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").
The ADSL has the following features:
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:
xportr_type()xportr_length()xportr_order()xportr_format()xportr_label()xportr_write()# Loading packages
library(dplyr)
library(labelled)
library(xportr)
library(admiral)
# Loading in our example data
adsl <- admiral::admiral_adslNOTE: Dataset can be created by using this command
admiral::use_ad_template("adsl").
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 <- readxl::read_xlsx(
system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr"), sheet = "Variables") %>%
dplyr::rename(type = "Data Type") %>%
rlang::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.
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.
look_for(adsl, details = TRUE)
pos variable label col_type values
1 STUDYID Study Identifier chr range: CDISCPILOT01 - CDI~
2 USUBJID Unique Subject Identifier chr range: 01-701-1015 - 01-7~
3 SUBJID Subject Identifier for th~ chr range: 1001 - 1448
4 RFSTDTC Subject Reference Start D~ chr range: 2012-07-09 - 2014-~
5 RFENDTC Subject Reference End Dat~ chr range: 2012-09-01 - 2015-~
6 RFXSTDTC Date/Time of First Study ~ chr range: 2012-07-09 - 2014-~
7 RFXENDTC Date/Time of Last Study T~ chr range: 2012-08-28 - 2015-~
8 RFICDTC Date/Time of Informed Con~ chr range:
9 RFPENDTC Date/Time of End of Parti~ chr range: 2012-08-13 - 2015-~
10 DTHDTC Date/Time of Death chr range: 2013-01-14 - 2014-~
11 DTHFL Subject Death Flag chr range: Y - Y
12 SITEID Study Site Identifier chr range: 701 - 718
13 AGE Age dbl range: 50 - 89
14 AGEU Age Units chr range: YEARS - YEARS
15 SEX Sex chr range: F - M
16 RACE Race chr range: AMERICAN INDIAN OR~
17 ETHNIC Ethnicity chr range: HISPANIC OR LATINO~
18 ARMCD Planned Arm Code chr range: Pbo - Xan_Lo
19 ARM Description of Planned Arm chr range: Placebo - Xanomeli~
20 ACTARMCD Actual Arm Code chr range: Pbo - Xan_Lo
21 ACTARM Description of Actual Arm chr range: Placebo - Xanomeli~
22 COUNTRY Country chr range: USA - USA
23 DMDTC Date/Time of Collection chr range: 2012-07-06 - 2014-~
24 DMDY Study Day of Collection dbl range: -37 - -2
25 TRT01P Description of Planned Arm chr range: Placebo - Xanomeli~
26 TRT01A Description of Actual Arm chr range: Placebo - Xanomeli~
27 TRTSDTM — dttm range: 2012-07-09 - 2014-~
28 TRTSTMF — chr range: H - H
29 TRTEDTM — dttm range: 2012-08-28 23:59:5~
30 TRTETMF — chr range: H - H
31 TRTSDT — date range: 2012-07-09 - 2014-~
32 TRTEDT — date range: 2012-08-28 - 2015-~
33 TRTDURD — dbl range: 1 - 212
34 SCRFDT — date range: 2012-08-13 - 2014-~
35 EOSDT — date range: 2012-09-01 - 2015-~
36 EOSSTT — chr range: COMPLETED - DISCON~
37 FRVDT — date range: 2013-02-18 - 2014-~
38 RANDDT — date range: 2012-07-09 - 2014-~
39 DTHDT — date range: 2013-01-14 - 2014-~
40 DTHADY — dbl range: 12 - 175
41 LDDTHELD — dbl range: 0 - 2
42 LSTALVDT — date range: 2012-09-01 - 2015-~
43 AGEGR1 — fct <18
18-64
>=65
44 SAFFL — chr range: Y - Y
45 RACEGR1 — chr range: Non-white - White
46 REGION1 — chr range: NA - NA
47 LDDTHGR1 — chr range: <= 30 - <= 30
48 DTH30FL — chr range: Y - Y
49 DTHA30FL — chr range:
50 DTHB30FL — chr range: Y - YUsing xport_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")
Now all appropriate types have been applied to the dataset as
seen below.
