Link mortality data onto an NHANES analytic dataset

Performs a left join of the parsed LMF onto a data frame containing NHANES participants, matched on the participant sequence number. Automatically handles multiple cycles by row-binding the appropriate LMF files before joining.

Usage

nhanes_mortality_link(
  nhanes_data,
  cycles = NULL,
  keep_vars = NULL,
  download = TRUE,
  seqn_col = "SEQN",
  cycle_col = "cycle"
)

Arguments

nhanes_data

A data frame containing NHANES participants.

cycles

Character vector of "YYYY-YYYY" cycle labels present in nhanes_data. Inferred from cycle_col when omitted.

keep_vars

Character vector of LMF variables to retain. Defaults to all: c("ELIGSTAT", "MORTSTAT", "UCOD_LEADING", "DIABETES", "HYPERTEN", "PERMTH_INT", "PERMTH_EXM").

download

Logical. Download missing LMF files automatically? Default TRUE.

seqn_col

Character. Name of the participant sequence-number column in nhanes_data. Default "SEQN" (nhanesR / CDC standard). Use "seqn" for nhanesdata output.

cycle_col

Character. Name of the cycle column in nhanes_data. Default "cycle" ("YYYY-YYYY" labels). Use "year" for nhanesdata output, where the column contains integer start years (e.g. 1999, 2001).

Value

nhanes_data with LMF columns appended. Rows with no mortality record (SEQNs absent from the LMF) will have NA for all LMF columns; this should not occur for continuous NHANES 1999-2018.

Details

Data from any source – nhanes_download(), nhanesA, or nhanesdata – can be linked by supplying the appropriate column name arguments. For example, nhanesdata stores the sequence number as seqn (integer) and the cycle as year (integer start year, e.g. 1999); pass seqn_col = "seqn", cycle_col = "year" and both are handled automatically.

See also

nhanes_survival_prep() to convert the linked data into a survival dataset; nhanes_lmf_cycles() for cycles with a public-use LMF; nhanes_stack() to row-bind multi-cycle data before linking.

Examples

# \donttest{
demo <- nhanes_download("DEMO", "2015-2016")
demo_mort <- nhanes_mortality_link(demo)
# }