4.1 External Data

Data may be directly imported into the R environment using packages. Most often, data will take the form of Comma Separated Values (.csv), Excel Spreadsheets (.xlsx), SAS (.sas7bdat) or JSON (.json).

Package Formats Reference
readr .csv, .txt Cheat Sheet
readxl .xls, .xlsx Cheat Sheet
haven .sas7bdat, .sas7bcat, .xpt Package Site
jsonlite .json Vignette

4.1.1 CDISC Datasets

The PHUSE Test Datasets Factory provides a convenient set CDISC datasets in xpt format to experiment with. You may access them through the following github repositories:

Below is an example of using the haven package to read in adsl.xpt directly from the ADaM repository. Note you can also chose to download these data and read them locally from your computer.

library(haven)

adsl <- read_xpt("https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/adsl.xpt")
STUDYID USUBJID SUBJID SITEID SITEGR1 ARM TRT01P TRT01PN TRT01A TRT01AN TRTSDT TRTEDT TRTDURD AVGDD CUMDOSE AGE AGEGR1 AGEGR1N AGEU RACE RACEN SEX ETHNIC SAFFL ITTFL EFFFL COMP8FL COMP16FL COMP24FL DISCONFL DSRAEFL DTHFL BMIBL BMIBLGR1 HEIGHTBL WEIGHTBL EDUCLVL DISONSDT DURDIS DURDSGR1 VISIT1DT RFSTDTC RFENDTC VISNUMEN RFENDT DCDECOD EOSSTT DCSREAS MMSETOT
CDISCPILOT01 01-701-1015 1015 701 701 Placebo Placebo 0 Placebo 0 2014-01-02 2014-07-02 182 0.0 0 63 <65 1 YEARS WHITE 1 F HISPANIC OR LATINO Y Y Y Y Y Y 25.1 25-<30 147.3 54.4 16 2010-04-30 43.9
=12
2013-12-26 2014-01-02 2014-07-02 12 2014-07-02 COMPLETED COMPLETED 23
CDISCPILOT01 01-701-1023 1023 701 701 Placebo Placebo 0 Placebo 0 2012-08-05 2012-09-01 28 0.0 0 64 <65 1 YEARS WHITE 1 M HISPANIC OR LATINO Y Y Y N N N Y Y 30.4
=30
162.6 80.3 14 2006-03-11 76.4
=12
2012-07-22 2012-08-05 2012-09-02 5 2012-09-02 ADVERSE EVENT DISCONTINUED Adverse Event 23
CDISCPILOT01 01-701-1028 1028 701 701 Xanomeline High Dose Xanomeline High Dose 81 Xanomeline High Dose 81 2013-07-19 2014-01-14 180 77.7 13986 71 65-80 2 YEARS WHITE 1 M NOT HISPANIC OR LATINO Y Y Y Y Y Y 31.4
=30
177.8 99.3 16 2009-12-16 42.8
=12
2013-07-11 2013-07-19 2014-01-14 12 2014-01-14 COMPLETED COMPLETED 23
CDISCPILOT01 01-701-1033 1033 701 701 Xanomeline Low Dose Xanomeline Low Dose 54 Xanomeline Low Dose 54 2014-03-18 2014-03-31 14 54.0 756 74 65-80 2 YEARS WHITE 1 M NOT HISPANIC OR LATINO Y Y Y N N N Y 28.8 25-<30 175.3 88.5 12 2009-08-02 55.3
=12
2014-03-10 2014-03-18 2014-04-14 5 2014-04-14 STUDY TERMINATED BY SPONSOR DISCONTINUED Sponsor Decision 23
CDISCPILOT01 01-701-1034 1034 701 701 Xanomeline High Dose Xanomeline High Dose 81 Xanomeline High Dose 81 2014-07-01 2014-12-30 183 76.9 14067 77 65-80 2 YEARS WHITE 1 F NOT HISPANIC OR LATINO Y Y Y Y Y Y 26.1 25-<30 154.9 62.6 9 2011-09-29 32.9
=12
2014-06-24 2014-07-01 2014-12-30 12 2014-12-30 COMPLETED COMPLETED 21