean as an intercept-only estimating equation",
        "The conditional case: Binder's (1992) weighted partial likelihood",
        "Why the numerator doesn't need weighting but the denominator does",
        "A runnable numeric demonstration",
        "Convergence of PEM toward Cox as $K \\to \\infty$",
        "Baseline cumulative hazard: three estimates, one true curve",
        "Design weights: conditional robustness vs. marginal sensitivity",
        "Discussion",
        "Current limitations of this document",
        "Session information"
      ],
      "created": "2026-08-09 22:56:00",
      "modified": "2026-08-09 22:56:00",
      "commits": 1
    },
    {
      "source": "nhanesR-overview.Rmd",
      "filename": "nhanesR-overview.html",
      "title": "Getting Started with nhanesR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What nhanesR does",
        "Installation",
        "Setup and options",
        "Default cache location",
        "Permanent configuration via .Rprofile",
        "Checking and changing settings interactively",
        "Function map",
        "Stage 1 — Discovery",
        "Stage 2 — Variable search",
        "Stage 3 — Download",
        "Stage 4 — Harmonize and stack",
        "Stage 5 — Mortality linkage",
        "Stage 6 — Survival analysis preparation",
        "Cache management",
        "Typical workflow",
        "Further reading"
      ],
      "created": "2026-05-28 19:42:26",
      "modified": "2026-08-24 20:17:02",
      "commits": 7
    },
    {
      "source": "analyte-harmonization.Rmd",
      "filename": "analyte-harmonization.html",
      "title": "Navigating Variable Name Changes and Analyte Gaps in NHANES",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The problem",
        "The quality gap in published NHANES research",
        "Two structural barriers to full-cycle, properly-weighted analyses",
        "A pragmatic, hypothesis-first approach",
        "The analytic panel",
        "The CDC catalog gap for 1999–2002 BIOPRO data",
        "Step 1: Discovering where an analyte lives",
        "Example 1: A well-behaved analyte",
        "Example 2: A variable with a prefix change",
        "Example 3: An analyte missing from one cycle",
        "Example 4: An analyte confined to a few cycles",
        "Example 5: A questionnaire variable with a case change",
        "Step 2: Downloading with automatic harmonisation",
        "Downloading ALP across all available cycles",
        "Downloading ALT across all available cycles",
        "Downloading AST across its available cycles",
        "Downloading the questionnaire variable with a case change",
        "Example 6: Disambiguation by component — serum versus urine albumin",
        "Step 3: Assembling the multi-analyte base",
        "Step 4: Derived variables",
        "What the manual approach looks like",
        "Using nhanesR with AI coding assistants",
        "Further reading",
        "Summary of functions used",
        "Session information"
      ],
      "created": "2026-06-02 22:50:04",
      "modified": "2026-06-23 06:05:32",
      "commits": 4
    },
    {
      "source": "nhanes-iii.Rmd",
      "filename": "nhanes-iii.html",
      "title": "NHANES III (1988-1994): Fixed-Width Files, Cotinine, and Mortality",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Download the files",
        "2. Read column positions from the SAS program",
        "3. Read only the columns you need",
        "The same steps with the package functions",
        "4. Missing-value codes",
        "5. Look up variables in the codebook",
        "6. Smoking status, checked against cotinine",
        "7. Link mortality",
        "8. Survey-weighted Cox model",
        "Notes"
      ],
      "created": "2026-09-30 23:53:37",
      "modified": "2026-10-03 04:21:33",
      "commits": 4
    },
    {
      "source": "nhanes-mortality-workflow.Rmd",
      "filename": "nhanes-mortality-workflow.html",
      "title": "NHANES Mortality Linkage: A Complete Workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Package options",
        "Background: NHANES structure",
        "1. What cycles and files are available?",
        "2. Discover variables",
        "3. Download laboratory data",
        "4. Download questionnaire data",
        "5. Harmonize across cycles",
        "6. Recode questionnaire variables",
        "7. Stack demographics and merge all components",
        "8. Link mortality and prepare the survival dataset",
        "9. Survey-weighted Cox model",
        "Choosing the correct survey weight",
        "Pooling across cycles",
        "Notes on data management",
        "Cross-cycle variable harmonization",
        "SEQN is a character identifier",
        "NHANES questionnaire coding",
        "Notes on the public-use LMF"
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