The intent of this package is to provide convenient access to study data in Castor via R.
Access to data in the API comes in three forms:
- Access to individual items (getStudyDataPoint, getStudy, getRecord, etc.)
- Access to pages of items in a list (getStudyDataPoints, getStudies, getRecords, etc.)
- Processed into a data frame for straightforward analysis (getStudyData)
# install.packages("remotes")
remotes::install_github("castoredc/castoRedc")In the package, user missing data is handled in the following way. For date variables, they are represented by 31-12-29XX, where XX (95-99) indicates the type of missing data. For numeric variables, they are represented by the values -99 to -95, where 95 to 99 represent the type of missing data in Castor. For non-numeric variables, they are represented by ##_USER_MISSING_XX## where XX (95-99) indicates the type of missing data.
If you want to test the package, for example when developing, please
fill in create_testing_credentials.R.
You should supply an example for each of the study, report, etc. Please
make sure that the record has a value in the field. And that the report
step is a child of the report.
See https://helpdesk.castoredc.com/article/124-application-programming-interface-api about generating your credentials.
Note: It is recommended that you read https://cran.r-project.org/web/packages/httr/vignettes/secrets.html about managing your credentials.
library(castoRedc)
castor_api <- CastorData$new(key = credentials$client_id,
secret = credentials$client_secret,
base_url = "https://data.castoredc.com")studies <- castor_api$getStudies()| crf_id | study_id | name | created_by | created_on | trial_registry_id | live | randomization_enabled | gcp_enabled | surveys_enabled | premium_support_enabled | main_contact | expected_centers | expected_records | slug | version | duration | domain | _links.self.href |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88 | 15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88 | PythonWrapperTest - Study | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2021-06-22 07:50:12 | TRUE | FALSE | TRUE | TRUE | FALSE | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 1 | 180 | ESXnzDc2zuKJ7fFjEnUCu5 | 0.21 | 12 | https://data.castoredc.com | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88 | |
| 1BCD52D3-7AB3-4EA9-8ABE-74B4B7087001 | 1BCD52D3-7AB3-4EA9-8ABE-74B4B7087001 | PythonWrapperTest - Client (Write) | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2022-06-28 07:13:41 | TRUE | TRUE | TRUE | TRUE | FALSE | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 1 | 100 | 8pDFJAdy4m3Kf8fZEMRxw6 | 0.01 | 24 | https://data.castoredc.com | https://data.castoredc.com/api/study/1BCD52D3-7AB3-4EA9-8ABE-74B4B7087001 | |
| C6073904-2B46-4F38-B359-A455FC255920 | C6073904-2B46-4F38-B359-A455FC255920 | PythonWrapperTest - Import | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2021-03-12 12:47:30 | TRUE | FALSE | FALSE | TRUE | FALSE | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 1 | 50 | ThTvYFAxJFodP35aATLKFd | 0.21 | 27 | https://data.castoredc.com | https://data.castoredc.com/api/study/C6073904-2B46-4F38-B359-A455FC255920 | |
| D234215B-D956-482D-BF17-71F2BB12A2FD | D234215B-D956-482D-BF17-71F2BB12A2FD | PythonWrapperTest - Client | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2019-09-23 08:12:48 | TRUE | TRUE | TRUE | TRUE | FALSE | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2 | 50 | python-wrapper | 0.61 | 15 | https://data.castoredc.com | https://data.castoredc.com/api/study/D234215B-D956-482D-BF17-71F2BB12A2FD | |
| D82A17DE-E280-4D69-B96A-4399872BBECC | D82A17DE-E280-4D69-B96A-4399872BBECC | PythonWrapperTest - SpecialCases | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 2022-01-03 13:52:27 | TRUE | FALSE | TRUE | TRUE | FALSE | B23ABCC4-3A53-FB32-7B78-3960CC907F25 | 1 | 500 | p8CPbd2rnbBFkb2oW5GFUg | 1.11 | 60 | https://data.castoredc.com | https://data.castoredc.com/api/study/D82A17DE-E280-4D69-B96A-4399872BBECC |
(example_study_id <- studies[["study_id"]][1])
#> [1] "15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88"study <- castor_api$getStudyData(example_study_id)
