DESCRIPTION: "NCHS" → "National Center
for Health Statistics (NCHS)" and "NDI" → "National Death Index (NDI)".DESCRIPTION.\dontrun{} with \donttest{} in examples; all examples
require CDC network access so none were unwrapped.\d regex in NH_describe documentation (unknown Rd macro on Windows);
replaced with [0-9].NHANES_2017_2020_MORT_2019_PUBLIC.dat; has_lmf_public set to FALSE
for that cycle.cli pluralization crash in nhanes_merge() when duplicate columns
are found ({i} and {?s} quantity conflict resolved with cli::qty()).\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.~ 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.DESCRIPTION.inst/WORDLIST to suppress spell-check NOTEs for domain abbreviations
(NHANES, NCHS, LMF, NDI) and "codebook".nhanes_harmonize(): the prefer_mgdl argument has been replaced by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.Initial release.
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.
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.