Package index • nhanesR

Discovery

Find available cycles and files

nhanes_cycles(): List available NHANES cycles
nhanes_manifest(): List available files for a NHANES cycle and component

Variable search

Search the CDC variable catalog by keyword

nhanes_search_variables(): Search NHANES variables by keyword
nhanes_variable_map(): Build a per-cycle variable map for an analyte

Download

Download and cache NHANES XPT files

nhanes_download(): Download and cache NHANES XPT data files
nhanes_download_analyte(): Download NHANES files for an analyte using the CDC variable catalog

NHANES III files

Fixed-width files: list, browse variables, choose columns, read

nhanes3_files(): List the NHANES III data files and their CDC addresses
nhanes3_download(): Download NHANES III files into the nhanesR cache
nhanes3_layout(): The variables in an NHANES III file: names, labels and column positions
nhanes3_read(): Read chosen columns of an NHANES III file

Harmonize, stack, and merge

Combine data across cycles and components

nhanes_harmonize(): Harmonize variable names across NHANES cycles and stack into one data frame
nhanes_stack(): Stack NHANES data across multiple cycles
nhanes_merge(): Merge NHANES component data frames by SEQN

Variable labelling

Attach CDC descriptions as Hmisc-style column labels

NH_label(): Attach CDC variable descriptions as Hmisc-style labels
NH_describe(): NHANES-annotated variable descriptions

Mortality linkage

Link National Center for Health Statistics (NCHS) Public-Use Linked Mortality Files

nhanes_mortality_link(): Link mortality data onto an NHANES analytic dataset
nhanes_mortality_download(): Download NHANES Public-Use Linked Mortality Files
nhanes_mortality_parse(): Parse NHANES Linked Mortality Files into data frames
nhanes_lmf_cycles(): List NHANES cycles with a public-use LMF

NHIS data download

Download and parse NHIS Household/Person survey files (1986-2018)

nhis_download(): Download and parse an NHIS Household or Person file
nhis_data_years(): List NHIS survey years with Household/Person data available

NHIS mortality linkage

Link NCHS Public-Use Linked Mortality Files onto NHIS data

nhis_mortality_link(): Link NHIS mortality data onto an NHIS analytic dataset
nhis_mortality_download(): Download NHIS Public-Use Linked Mortality Files
nhis_mortality_parse(): Parse NHIS Linked Mortality Files into data frames
nhis_lmf_years(): List NHIS survey years with a public-use LMF

Survival analysis

Prepare and summarise survival datasets

nhanes_survival_prep(): Prepare an NHANES-LMF dataset for survival analysis
nhanes_followup_summary(): Summarize mortality follow-up by cycle
nhanes_ucod_labels(): Lookup table for UCOD_LEADING cause-of-death codes

Descriptive mortality rates

Deaths, person-years and crude rates in cells, with all margins

mortality_tabulation(): Tabulate deaths, person-years and crude mortality rates
tabulation_grid(): Pivot a mortality tabulation into a two-way grid

Survey-weighted Cox models

Fuse rms and survey Cox fits; compute weighted baseline hazard

svycph_fuse(): Fuse svycoxph and cph objects for rms ecosystem compatibility
weighted_basehaz(): Compute survey-weighted cumulative baseline hazard with variance
svycph_set_basehaz(): Substitute weighted baseline hazard into a fused cph object

Cache management

nhanes_cache_dir(): Get or set the nhanesR local cache directory