Skip to contents

Read chosen columns of an NHANES III file

Source: R/nhanes3.R
nhanes3_read.Rd

Reads only the columns you ask for from the large fixed-width .dat file, using the positions in its SAS program (nhanes3_layout()). Choose the columns by name with vars, or, in an interactive session, leave vars out to pick them from a list (use pattern to shorten the list first). SEQN, the respondent ID used to link files and mortality, is always included when the file has it.

Usage

nhanes3_read(
  file,
  vars = NULL,
  pattern = NULL,
  recode = NULL,
  id = "SEQN",
  dat_file = NULL,
  sas_file = NULL,
  n_max = Inf
)

Arguments

file

A file name from nhanes3_files(), or the path to a .sas program (then give dat_file too).

vars

Character vector of variable names to read. If NULL in an interactive session, you choose from a list; otherwise an error asks you to supply them.

pattern

Optional regular expression that narrows the interactive list (name or label), as in nhanes3_layout().

recode

Names of numeric variables (among vars) whose all-8s and all-9s codes become NA. Default none.

id

Name of the ID column to always include, or NULL for none.

dat_file

Path to the .dat file, if you already have it; otherwise the cached copy is used, downloaded on first use (about 195 MB for the exam file).

sas_file

Path to the .sas program, if you already have it.

n_max

Maximum number of rows to read (default all), useful for a quick look.

Value

A tibble with the requested columns (numeric, except any $ character columns). It carries attr(, "width"), the width of each field, and attr(, "var_labels"), the SAS labels.

Details

NHANES III stores "blank but applicable" as all 8s and "don't know" as all 9s, sized to the field (8/9 for a one-character item, 88888/99999 for a five-character measurement). Left in place they look like real values. recode turns these into NA for the variables you name. It is not applied to everything: IDs, weights and age have no such codes, and many items have special codes of their own (666 for "varies", 777 for "less than 1 per day"), so check the codebook (nhanes3_download() with what = "codebook") first.

See also

nhanes3_layout(), nhanes3_files(), nhanes_mortality_parse() for the NHANES III linked mortality file.

Examples

if (FALSE) { # \dontrun{
exam <- nhanes3_read("exam", c("HSSEX", "HSAGEIR", "BMPHT", "BMPWT", "WTPFEX6"),
                     recode = c("BMPHT", "BMPWT"))
} # }