look_for(adsl_type, details = TRUE)
pos variable label col_type values
1 STUDYID — dbl range:
2 USUBJID — dbl range:
3 SUBJID — dbl range: 1001 - 1448
4 RFSTDTC — dbl range:
5 RFENDTC — dbl range:
6 RFXSTDTC — dbl range:
7 RFXENDTC — dbl range:
8 RFICDTC — dbl range:
9 RFPENDTC — dbl range:
10 DTHDTC — dbl range:
11 DTHFL — dbl range:
12 SITEID — dbl range: 701 - 718
13 AGE — dbl range: 50 - 89
14 AGEU — dbl range:
15 SEX — dbl range:
16 RACE — dbl range:
17 ETHNIC — dbl range:
18 ARMCD — dbl range:
19 ARM — dbl range:
20 ACTARMCD — dbl range:
21 ACTARM — dbl range:
22 COUNTRY — dbl range:
23 DMDTC — dbl range:
24 DMDY — dbl range: -37 - -2
25 TRT01P — dbl range:
26 TRT01A — dbl range:
27 TRTSDTM — dbl range: 1341792000 - 1409616000
28 TRTSTMF — chr range: H - H
29 TRTEDTM — dbl range: 1346198399 - 1425599999
30 TRTETMF — chr range: H - H
31 TRTSDT — dbl range: 15530 - 16315
32 TRTEDT — dbl range: 15580 - 16499
33 TRTDURD — dbl range: 1 - 212
34 SCRFDT — dbl range: 15565 - 16181
35 EOSDT — dbl range: 15584 - 16499
36 EOSSTT — dbl range:
37 FRVDT — dbl range: 15754 - 16389
38 RANDDT — chr range: 2012-07-09 - 2014-09-02
39 DTHDT — dbl range: 15719 - 16375
40 DTHADY — dbl range: 12 - 175
41 LDDTHELD — dbl range: 0 - 2
42 LSTALVDT — dbl range: 15584 - 16499
43 AGEGR1 — dbl range: 2 - 3
44 SAFFL — dbl range:
45 RACEGR1 — dbl range:
46 REGION1 — dbl range:
47 LDDTHGR1 — dbl range:
48 DTH30FL — dbl range:
49 DTHA30FL — dbl range:
50 DTHB30FL — dbl range: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.
str(adsl) tbl_df [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" "2012-08-05" ...
$ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
$ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" "2012-09-01 23:59:59" ...
$ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
$ TRTSDT : Date[1:306], format: "2014-01-02" "2012-08-05" ...
$ TRTEDT : Date[1:306], format: "2014-07-02" "2012-09-01" ...
$ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
$ SCRFDT : Date[1:306], format: NA NA ...
$ EOSDT : Date[1:306], format: "2014-07-02" "2012-09-02" ...
$ EOSSTT : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
$ FRVDT : Date[1:306], format: NA "2013-02-18" ...
$ RANDDT : Date[1:306], format: "2014-01-02" "2012-08-05" ...
$ DTHDT : Date[1:306], format: NA 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" "2012-09-02" ...
$ 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`str(adsl_length) tbl_df [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" "2012-08-05" ...
$ TRTSTMF : chr [1:306] "H" "H" "H" "H" ...
..- attr(*, "width")= num 200
$ TRTEDTM : POSIXct[1:306], format: "2014-07-02 23:59:59" "2012-09-01 23:59:59" ...
$ TRTETMF : chr [1:306] "H" "H" "H" "H" ...
..- attr(*, "width")= num 200
$ TRTSDT : Date[1:306], format: "2014-01-02" "2012-08-05" ...
$ TRTEDT : Date[1:306], format: "2014-07-02" "2012-09-01" ...
$ TRTDURD : num [1:306] 182 28 180 14 183 26 NA 190 10 55 ...
..- attr(*, "width")= num 8
$ SCRFDT : Date[1:306], format: NA NA ...
$ EOSDT : Date[1:306], format: "2014-07-02" "2012-09-02" ...
$ EOSSTT : chr [1:306] "COMPLETED" "DISCONTINUED" "COMPLETED" "DISCONTINUED" ...
..- attr(*, "width")= num 200
$ FRVDT : Date[1:306], format: NA "2013-02-18" ...
$ RANDDT : Date[1:306], format: "2014-01-02" "2012-08-05" ...
$ DTHDT : Date[1:306], format: NA 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" "2012-09-02" ...
$ 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!
Please note that the order of the ADSL variables, see
above, does not match 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.
adsl_order <- xportr_order(adsl,var_spec, domain = "ADSL", verbose = "message") Now we apply formats to the dataset. These will typically be
DATE9., DATETIME20 or TIME5, but
many others can be used. Notice that 8 Date/Time variables are missing a
format in our ADSL dataset. Here we just take a peak at a
few TRT variables, which have a NULL
format.
attr(adsl$TRTSDT, "format.sas")
NULL
attr(adsl$TRTEDT, "format.sas")
NULL
attr(adsl$TRTSDTM, "format.sas")
NULL
attr(adsl$TRTEDTM, "format.sas")
NULLUsing our xportr_format() we apply our formats.