|
|
|
fields <- castor_api$getFields(example_study_id)| id | parent_id | field_id | field_number | field_label | field_variable_name | field_type | field_required | field_hidden | field_info | field_units | field_min | field_min_label | field_max | field_max_label | field_enforce_decimals | field_slider_step | field_slider_step_value | field_image | report_id | field_length | additional_config | exclude_on_data_export | option_group | metadata_points | validations | dependency_parents | dependency_children | randomize_option_order | _links.self.href | option_group.id | option_group.name | option_group.description | option_group.layout | option_group.fields | option_group.options |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 00A3BB37-1532-400E-8BBC-529FF5D63317 | 6D2A7286-685C-4A78-9641-929E233E41E2 | 00A3BB37-1532-400E-8BBC-529FF5D63317 | 7 | Record all relevant received therapy | NA | repeated_measures | 0 | 0 | NA | NA | NA | NA | NA | F3F1C353-A3DC-42B4-8B47-B2DF56E8B3BF | NA | {“showReportOfAllPhases”:“0”} | FALSE | NA | NULL | NULL | NULL | NULL | FALSE | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/field/00A3BB37-1532-400E-8BBC-529FF5D63317 | NA | NA | NA | NA | NULL | NULL | |||||
| 02E4E21B-0AAA-4C89-980F-414D37E25BE5 | 88CA5E48-2A1B-4179-9908-F090B62E44A0 | 02E4E21B-0AAA-4C89-980F-414D37E25BE5 | 1 | To randomize this patient, click on the ‘Randomize’ button in the Randomization tab. | NA | remark | 0 | 0 | NA | NA | NA | NA | NA | NA | FALSE | NA | NULL | NULL | NULL | NULL | FALSE | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/field/02E4E21B-0AAA-4C89-980F-414D37E25BE5 | NA | NA | NA | NA | NULL | NULL | |||||||
| 04E40C4C-3AA0-42D3-AE27-F40879366A84 | 4E1682D3-9611-4B1A-84C4-14FCEBA15248 | 04E40C4C-3AA0-42D3-AE27-F40879366A84 | 1 | Describe the adverse event | AE_type | textarea | 1 | 0 | NA | NA | NA | NA | NA | NA | FALSE | NA | NULL | NULL | NULL | NULL | FALSE | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/field/04E40C4C-3AA0-42D3-AE27-F40879366A84 | NA | NA | NA | NA | NULL | NULL |
forms <- castor_api$getForms(example_study_id)| id | form_id | form_name | form_order | form_description | _embedded.visit.id | _embedded.visit.visit_id | _embedded.visit.visit_description | _embedded.visit.visit_name | _embedded.visit.visit_duration | _embedded.visit.visit_number | _embedded.visit.visit_order | _embedded.visit._links.self.href | _links.self.href |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10B74382-3EA9-4107-85BC-C33B9BA078CA | 10B74382-3EA9-4107-85BC-C33B9BA078CA | Physical exam | 8 | This is a copy of the Baseline Physical exam step. | 62EDEB24-7616-4476-912D-2F280FB56E36 | 62EDEB24-7616-4476-912D-2F280FB56E36 | NA | Follow-up Visit | NA | NA | 3 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/62EDEB24-7616-4476-912D-2F280FB56E36 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/10B74382-3EA9-4107-85BC-C33B9BA078CA |
| 287CE537-8910-4A0A-95A2-3683E48B548E | 287CE537-8910-4A0A-95A2-3683E48B548E | Study inclusion | 2 | This form contains Inclusion Criteria information. | EFEDE30F-0D61-468D-B67D-92465ACB0108 | EFEDE30F-0D61-468D-B67D-92465ACB0108 | NA | Informed Consent and Inclusion | NA | NA | 1 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/EFEDE30F-0D61-468D-B67D-92465ACB0108 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/287CE537-8910-4A0A-95A2-3683E48B548E |
| 2D15033E-59B8-4BF3-A5BA-5AF82F1870C1 | 2D15033E-59B8-4BF3-A5BA-5AF82F1870C1 | Demographics | 3 | This form contains Demographic information. | EFEDE30F-0D61-468D-B67D-92465ACB0108 | EFEDE30F-0D61-468D-B67D-92465ACB0108 | NA | Informed Consent and Inclusion | NA | NA | 1 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/EFEDE30F-0D61-468D-B67D-92465ACB0108 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/2D15033E-59B8-4BF3-A5BA-5AF82F1870C1 |
| 31B909EC-39C5-4C94-ADAF-30C62E039288 | 31B909EC-39C5-4C94-ADAF-30C62E039288 | Laboratory | 7 | This form contains hematology and biochemistry data. | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | NA | Baseline | NA | NA | 2 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/31B909EC-39C5-4C94-ADAF-30C62E039288 |
