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Getting Started with xportr

The demo will make use of a small ADSL data set that is apart of the {admiral} package. The script that generates this ADSL dataset can be created by using this command admiral::use_ad_template("adsl"). For a deeper discussion into xportr be sure to check out the Deep Dive User Guide.

The ADSL has the following features:

  • 306 observations
  • 48 variables
  • Data types other than character and numeric
  • Missing labels on variables
  • Missing label for data set
  • Order of variables not following specification file
  • Formats missing

To create a fully compliant v5 xpt ADSL dataset, that was developed using R, we will need to apply the 6 main functions within the xportr package:

# Loading packages
library(dplyr)
library(labelled)
library(xportr)
library(admiral)
library(rlang)
library(readxl)

# Loading in our example data
adsl <- admiral::admiral_adsl

NOTE: The ADSL dataset can be created by using this command admiral::use_ad_template("adsl").

Preparing your Specification Files

In order to make use of the functions within xportr you will need to create an R data frame that contains your specification file. You will most likely need to do some pre-processing of your spec sheets after loading in the spec files for them to work appropriately with the xportr functions. Please see our example spec sheets in system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr") to see how xportr expects the specification sheets.

var_spec <- read_xlsx(
  system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr"),
  sheet = "Variables"
) %>%
  rename(type = "Data Type") %>%
  set_names(tolower)

Below is a quick snapshot of the specification file pertaining to the ADSL data set, which we will make use of in the 6 xportr function calls below. Take note of the order, label, type, length and format columns.

xportr_type()

NOTE: We make use of str() to expose the attributes (length, labels, formats, type) of the datasets. We have suppressed these calls for the sake of brevity.

In order to be compliant with transport v5 specifications an xpt file can only have two data types: character and numeric/dbl. Currently the ADSL data set has chr, dbl, time, factor and date.

  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
    ..- attr(*, "label")= chr "Study Identifier"
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
    ..- attr(*, "label")= chr "Unique Subject Identifier"
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
    ..- attr(*, "label")= chr "Subject Identifier for the Study"
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Subject Reference Start Date/Time"
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
    ..- attr(*, "label")= chr "Subject Reference End Date/Time"
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Date/Time of First Study Treatment"
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
    ..- attr(*, "label")= chr "Date/Time of Last Study Treatment"
   $ RFICDTC : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Informed Consent"
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
    ..- attr(*, "label")= chr "Date/Time of End of Participation"
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Death"
   $ DTHFL   : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Subject Death Flag"
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
    ..- attr(*, "label")= chr "Study Site Identifier"
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
    ..- attr(*, "label")= chr "Age"
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
    ..- attr(*, "label")= chr "Age Units"
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
    ..- attr(*, "label")= chr "Sex"
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
    ..- attr(*, "label")= chr "Race"
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
    ..- attr(*, "label")= chr "Ethnicity"
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Planned Arm Code"
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Actual Arm Code"
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
    ..- attr(*, "label")= chr "Country"
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
    ..- attr(*, "label")= chr "Date/Time of Collection"
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
    ..- attr(*, "label")= chr "Study Day of Collection"
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LSTALVDT: Date[1:306], format: "2014-07-02" ...
   $ AGEGR1  : Factor w/ 3 levels "<18","18-64",..: 2 2 3 3 3 3 2 3 3 3 ...
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
   $ DTH30FL : chr [1:306] NA NA NA NA ...
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
   $ DTHB30FL: chr [1:306] NA NA NA NA ...

Using xportr_type() and the supplied specification file, we can coerce the variables in the ADSL set to be either numeric or character.

adsl_type <- xportr_type(adsl, var_spec, domain = "ADSL", verbose = "message")
  
  ── Variable type mismatches found. ──
  
2 variables coerced
  Variable type(s) in dataframe don't match metadata:
  `LSTALVDT` and `AGEGR1`

Now all appropriate types have been applied to the dataset as seen below.