adsl_fmt <- adsl %>% xportr_format(var_spec, domain = "ADSL", "message")attr(adsl_fmt$TRTSDT, "format.sas")
[1] "DATE9."
attr(adsl_fmt$TRTEDT, "format.sas")
[1] "DATE9."
attr(adsl_fmt$TRTSDTM, "format.sas")
[1] "DATETIME20."
attr(adsl_fmt$TRTEDTM, "format.sas")
[1] "DATETIME20."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 variable label.
look_for(adsl, details = FALSE)
pos variable label
1 STUDYID Study Identifier
2 USUBJID Unique Subject Identifier
3 SUBJID Subject Identifier for the Study
4 RFSTDTC Subject Reference Start Date/Time
5 RFENDTC Subject Reference End Date/Time
6 RFXSTDTC Date/Time of First Study Treatment
7 RFXENDTC Date/Time of Last Study Treatment
8 RFICDTC Date/Time of Informed Consent
9 RFPENDTC Date/Time of End of Participation
10 DTHDTC Date/Time of Death
11 DTHFL Subject Death Flag
12 SITEID Study Site Identifier
13 AGE Age
14 AGEU Age Units
15 SEX Sex
16 RACE Race
17 ETHNIC Ethnicity
18 ARMCD Planned Arm Code
19 ARM Description of Planned Arm
20 ACTARMCD Actual Arm Code
21 ACTARM Description of Actual Arm
22 COUNTRY Country
23 DMDTC Date/Time of Collection
24 DMDY Study Day of Collection
25 TRT01P Description of Planned Arm
26 TRT01A Description of Actual Arm
27 TRTSDTM —
28 TRTSTMF —
29 TRTEDTM —
30 TRTETMF —
31 TRTSDT —
32 TRTEDT —
33 TRTDURD —
34 SCRFDT —
35 EOSDT —
36 EOSSTT —
37 FRVDT —
38 RANDDT —
39 DTHDT —
40 DTHADY —
41 LDDTHELD —
42 LSTALVDT —
43 AGEGR1 —
44 SAFFL —
45 RACEGR1 —
46 REGION1 —
47 LDDTHGR1 —
48 DTH30FL —
49 DTHA30FL —
50 DTHB30FL —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_update <- 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`look_for(adsl_update, details = FALSE)
pos variable label
1 STUDYID Study Identifier
2 USUBJID Unique Subject Identifier
3 SUBJID Subject Identifier for the Study
4 RFSTDTC Subject Reference Start Date/Time
5 RFENDTC Subject Reference End Date/Time
6 RFXSTDTC Date/Time of First Study Treatment
7 RFXENDTC Date/Time of Last Study Treatment
8 RFICDTC Date/Time of Informed Consent
9 RFPENDTC Date/Time of End of Participation
10 DTHDTC Date / Time of Death
11 DTHFL Subject Death Flag
12 SITEID Study Site Identifier
13 AGE Age
14 AGEU Age Units
15 SEX Sex
16 RACE Race
17 ETHNIC Ethnicity
18 ARMCD Planned Arm Code
19 ARM Description of Planned Arm
20 ACTARMCD Actual Arm Code
21 ACTARM Description of Actual Arm
22 COUNTRY Country
23 DMDTC Date/Time of Collection
24 DMDY Study Day of Collection
25 TRT01P Planned Treatment for Period 01
26 TRT01A Actual Treatment for Period 01
27 TRTSDTM Datetime of First Exposure to Treatment
28 TRTSTMF
29 TRTEDTM Datetime of Last Exposure to Treatment
30 TRTETMF
31 TRTSDT Date of First Exposure to Treatment
32 TRTEDT Date of Last Exposure to Treatment
33 TRTDURD Total Duration of Trt (days)
34 SCRFDT Screen Failure Date
35 EOSDT End of Study Date
36 EOSSTT End of Study Status
37 FRVDT Final Retrievel Visit Date
38 RANDDT
39 DTHDT Death Date
40 DTHADY Relative Day of Death
41 LDDTHELD Elapsed Days from Last Dose to Death
42 LSTALVDT Date Last Known Alive
43 AGEGR1 Pooled Age Group 1
44 SAFFL Safety Population Flag
45 RACEGR1 Pooled Race Group 1
46 REGION1 Geographic Region 1
47 LDDTHGR1 Last Does to Death Group
48 DTH30FL Under 30 Group
49 DTHA30FL Over 30 Group
50 DTHB30FL Over 30 plus 30 days GroupFinally, we arrive at exporting the R data frame object as a xpt file
with the function 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", "message") %>%
xportr_write("adsl.xpt", label = "Subject-Level Analysis Dataset")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.
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.