| 4366B99E-610D-4082-BEC8-F93A59A8F01A | 4366B99E-610D-4082-BEC8-F93A59A8F01A | Consent | 1 | This form contains informed consent information. | EFEDE30F-0D61-468D-B67D-92465ACB0108 | EFEDE30F-0D61-468D-B67D-92465ACB0108 | NA | Informed Consent and Inclusion | NA | NA | 1 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/EFEDE30F-0D61-468D-B67D-92465ACB0108 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/4366B99E-610D-4082-BEC8-F93A59A8F01A |
| 5349E9D7-A0E6-49A2-93A4-B66A38291048 | 5349E9D7-A0E6-49A2-93A4-B66A38291048 | Physical exam | 6 | This form contains physical exam data from the first visit. | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | NA | Baseline | NA | NA | 2 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/5349E9D7-A0E6-49A2-93A4-B66A38291048 |
| 6D2A7286-685C-4A78-9641-929E233E41E2 | 6D2A7286-685C-4A78-9641-929E233E41E2 | Medical history | 4 | This form contains Medical history information. | EFEDE30F-0D61-468D-B67D-92465ACB0108 | EFEDE30F-0D61-468D-B67D-92465ACB0108 | NA | Informed Consent and Inclusion | NA | NA | 1 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/EFEDE30F-0D61-468D-B67D-92465ACB0108 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/6D2A7286-685C-4A78-9641-929E233E41E2 |
| 88CA5E48-2A1B-4179-9908-F090B62E44A0 | 88CA5E48-2A1B-4179-9908-F090B62E44A0 | Randomization | 5 | This form includes information on the randomization. | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | NA | Baseline | NA | NA | 2 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/88CA5E48-2A1B-4179-9908-F090B62E44A0 |
| 8FC6AD28-3C81-4958-9B13-B249B2CA2D72 | 8FC6AD28-3C81-4958-9B13-B249B2CA2D72 | Medication | 11 | In this step you can record medication intake. | 3102EBF4-1525-4F83-94CF-840C51E64CCA | 3102EBF4-1525-4F83-94CF-840C51E64CCA | NA | Unscheduled visits and Medication | NA | NA | 4 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/3102EBF4-1525-4F83-94CF-840C51E64CCA | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/8FC6AD28-3C81-4958-9B13-B249B2CA2D72 |
| 90226AC6-F20E-48DC-83BC-C094CDC589BD | 90226AC6-F20E-48DC-83BC-C094CDC589BD | Unscheduled visit | 10 | In this step you can record unscheduled visits. | 3102EBF4-1525-4F83-94CF-840C51E64CCA | 3102EBF4-1525-4F83-94CF-840C51E64CCA | NA | Unscheduled visits and Medication | NA | NA | 4 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/3102EBF4-1525-4F83-94CF-840C51E64CCA | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/90226AC6-F20E-48DC-83BC-C094CDC589BD |
| FEABD311-4C21-4602-B722-37EECC90A622 | FEABD311-4C21-4602-B722-37EECC90A622 | Laboratory | 9 | To copy a step, click on the cogwheel next to it. | 62EDEB24-7616-4476-912D-2F280FB56E36 | 62EDEB24-7616-4476-912D-2F280FB56E36 | NA | Follow-up Visit | NA | NA | 3 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/62EDEB24-7616-4476-912D-2F280FB56E36 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/repeating-data-instance/FEABD311-4C21-4602-B722-37EECC90A622 |
visits <- castor_api$getVisits(example_study_id)| id | visit_id | visit_description | visit_name | visit_duration | visit_number | visit_order | _links.self.href |
|---|---|---|---|---|---|---|---|
| 3102EBF4-1525-4F83-94CF-840C51E64CCA | 3102EBF4-1525-4F83-94CF-840C51E64CCA | NA | Unscheduled visits and Medication | NA | NA | 4 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/3102EBF4-1525-4F83-94CF-840C51E64CCA |
| 62EDEB24-7616-4476-912D-2F280FB56E36 | 62EDEB24-7616-4476-912D-2F280FB56E36 | NA | Follow-up Visit | NA | NA | 3 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/62EDEB24-7616-4476-912D-2F280FB56E36 |
| 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | 65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 | NA | Baseline | NA | NA | 2 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/65B46EAC-5CE4-4E54-8C27-87F2A0FBA318 |
| EFEDE30F-0D61-468D-B67D-92465ACB0108 | EFEDE30F-0D61-468D-B67D-92465ACB0108 | NA | Informed Consent and Inclusion | NA | NA | 1 | https://data.castoredc.com/api/study/15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88/visit/EFEDE30F-0D61-468D-B67D-92465ACB0108 |