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  "Package": "nhanesR",
  "Type": "Package",
  "Title": "Download, Parse, and Analyze NHANES Data with Mortality Linkage",
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  "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>.",
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  "Encoding": "UTF-8",
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    "NH_label",
    "nhanes_cache_dir",
    "nhanes_cycles",
    "nhanes_download",
    "nhanes_download_analyte",
    "nhanes_followup_summary",
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    "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",
    "svycph_fuse",
    "svycph_set_basehaz",
    "weighted_basehaz"
  ],
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    {
      "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",
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      "topics": [
        "nhanes_variable_map"
      ]
    },
    {
      "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": "weighted_basehaz",
      "title": "Compute survey-weighted cumulative baseline hazard with variance",
      "topics": [
        "weighted_basehaz"
      ]
    }
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      "headings": [
        "What nhanesR does",
        "Installation",
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        "Default cache location",
        "Permanent configuration via .Rprofile",
        "Checking and changing settings interactively",
        "Function map",
        "Stage 1 — Discovery",
        "Stage 2 — Variable search",
        "Stage 3 — Download",
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      "headings": [
        "The problem",
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        "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",
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        "Example 2: A variable with a prefix change",
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        "Example 4: An analyte confined to a few cycles",
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        "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",
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      "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",
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        "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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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Why not just use cph()?",
        "Why not just use svycoxph()?",
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        "Key references",
        "Step 1: Examine object structures",
        "Comparing weighted and unweighted estimates",
        "Step 2: Identify Design slot dependencies",
        "Step 3: Implement the fusion",
        "Comparing anova.rms() output: survey-correct vs naive",
        "Step 4: Survey-weighted baseline hazard",
        "Step 5: Degrees of freedom correction",
        "Conclusions and current limitations",
        "What works",
        "Empirical demonstration of design effects",
        "When survey weighting is and is not necessary",
        "Current limitations",
        "The nhanesR package",
        "A broader methodological agenda",
        "Session information"
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      "source": "uacr-bridging.Rmd",
      "filename": "uacr-bridging.html",
      "title": "Urinary Albumin-to-Creatinine Ratio Across NHANES Cycles",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Step 1 — Locate the variables",
        "Step 2 — Download and stack",
        "Step 3 — Calculate UACR",
        "Step 4 — Method comparability and bridging",
        "Known method changes",
        "Bridging equations for serum creatinine",
        "Step 5 — Survival analysis with survey weights",
        "Notes and caveats",
        "See also"
      ],
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      "modified": "2026-07-17 13:10:02",
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