  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
    ..- attr(*, "label")= chr "Study Identifier"
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
    ..- attr(*, "label")= chr "Unique Subject Identifier"
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
    ..- attr(*, "label")= chr "Subject Identifier for the Study"
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Subject Reference Start Date/Time"
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
    ..- attr(*, "label")= chr "Subject Reference End Date/Time"
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Date/Time of First Study Treatment"
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
    ..- attr(*, "label")= chr "Date/Time of Last Study Treatment"
   $ RFICDTC : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Informed Consent"
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
    ..- attr(*, "label")= chr "Date/Time of End of Participation"
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Death"
   $ DTHFL   : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Subject Death Flag"
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
    ..- attr(*, "label")= chr "Study Site Identifier"
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
    ..- attr(*, "label")= chr "Age"
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
    ..- attr(*, "label")= chr "Age Units"
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
    ..- attr(*, "label")= chr "Sex"
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
    ..- attr(*, "label")= chr "Race"
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
    ..- attr(*, "label")= chr "Ethnicity"
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Planned Arm Code"
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Actual Arm Code"
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
    ..- attr(*, "label")= chr "Country"
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
    ..- attr(*, "label")= chr "Date/Time of Collection"
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
    ..- attr(*, "label")= chr "Study Day of Collection"
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LSTALVDT: num [1:306] 16253 15585 16084 16174 16434 ...
   $ AGEGR1  : chr [1:306] "18-64" "18-64" ">=65" ">=65" ...
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
   $ DTH30FL : chr [1:306] NA NA NA NA ...
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
   $ DTHB30FL: chr [1:306] NA NA NA NA ...
   - attr(*, "_xportr.df_arg_")= chr "ADSL"

xportr_length()

Next we can apply the lengths from a variable level specification file to the data frame. xportr_length() will identify variables that are missing from your specification file. The function will also alert you to how many lengths have been applied successfully. Before we apply the lengths lets verify that no lengths have been applied to the original dataframe.

  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
    ..- attr(*, "label")= chr "Study Identifier"
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
    ..- attr(*, "label")= chr "Unique Subject Identifier"
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
    ..- attr(*, "label")= chr "Subject Identifier for the Study"
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Subject Reference Start Date/Time"
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
    ..- attr(*, "label")= chr "Subject Reference End Date/Time"
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Date/Time of First Study Treatment"
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
    ..- attr(*, "label")= chr "Date/Time of Last Study Treatment"
   $ RFICDTC : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Informed Consent"
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
    ..- attr(*, "label")= chr "Date/Time of End of Participation"
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Death"
   $ DTHFL   : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Subject Death Flag"
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
    ..- attr(*, "label")= chr "Study Site Identifier"
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
    ..- attr(*, "label")= chr "Age"
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
    ..- attr(*, "label")= chr "Age Units"
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
    ..- attr(*, "label")= chr "Sex"
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
    ..- attr(*, "label")= chr "Race"
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
    ..- attr(*, "label")= chr "Ethnicity"
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Planned Arm Code"
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Actual Arm Code"
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
    ..- attr(*, "label")= chr "Country"
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
    ..- attr(*, "label")= chr "Date/Time of Collection"
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
    ..- attr(*, "label")= chr "Study Day of Collection"
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LSTALVDT: Date[1:306], format: "2014-07-02" ...
   $ AGEGR1  : Factor w/ 3 levels "<18","18-64",..: 2 2 3 3 3 3 2 3 3 3 ...
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
   $ DTH30FL : chr [1:306] NA NA NA NA ...
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
   $ DTHB30FL: chr [1:306] NA NA NA NA ...

No lengths have been applied to the variables as seen in the printout - the lengths would be in the attr() part of each variables. Let’s now use xportr_length() to apply our lengths from the specification file.

adsl_length <- adsl %>% xportr_length(var_spec, domain = "ADSL", "message")
  
