Read and write Dataset-JSON files.
# install.packages("remotes")
remotes::install_github("ramiromagno/dataset.json")Examples Dataset-JSON files are borrowed from DataExchange-DatasetJson/examples.
For the bundled example files, run:
library(dataset.json)
print(ds_json_example_path(), n = Inf)
#> # A tibble: 33 × 4
#> name file rel_path abs_path
#> <chr> <chr> <chr> <chr>
#> 1 adae adae.json adam/adae.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 2 adcibc adcibc.json adam/adcibc.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 3 adsl adsl.json adam/adsl.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 4 adtte adtte.json adam/adtte.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 5 ae_i18n ae_i18n.json sdtm/ae_i18n.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 6 ae ae.json sdtm/ae.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 7 cm cm.json sdtm/cm.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 8 dd dd.json sdtm/dd.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 9 di di.json sdtm/di.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 10 dm dm.json sdtm/dm.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 11 ds ds.json sdtm/ds.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 12 ec ec.json sdtm/ec.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 13 ex ex.json sdtm/ex.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 14 fa fa.json sdtm/fa.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 15 ft ft.json sdtm/ft.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 16 ie ie.json sdtm/ie.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 17 lb lb.json sdtm/lb.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 18 mh mh.json sdtm/mh.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 19 oe oe.json sdtm/oe.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 20 qsph qsph.json sdtm/qsph.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 21 qssl qssl.json sdtm/qssl.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 22 relrec relrec.json sdtm/relrec.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 23 rs rs.json sdtm/rs.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 24 se se.json sdtm/se.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 25 suppdm suppdm.json sdtm/suppdm.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 26 suppec suppec.json sdtm/suppec.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 27 sv sv.json sdtm/sv.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 28 ta ta.json sdtm/ta.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 29 te te.json sdtm/te.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 30 ti ti.json sdtm/ti.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 31 ts ts.json sdtm/ts.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 32 tv tv.json sdtm/tv.json /home/rmagno/R/x86_64-pc-linux-gnu-li…
#> 33 vs vs.json sdtm/vs.json /home/rmagno/R/x86_64-pc-linux-gnu-li…Here is an example where you read a Adverse Events domain dataset:
# Example file: ae.json
ae <- read_ds_json(ds_json_example_path("ae"))
# Domain
ae@clinicalData@itemGroupData@name
#> [1] "AE"
ae@clinicalData@itemGroupData@label
#> [1] "Adverse Events"
# Dataset
ae@clinicalData@itemGroupData@itemData
#> # A tibble: 74 × 38
#> ITEMGROUPDATASEQ STUDYID DOMAIN USUBJID AESEQ AELNKID AETERM AELLT AELLTCD
#> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 1 CDISCPILO… AE CDISC0… 1 1 INJEC… <NA> <NA>
#> 2 2 CDISCPILO… AE CDISC0… 2 2 FATIG… <NA> <NA>
#> 3 3 CDISCPILO… AE CDISC0… 1 1 INJEC… <NA> <NA>
#> 4 4 CDISCPILO… AE CDISC0… 2 2 SHOUL… <NA> <NA>
#> 5 5 CDISCPILO… AE CDISC0… 3 3 JOINT… <NA> <NA>
#> 6 6 CDISCPILO… AE CDISC0… 4 4 INCON… <NA> <NA>
#> 7 7 CDISCPILO… AE CDISC0… 5 5 INJEC… <NA> <NA>
#> 8 8 CDISCPILO… AE CDISC0… 6 6 SKIN … <NA> <NA>
#> 9 9 CDISCPILO… AE CDISC0… 7 7 CONFU… <NA> <NA>
#> 10 10 CDISCPILO… AE CDISC0… 8 8 DYSPN… <NA> <NA>
#> # ℹ 64 more rows
#> # ℹ 29 more variables: AEDECOD <chr>, AEPTCD <chr>, AEHLT <chr>, AEHLTCD <chr>,
#> # AEHLGT <chr>, AEHLGTCD <chr>, AEBODSYS <chr>, AEBDSYCD <chr>, AESOC <chr>,
#> # AESOCCD <chr>, AESEV <chr>, AESER <chr>, AEACN <chr>, AEREL <chr>,
#> # AEOUT <chr>, AESCAN <chr>, AESCONG <chr>, AESDISAB <chr>, AESDTH <chr>,
#> # AESHOSP <chr>, AESLIFE <chr>, AESOD <chr>, EPOCH <chr>, AESTDTC <chr>,
#> # AEENDTC <chr>, AESTDY <dbl>, AEENDY <dbl>, AEENRTPT <chr>, AEENTPT <chr>And here an example of an ADaM dataset: Subject-Level Analysis.
# Example file: adsl.json
adsl <- read_ds_json(ds_json_example_path("adsl"))
# Domain
adsl@clinicalData@itemGroupData@name
#> [1] "ADSL"
adsl@clinicalData@itemGroupData@label
#> [1] "Subject-Level Analysis"
# Dataset
adsl@clinicalData@itemGroupData@itemData
#> # A tibble: 254 × 50
#> ITEMGROUPDATASEQ STUDYID USUBJID SUBJID SITEID SITEGR1 ARM TRT01P TRT01PN
#> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 1 CDISCPIL… 01-701… 1015 701 701 Plac… Place… 0
#> 2 2 CDISCPIL… 01-701… 1023 701 701 Plac… Place… 0
#> 3 3 CDISCPIL… 01-701… 1028 701 701 Xano… Xanom… 81
#> 4 4 CDISCPIL… 01-701… 1033 701 701 Xano… Xanom… 54
#> 5 5 CDISCPIL… 01-701… 1034 701 701 Xano… Xanom… 81
#> 6 6 CDISCPIL… 01-701… 1047 701 701 Plac… Place… 0
#> 7 7 CDISCPIL… 01-701… 1097 701 701 Xano… Xanom… 54
#> 8 8 CDISCPIL… 01-701… 1111 701 701 Xano… Xanom… 54
#> 9 9 CDISCPIL… 01-701… 1115 701 701 Xano… Xanom… 54
#> 10 10 CDISCPIL… 01-701… 1118 701 701 Plac… Place… 0
#> # ℹ 244 more rows
#> # ℹ 41 more variables: TRT01A <chr>, TRT01AN <dbl>, TRTSDT <dbl>, TRTEDT <dbl>,
#> # TRTDURD <dbl>, AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>,
#> # AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>,
#> # ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>,
#> # COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>,
#> # BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, …TODO.