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Changelog

Source: NEWS.md

nhanesR 0.1.4

CRAN resubmission fixes

  • Expanded all unexpanded acronyms in DESCRIPTION: “NCHS” → “National Center for Health Statistics (NCHS)” and “NDI” → “National Death Index (NDI)”.
  • Added NHANES methodology URL reference to DESCRIPTION.
  • Replaced all \dontrun{} with \donttest{} in examples; all examples require CDC network access so none were unwrapped.
  • Fixed \d regex in NH_describe documentation (unknown Rd macro on Windows); replaced with [0-9].

Bug fixes

  • Removed “2017-2020” from the internal LMF registry: CDC has not published NHANES_2017_2020_MORT_2019_PUBLIC.dat; has_lmf_public set to FALSE for that cycle.
  • Fixed cli pluralization crash in nhanes_merge() when duplicate columns are found ({i} and {?s} quantity conflict resolved with cli::qty()).
  • Fixed several example bugs exposed by switching from \dontrun to \donttest: missing cycles argument in nhanes_download_analyte() calls; list passed to nhanes_mortality_link() instead of a stacked data frame; undefined linked_data object in nhanes_followup_summary() example.

nhanesR 0.1.3

Bug fixes

  • Default cache directory changed from a platform-specific path under ~ to file.path(tempdir(), "nhanesR"). This prevents nhanesR from writing to the user’s home filespace without explicit consent, in compliance with CRAN Policy. To retain a persistent cache across sessions, set nhanesR.cache_dir in ~/.Rprofile.
  • nhanes_cache_dir("~/my_nhanes_cache") example wrapped in \dontrun{} to prevent directory creation during R CMD CHECK.

nhanesR 0.1.2

Bug fixes

  • Fixed broken CDC mortality linkage URL in three vignettes (CDC reorganised their site; updated to current NCHS Data Linkage landing page).
  • Removed non-standard sentence from DESCRIPTION.
  • Added inst/WORDLIST to suppress spell-check NOTEs for domain abbreviations (NHANES, NCHS, LMF, NDI) and “codebook”.

nhanesR 0.1.1

Breaking changes

  • nhanes_harmonize(): the prefer_mgdl argument has been replaced by units = c("conventional", "SI", "both"). The default ("conventional") preserves prior behaviour; set units = "SI" to retain SI columns and drop conventional duplicates instead.

nhanesR 0.1.0

Initial release.

New functions

  • nhanes_cycles() — list all continuous NHANES cycles (1999–present) and optionally NHANES III (1988–1994), with cycle labels, begin/end years, and file-name suffixes.

  • nhanes_manifest() — query the CDC data catalog for available files within a given cycle and component.

  • nhanes_download() — download one or more NHANES XPT files from CDC, parse them into R data frames, and cache them locally. Falls back to foreign::read.xport() when haven::read_xpt() cannot parse older files.

  • nhanes_stack() — row-bind per-cycle data frames into a single data frame, filling columns absent in some cycles with NA.

  • nhanes_merge() — join NHANES components by SEQN (and optionally cycle), with survey-design-aware defaults.

  • nhanes_mortality_link() — download the NCHS Public-Use Linked Mortality Files (LMF) for the relevant cycles and left-join them onto an analytic dataset by SEQN. Mortality follow-up runs through December 31, 2019.

  • nhanes_survival_prep() — prepare a survival analysis dataset from a mortality-linked data frame: removes ineligible participants (ELIGSTAT != 1), creates time and event columns, optionally creates event_cause for cause-specific mortality, and warns about asymmetric follow-up across cycles.

  • nhanes_followup_summary() — summarize follow-up time and event rates by cycle.

  • nhanes_ucod_labels() — return the 11-category ICD-10 underlying cause-of- death recode used in the public-use LMF.

  • nhanes_search_variables() — search the CDC NHANES variable catalog for variables whose name or description matches a keyword. Results are cached locally. The summarize argument (default TRUE) collapses one-row-per-cycle output into one row per unique variable name, with comma-separated file names, cycles, and an n_cycles count.

  • nhanes_variable_map() — wraps nhanes_search_variables() to return a single-row-per-cycle lookup table (cycle, variable_name, file_name) for a given analyte. Automatically drops comment-code variables, prefers non-SI variables when both exist in a cycle, and accepts a keep_vars argument to disambiguate serum from urine forms of the same analyte (e.g. serum creatinine vs. urinary creatinine).

  • nhanes_cache_dir() — view or change the local cache directory.

Bug fixes and infrastructure

  • Fixed CDC data file URLs: CDC reorganized all NHANES file paths from /Nchs/Nhanes/{cycle}/ to /Nchs/Data/Nhanes/Public/{begin_year}/DataFiles/. All download functions updated accordingly.

  • Added Content-Type check in the HTTP download helper: CDC returns HTTP 200 with an HTML error page when a file has moved; nhanesR now detects this and aborts with an informative message rather than saving a corrupt file.

  • Added foreign::read.xport() fallback for XPT files that haven::read_xpt() cannot parse (affects some files from NHANES cycles prior to 2003).

  • MD5 hash sidecar files (.md5) are written alongside every cached RDS to detect corruption and trigger re-download when needed.

Vignette

  • Added “NHANES Mortality Linkage: A Complete Workflow” vignette illustrating the full pipeline from file discovery through survey-weighted Cox proportional hazards modeling, using serum total cholesterol and cardiovascular mortality across ten cycles (1999–2018) as a worked example.