  ── Variable lengths missing from metadata. ──
  
3 lengths resolved
  Variable(s) present in dataframe but doesn't exist in
  `metadata`.Problem with `TRTSTMF`, `TRTETMF`, and `RANDDT`
  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
    ..- attr(*, "label")= chr "Study Identifier"
    ..- attr(*, "width")= num 21
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
    ..- attr(*, "label")= chr "Unique Subject Identifier"
    ..- attr(*, "width")= num 30
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
    ..- attr(*, "label")= chr "Subject Identifier for the Study"
    ..- attr(*, "width")= num 8
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Subject Reference Start Date/Time"
    ..- attr(*, "width")= num 19
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
    ..- attr(*, "label")= chr "Subject Reference End Date/Time"
    ..- attr(*, "width")= num 19
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Date/Time of First Study Treatment"
    ..- attr(*, "width")= num 19
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
    ..- attr(*, "label")= chr "Date/Time of Last Study Treatment"
    ..- attr(*, "width")= num 19
   $ RFICDTC : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Informed Consent"
    ..- attr(*, "width")= num 19
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
    ..- attr(*, "label")= chr "Date/Time of End of Participation"
    ..- attr(*, "width")= num 19
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Death"
    ..- attr(*, "width")= num 19
   $ DTHFL   : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Subject Death Flag"
    ..- attr(*, "width")= num 2
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
    ..- attr(*, "label")= chr "Study Site Identifier"
    ..- attr(*, "width")= num 5
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
    ..- attr(*, "label")= chr "Age"
    ..- attr(*, "width")= num 8
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
    ..- attr(*, "label")= chr "Age Units"
    ..- attr(*, "width")= num 10
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
    ..- attr(*, "label")= chr "Sex"
    ..- attr(*, "width")= num 1
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
    ..- attr(*, "label")= chr "Race"
    ..- attr(*, "width")= num 60
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
    ..- attr(*, "label")= chr "Ethnicity"
    ..- attr(*, "width")= num 100
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Planned Arm Code"
    ..- attr(*, "width")= num 20
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
    ..- attr(*, "width")= num 200
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Actual Arm Code"
    ..- attr(*, "width")= num 20
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
    ..- attr(*, "width")= num 200
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
    ..- attr(*, "label")= chr "Country"
    ..- attr(*, "width")= num 3
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
    ..- attr(*, "label")= chr "Date/Time of Collection"
    ..- attr(*, "width")= num 19
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
    ..- attr(*, "label")= chr "Study Day of Collection"
    ..- attr(*, "width")= num 8
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
    ..- attr(*, "width")= num 40
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
    ..- attr(*, "width")= num 40
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
    ..- attr(*, "width")= num 200
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
    ..- attr(*, "width")= num 200
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
    ..- attr(*, "width")= num 8
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
    ..- attr(*, "width")= num 200
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
    ..- attr(*, "width")= num 8
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
    ..- attr(*, "width")= num 8
   $ LSTALVDT: Date[1:306], format: "2014-07-02" ...
   $ AGEGR1  : Factor w/ 3 levels "<18","18-64",..: 2 2 3 3 3 3 2 3 3 3 ...
    ..- attr(*, "width")= num 20
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
    ..- attr(*, "width")= num 2
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
    ..- attr(*, "width")= num 200
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
    ..- attr(*, "width")= num 80
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
    ..- attr(*, "width")= num 200
   $ DTH30FL : chr [1:306] NA NA NA NA ...
    ..- attr(*, "width")= num 200
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
    ..- attr(*, "width")= num 200
   $ DTHB30FL: chr [1:306] NA NA NA NA ...
    ..- attr(*, "width")= num 200
   - attr(*, "_xportr.df_arg_")= chr "ADSL"

Note the additional attr(*, "width")= after each variable with the width. These have been directly applied from the specification file that we loaded above!

xportr_order()

Please note that the order of the ADSL variables, see above, does not match the specification file order column. We can quickly remedy this with a call to xportr_order(). Note that the variable SITEID has been moved as well as many others to match the specification file order column. Variables not in the spec are moved to the end of the data and a message is written to the console.

adsl_order <- xportr_order(adsl, var_spec, domain = "ADSL", verbose = "message")
  
  ── 3 variables not in spec and moved to end ──
  
  Variable moved to end in `.df`: `TRTSTMF`, `TRTETMF`, and `RANDDT`
  ── 48 reordered in dataset ──
  
  
  
