xportr: Wrapper to apply all core xportr functions and write xpt

In xportr: Utilities to Output CDISC SDTM/ADaM XPT Files

Wrapper to apply all core xportr functions and write xpt

Description

Wrapper to apply all core xportr functions and write xpt

Usage

xportr(
  .df,
  var_metadata = NULL,
  df_metadata = NULL,
  domain = NULL,
  verbose = NULL,
  path,
  strict_checks = FALSE
)

Arguments

.df	A data frame of CDISC standard.
var_metadata	A data frame containing variable level metadata
df_metadata	A data frame containing dataset level metadata.
domain	Appropriate CDISC dataset name, e.g. ADAE, DM. Used to subset the metadata object.
verbose	The action this function takes when an action is taken on the dataset or function validation finds an issue. See 'Messaging' section for details. Options are 'stop', 'warn', 'message', and 'none'
path	Path where transport file will be written. File name sans will be used as xpt name.
strict_checks	If TRUE, xpt validation will report errors and not write out the dataset. If FALSE, xpt validation will report warnings and continue with writing out the dataset. Defaults to FALSE

Value

Returns the input dataframe invisibly

Examples

data("adsl_xportr", "dataset_spec", "var_spec")
adsl <- adsl_xportr

library(magrittr)
test_dir <- tempdir()

pipeline_path <- file.path(test_dir, "adslpipe.xpt")
xportr_path <- file.path(test_dir, "adslxptr.xpt")

dataset_spec_low <- setNames(dataset_spec, tolower(names(dataset_spec)))
names(dataset_spec_low)[[2]] <- "label"

var_spec_low <- setNames(var_spec, tolower(names(var_spec)))
names(var_spec_low)[[5]] <- "type"

adsl %>%
  xportr_metadata(var_spec_low, "ADSL", verbose = "none") %>%
  xportr_type() %>%
  xportr_length() %>%
  xportr_label() %>%
  xportr_order() %>%
  xportr_format() %>%
  xportr_df_label(dataset_spec_low) %>%
  xportr_write(pipeline_path)

# `xportr()` can be used to apply a whole pipeline at once
xportr(
  adsl,
  var_metadata = var_spec_low,
  df_metadata = dataset_spec_low,
  domain = "ADSL",
  verbose = "none",
  path = xportr_path
)

xportr documentation built on Oct. 8, 2024, 1:08 a.m.