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)
#> 
#> ── Variable lengths missing from metadata. ──
#> 
#> ✔ 30 lengths resolved `RFXSTDTC`, `RFXENDTC`, `RFICDTC`, `RFPENDTC`, `DTHDTC`, `ARMCD`, `ACTARMCD`, `ACTARM`, `COUNTRY`, `DMDTC`, `DMDY`, `TRTSDTM`, `TRTSTMF`, `TRTEDTM`, `TRTETMF`, `SCRFDT`, `EOSDT`, `FRVDT`, `RANDDT`, `DTHDT`, `DTHDTF`, `DTHADY`, `LDDTHELD`, `LSTALVDT`, `RACEGR1`, `REGION1`, `LDDTHGR1`, `DTH30FL`, `DTHA30FL`, and `DTHB30FL`
#> 
#> ── Variable labels missing from metadata. ──
#> 
#> ✔ 30 labels skipped
#> 
#> ── 30 variables not in spec and moved to end ──
#> 
#> ── 42 reordered in dataset ──
#> 

# `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
)
#> ── Variable lengths missing from metadata. ──
#> 
#> ✔ 30 lengths resolved `RFXSTDTC`, `RFXENDTC`, `RFICDTC`, `RFPENDTC`, `DTHDTC`, `ARMCD`, `ACTARMCD`, `ACTARM`, `COUNTRY`, `DMDTC`, `DMDY`, `TRTSDTM`, `TRTSTMF`, `TRTEDTM`, `TRTETMF`, `SCRFDT`, `EOSDT`, `FRVDT`, `RANDDT`, `DTHDT`, `DTHDTF`, `DTHADY`, `LDDTHELD`, `LSTALVDT`, `RACEGR1`, `REGION1`, `LDDTHGR1`, `DTH30FL`, `DTHA30FL`, and `DTHB30FL`
#> 
#> ── Variable labels missing from metadata. ──
#> 
#> ✔ 30 labels skipped
#> 
#> ── 30 variables not in spec and moved to end ──
#> 
#> ── 42 reordered in dataset ──
#>