  Variable reordered in `.df`: `SITEID`, `USUBJID`, `SUBJID`, `COUNTRY`, `AGE`, `AGEU`, `AGEGR1`, `SEX`, `RACE`, `RACEGR1`, `ETHNIC`, `RFSTDTC`, `RFENDTC`, `RFXSTDTC`, `RFXENDTC`, `RFICDTC`, `RFPENDTC`, `DMDTC`, `DMDY`, `SAFFL`, `ARM`, `ARMCD`, `ACTARM`, `ACTARMCD`, `TRT01P`, `TRT01A`, `TRTSDTM`, `TRTSDT`, `TRTEDT`, `DTHFL`, `DTHDTC`, `DTHDT`, `DTHADY`, `REGION1`, `TRTDURD`, `LDDTHELD`, `LSTALVDT`, `LDDTHGR1`, `DTH30FL`, `DTHA30FL`, `DTHB30FL`, `FRVDT`, `SCRFDT`, `EOSDT`, `EOSSTT`, `TRTSTMF`, `TRTETMF`, and `RANDDT`

xportr_format()

Now we apply formats to the dataset. These will typically be DATE9., DATETIME20 or TIME5, but many others can be used. Notice that in the ADSL dataset there are 8 Date/Time variables and they are missing formats. Here we just take a peak at a few TRT variables, which have a NULL format.

  # A tibble: 4 × 2
    Variable Format
    
  1 TRTSDT   
  2 TRTEDT   
  3 TRTSDTM  
  4 TRTEDTM  

Using our xportr_format() we can apply our formats to the dataset.

adsl_fmt <- adsl %>% xportr_format(var_spec, domain = "ADSL")
  # A tibble: 4 × 2
    Variable Format     
          
  1 TRTSDT   DATE9.     
  2 TRTEDT   DATE9.     
  3 TRTSDTM  DATETIME20.
  4 TRTEDTM  DATETIME20.

NOTE: You can use attr(data$variable, which = "format") to inspect formats applied to a dataframe. The above output has these individual calls bound together for easier viewing.

xportr_label()

Please observe that our ADSL dataset is missing many variable labels. Sometimes these labels can be lost while using R’s function. However, a CDISC compliant data set needs to have each variable with a label.

  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
   $ RFICDTC : chr [1:306] NA NA NA NA ...
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
   $ DTHFL   : chr [1:306] NA NA NA NA ...
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
   $ LSTALVDT: Date[1:306], format: "2014-07-02" ...
   $ AGEGR1  : Factor w/ 3 levels "<18","18-64",..: 2 2 3 3 3 3 2 3 3 3 ...
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
   $ DTH30FL : chr [1:306] NA NA NA NA ...
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
   $ DTHB30FL: chr [1:306] NA NA NA NA ...

Using the xport_label function we can take the specifications file and label all the variables available. xportr_label will produce a warning message if you the variable in the data set is not in the specification file.

adsl_lbl <- adsl %>% xportr_label(var_spec, domain = "ADSL", "message")
  ── Variable labels missing from metadata. ──
  
