prep_prepare_dataframes: Prepare and verify study data with metadata

In dataquieR: Data Quality in Epidemiological Research

Prepare and verify study data with metadata

Description

This function ensures, that a data frame ds1 with suitable variable names study_data and meta_data exist as base data.frames.

Usage

prep_prepare_dataframes(
  .study_data,
  .meta_data,
  .label_col,
  .replace_hard_limits,
  .replace_missings,
  .sm_code = NULL,
  .allow_empty = FALSE
)

Arguments

.study_data	if provided, use this data set as study_data
.meta_data	if provided, use this data set as meta_data
.label_col	if provided, use this as label_col
.replace_hard_limits	replace HARD_LIMIT violations by NA, defaults to FALSE.
.replace_missings	replace missing codes, defaults to TRUE
.sm_code	missing code for NAs, if they have been re-coded by util_combine_missing_lists
.allow_empty	allow ds1 to be empty. i.e., 0 rows and/or 0 columns

Details

This function defines ds1 and modifies study_data and meta_data in the environment of its caller (see eval.parent). It also defines or modifies the object label_col in the calling environment. Almost all functions exported by dataquieR call this function initially, so that aspects common to all functions live here, e.g. testing, if an argument meta_data has been given and features really a data.frame. It verifies the existence of required metadata attributes (VARATT_REQUIRE_LEVELS). It can also replace missing codes by NAs, and calls prep_study2meta to generate a minimum set of metadata from the study data on the fly (should be amended, so on-the-fly-calling is not recommended for an instructive use of dataquieR).

The function also detects tibbles, which are then converted to base-R data.frames, which are expected by dataquieR.

Different from the other utility function that work in the caller's environment, so it modifies objects in the calling function. It defines a new object ds1, it modifies study_data and/or meta_data and label_col.

Value

ds1 the study data with mapped column names

See Also

acc_margins

Examples

## Not run: 
acc_test1 <- function(resp_variable, aux_variable,
                      time_variable, co_variables,
                      group_vars, study_data, meta_data) {
  prep_prepare_dataframes()
  invisible(ds1)
}
acc_test2 <- function(resp_variable, aux_variable,
                      time_variable, co_variables,
                      group_vars, study_data, meta_data, label_col) {
  ds1 <- prep_prepare_dataframes(study_data, meta_data)
  invisible(ds1)
}
environment(acc_test1) <- asNamespace("dataquieR")
# perform this inside the package (not needed for functions that have been
# integrated with the package already)

environment(acc_test2) <- asNamespace("dataquieR")
# perform this inside the package (not needed for functions that have been
# integrated with the package already)
acc_test3 <- function(resp_variable, aux_variable, time_variable,
                      co_variables, group_vars, study_data, meta_data,
                      label_col) {
  prep_prepare_dataframes()
  invisible(ds1)
}
acc_test4 <- function(resp_variable, aux_variable, time_variable,
                      co_variables, group_vars, study_data, meta_data,
                      label_col) {
  ds1 <- prep_prepare_dataframes(study_data, meta_data)
  invisible(ds1)
}
environment(acc_test3) <- asNamespace("dataquieR")
# perform this inside the package (not needed for functions that have been
# integrated with the package already)

environment(acc_test4) <- asNamespace("dataquieR")
# perform this inside the package (not needed for functions that have been
# integrated with the package already)
load(system.file("extdata/meta_data.RData", package = "dataquieR"))
load(system.file("extdata/study_data.RData", package = "dataquieR"))
try(acc_test1())
try(acc_test2())
acc_test1(study_data = study_data)
try(acc_test1(meta_data = meta_data))
try(acc_test2(study_data = 12, meta_data = meta_data))
print(head(acc_test1(study_data = study_data, meta_data = meta_data)))
print(head(acc_test2(study_data = study_data, meta_data = meta_data)))
print(head(acc_test3(study_data = study_data, meta_data = meta_data)))
print(head(acc_test3(study_data = study_data, meta_data = meta_data,
  label_col = LABEL)))
print(head(acc_test4(study_data = study_data, meta_data = meta_data)))
print(head(acc_test4(study_data = study_data, meta_data = meta_data,
  label_col = LABEL)))
try(acc_test2(study_data = NULL, meta_data = meta_data))

## End(Not run)

dataquieR documentation built on July 26, 2023, 6:10 p.m.