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Extract data by form from MACRO dataset

extract_form.Rd

Extract data by form from MACRO dataset. Data will be transformed to long format adding a new column of `visit`.

Usage

extract_form(
  data,
  form,
  visit = NULL,
  vars_keep = NULL,
  dlu = cctu_env$dlu,
  rm_empty = getOption("cctu_rm_empty", default = "both")
)

Arguments

data

A data.frame from macro dataset.

form

Name of the form in the DLU file, see tidy_dlu.

visit

A character string or vector of visit name in the DLU file, see tidy_dlu.

vars_keep

Parameters to keep in the output data. This is useful if you want to keep treatment arm or age variable.

dlu

A DLU data.frame

rm_empty

Remove empty "rows", "cols", or "both" (default), or not "none". The remove_blank_rows_cols function will be used to clean the empty rows and/or columns. Use options(cctu_rm_empty = "none") to set global options.

Value

A data.table object.

See also

tidy_dlu data.table read_data remove_blank_rows_cols

Examples


# Read MACRO data
dt <- read.csv(system.file("extdata", "pilotdata.csv", package="cctu"),
               colClasses = "character")
dlu <- read.csv(system.file("extdata", "pilotdata_dlu.csv", package="cctu"))
clu <- read.csv(system.file("extdata", "pilotdata_clu.csv", package="cctu"))

# Create subjid
dt$subjid <- substr(dt$USUBJID, 8, 11)

df <- apply_macro_dict(dt, dlu = dlu, clu = clu, clean_names = FALSE)

# Following can give you the same dlu file used by apply_macro_dict
dlu <- tidy_dlu(dlu, clean_names = FALSE)

# Extract data from Lab form
lb <- extract_form(df, "Lab")

# Extract screening visit data from lab form
lb_base <- extract_form(df, "Lab", visit = "SCREENING")