3 labels skipped
  Variable(s) present in dataframe but doesn't exist in `metadata`.
  ✖ Problem with `TRTSTMF`, `TRTETMF`, and `RANDDT`
str(adsl_lbl)
  tibble [306 × 50] (S3: tbl_df/tbl/data.frame)
   $ STUDYID : chr [1:306] "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" "CDISCPILOT01" ...
    ..- attr(*, "label")= chr "Study Identifier"
   $ USUBJID : chr [1:306] "01-701-1015" "01-701-1023" "01-701-1028" "01-701-1033" ...
    ..- attr(*, "label")= chr "Unique Subject Identifier"
   $ SUBJID  : chr [1:306] "1015" "1023" "1028" "1033" ...
    ..- attr(*, "label")= chr "Subject Identifier for the Study"
   $ RFSTDTC : chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Subject Reference Start Date/Time"
   $ RFENDTC : chr [1:306] "2014-07-02" "2012-09-02" "2014-01-14" "2014-04-14" ...
    ..- attr(*, "label")= chr "Subject Reference End Date/Time"
   $ RFXSTDTC: chr [1:306] "2014-01-02" "2012-08-05" "2013-07-19" "2014-03-18" ...
    ..- attr(*, "label")= chr "Date/Time of First Study Treatment"
   $ RFXENDTC: chr [1:306] "2014-07-02" "2012-09-01" "2014-01-14" "2014-03-31" ...
    ..- attr(*, "label")= chr "Date/Time of Last Study Treatment"
   $ RFICDTC : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date/Time of Informed Consent"
   $ RFPENDTC: chr [1:306] "2014-07-02T11:45" "2013-02-18" "2014-01-14T11:10" "2014-09-15" ...
    ..- attr(*, "label")= chr "Date/Time of End of Participation"
   $ DTHDTC  : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Date / Time of Death"
   $ DTHFL   : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Subject Death Flag"
   $ SITEID  : chr [1:306] "701" "701" "701" "701" ...
    ..- attr(*, "label")= chr "Study Site Identifier"
   $ AGE     : num [1:306] 63 64 71 74 77 85 59 68 81 84 ...
    ..- attr(*, "label")= chr "Age"
   $ AGEU    : chr [1:306] "YEARS" "YEARS" "YEARS" "YEARS" ...
    ..- attr(*, "label")= chr "Age Units"
   $ SEX     : chr [1:306] "F" "M" "M" "M" ...
    ..- attr(*, "label")= chr "Sex"
   $ RACE    : chr [1:306] "WHITE" "WHITE" "WHITE" "WHITE" ...
    ..- attr(*, "label")= chr "Race"
   $ ETHNIC  : chr [1:306] "HISPANIC OR LATINO" "HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" "NOT HISPANIC OR LATINO" ...
    ..- attr(*, "label")= chr "Ethnicity"
   $ ARMCD   : chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Planned Arm Code"
   $ ARM     : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Planned Arm"
   $ ACTARMCD: chr [1:306] "Pbo" "Pbo" "Xan_Hi" "Xan_Lo" ...
    ..- attr(*, "label")= chr "Actual Arm Code"
   $ ACTARM  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Description of Actual Arm"
   $ COUNTRY : chr [1:306] "USA" "USA" "USA" "USA" ...
    ..- attr(*, "label")= chr "Country"
   $ DMDTC   : chr [1:306] "2013-12-26" "2012-07-22" "2013-07-11" "2014-03-10" ...
    ..- attr(*, "label")= chr "Date/Time of Collection"
   $ DMDY    : num [1:306] -7 -14 -8 -8 -7 -21 NA -9 -13 -7 ...
    ..- attr(*, "label")= chr "Study Day of Collection"
   $ TRT01P  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Planned Treatment for Period 01"
   $ TRT01A  : chr [1:306] "Placebo" "Placebo" "Xanomeline High Dose" "Xanomeline Low Dose" ...
    ..- attr(*, "label")= chr "Actual Treatment for Period 01"
   $ TRTSDTM : POSIXct[1:306], format: "2014-01-02" ...
   $ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
    ..- attr(*, "label")= chr ""
   $ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" ...
   $ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
    ..- attr(*, "label")= chr ""
   $ TRTSDT  : Date[1:306], format: "2014-01-02" ...
   $ TRTEDT  : Date[1:306], format: "2014-07-02" ...
   $ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
    ..- attr(*, "label")= chr "Total Duration of Trt  (days)"
   $ SCRFDT  : Date[1:306], format: NA ...
   $ EOSDT   : Date[1:306], format: "2014-07-02" ...
   $ EOSSTT  : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
    ..- attr(*, "label")= chr "End of Study Status"
   $ FRVDT   : Date[1:306], format: NA ...
   $ RANDDT  : Date[1:306], format: "2014-01-02" ...
   $ DTHDT   : Date[1:306], format: NA ...
   $ DTHADY  : num [1:306] NA NA NA NA NA NA NA NA NA NA ...
    ..- attr(*, "label")= chr "Relative Day of Death"
   $ LDDTHELD: num [1:306] NA NA NA NA NA NA NA NA NA NA ...
    ..- attr(*, "label")= chr "Elapsed Days from Last Dose to Death"
   $ LSTALVDT: Date[1:306], format: "2014-07-02" ...
   $ AGEGR1  : Factor w/ 3 levels "<18","18-64",..: 2 2 3 3 3 3 2 3 3 3 ...
    ..- attr(*, "label")= chr "Pooled Age Group 1"
   $ SAFFL   : chr [1:306] "Y" "Y" "Y" "Y" ...
    ..- attr(*, "label")= chr "Safety Population Flag"
   $ RACEGR1 : chr [1:306] "White" "White" "White" "White" ...
    ..- attr(*, "label")= chr "Pooled Race Group 1"
   $ REGION1 : chr [1:306] "NA" "NA" "NA" "NA" ...
    ..- attr(*, "label")= chr "Geographic Region 1"
   $ LDDTHGR1: chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Last Does to Death Group"
   $ DTH30FL : chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Under 30  Group"
   $ DTHA30FL: chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Over 30  Group"
   $ DTHB30FL: chr [1:306] NA NA NA NA ...
    ..- attr(*, "label")= chr "Over 30 plus 30 days Group"
   - attr(*, "_xportr.df_arg_")= chr "ADSL"

