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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argument has been replaced by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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.