extract_form: Extract data by form from MACRO dataset

In shug0131/cctu: In-House Functions for Report Writing at Cambridge Clinical Trials Unit

Extract data by form from MACRO dataset

Description

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")

shug0131/cctu documentation built on Feb. 15, 2025, 3:27 p.m.