xportr_write()

Finally, we arrive at exporting the R data frame object as a xpt file with xportr_write(). The xpt file will be written directly to your current working directory. To make it more interesting, we have put together all six functions with the magrittr pipe, %>%. A user can now apply types, length, variable labels, formats, data set label and write out their final xpt file in one pipe! Appropriate warnings and messages will be supplied to a user to the console for any potential issues before sending off to standard clinical data set validator application or data reviewers.

adsl %>%
  xportr_type(var_spec, "ADSL", "message") %>%
  xportr_length(var_spec, "ADSL", "message") %>%
  xportr_label(var_spec, "ADSL", "message") %>%
  xportr_order(var_spec, "ADSL", "message") %>%
  xportr_format(var_spec, "ADSL") %>%
  xportr_write("adsl.xpt", label = "Subject-Level Analysis Dataset")
  
  ── Variable type mismatches found. ──
  
2 variables coerced
  Variable type(s) in dataframe don't match metadata: `LSTALVDT` and `AGEGR1`
  
  
  ── Variable lengths missing from metadata. ──
  
  
  
  ✔ 3 lengths resolved
  
  Variable(s) present in dataframe but doesn't exist in `metadata`.Problem with `TRTSTMF`, `TRTETMF`, and `RANDDT`
  
  
  ── Variable labels missing from metadata. ──
  
  
  
3 labels skipped
  
  Variable(s) present in dataframe but doesn't exist in `metadata`.
  ✖ Problem with `TRTSTMF`, `TRTETMF`, and `RANDDT`
  
  
  ── 3 variables not in spec and moved to end ──
  
  
  
  Variable moved to end in `.df`: `TRTSTMF`, `TRTETMF`, and `RANDDT`
  ── 48 reordered in dataset ──
  
  
  
  Variable reordered in `.df`: `SITEID`, `USUBJID`, `SUBJID`, `COUNTRY`, `AGE`, `AGEU`, `AGEGR1`, `SEX`, `RACE`, `RACEGR1`, `ETHNIC`, `RFSTDTC`, `RFENDTC`, `RFXSTDTC`, `RFXENDTC`, `RFICDTC`, `RFPENDTC`, `DMDTC`, `DMDY`, `SAFFL`, `ARM`, `ARMCD`, `ACTARM`, `ACTARMCD`, `TRT01P`, `TRT01A`, `TRTSDTM`, `TRTSDT`, `TRTEDT`, `DTHFL`, `DTHDTC`, `DTHDT`, `DTHADY`, `REGION1`, `TRTDURD`, `LDDTHELD`, `LSTALVDT`, `LDDTHGR1`, `DTH30FL`, `DTHA30FL`, `DTHB30FL`, `FRVDT`, `SCRFDT`, `EOSDT`, `EOSSTT`, `TRTSTMF`, `TRTETMF`, and `RANDDT`

That’s it! We now have a xpt file created in R with all appropriate types, lengths, labels, ordering and formats from our specification file. If you are interested in exploring more of the custom warnings and error messages as well as more background on xpt generation be sure to check out the Deep Dive User Guide.

As always, we welcome your feedback. If you spot a bug, would like to see a new feature, or if any documentation is unclear - submit an issue on xportr’s GitHub page.