/castoRedc

R wrapper to Castor EDC API

Primary LanguageRMIT LicenseMIT

Castor API R Package

The intent of this package is to provide convenient access to study data in Castor via R.

Package Structure

Access to data in the API comes in three forms:

  1. Access to individual items (getStudyDataPoint, getStudy, getRecord, etc.)
  2. Access to pages of items in a list (getStudyDataPoints, getStudies, getRecords, etc.)
  3. Processed into a data frame for straightforward analysis (getStudyData)

Installation

# install.packages("remotes")
remotes::install_github("castoredc/castoRedc")

Missing data

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.

Testing

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.

Usage

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)
Participant_ID Site_Abbreviation Randomization_Group Participant_Creation ic_date ic_versions#Other ic_versions#Main study CF ic_main_version ic_language#English ic_language#Dutch
1 110001 FGV NA 2021-06-22 09:51:49 2021-06-22 FALSE FALSE 2.5 FALSE FALSE
2 110002 FGV NA 2021-06-22 09:59:01 NA FALSE FALSE NA FALSE FALSE
NA NA NA NA NA NA NA NA NA NA NA
NA.1 NA NA NA NA NA NA NA NA NA NA
NA.2 NA NA NA NA NA NA NA NA NA NA
repeating_data_name created_on Participant_ID repeating_data_inst_name AE_type AE_SAE AE_severity AE_stopdate AE_expected AE_outcome AE_action AE_relation AE_startdate
Adverse event 2021-06-22 09:55:13 110001 Adverse event - 22-06-2021 09:55:12 A bug in the API Yes Life-threatening 24-06-2021 Yes Resolved Medical intervention Definitely related 23-06-2021
Adverse event 2021-06-22 09:58:13 110001 Adverse event - 22-06-2021 09:58:12 NA NA NA NA NA NA NA NA NA
repeating_data_name created_on Participant_ID repeating_data_inst_name comorbidities
Comorbidities 2021-06-22 09:56:07 110001 Comorbidities - 22-06-2021 09:56:06 {“file_name”:“Y29tb3JiaWRpdGllcy50eHQ=”,“mime_type”:“text/plain”,“file_size”:48,“storage_path”:“B2CF4AB1-CCCF-43CD-9933-13DE879C1AB5”,“key”:{“generation”:{“metadata”:[],“version”:[“rb”,1]},“storage”:{“metadata”:{“ciphertext”:“CiQAsmjNQAKXE4sQbDJagktdyNPH7fbo6bCMPRGYrSp/hYls7U0SSQAAsqYVDFxH1mKbO5tgQ3RmzxhkmAvUKA7LDzwqaU1gcdWuKvplMjniW1OjZwW8qntb+a60NG12EN9k6YSifTl6749JXjB/4Fw=”,“key_version”:“1”,“project”:“castoredc-kms”,“location”:“europe-west4”,“keyring”:“15E88A04-9CB8-4B30-9A3C-B1DBFC96CD88”,“keyname”:“41B6FFD8-61BB-4D06-B5B1-58D8D2875C68”},“version”:[“google”,1]}},“algorithm”:{“version”:[“sodium”,1],“attributes”:{“nonce”:“0021a3e7a6cf3b8a686d184d499503df435a4232b0356476”}}}
repeating_data_name created_on Participant_ID repeating_data_inst_name med_stop med_name med_dose med_start med_units
Medication 2021-06-22 09:54:28 110001 Medication - 22-06-2021 09:54:28 28-06-2021 Diclofenac 150 25-06-2021 mg/day
Medication 2021-06-22 09:58:27 110001 Medication - 22-06-2021 09:58:26 NA NA NA NA NA
repeating_data_name created_on Participant_ID repeating_data_inst_name unsvis_sbp unsvis_dbp unsvis_date unsvis_weight unsvis_hr unsvis_type
Unscheduled visit 2021-06-22 09:57:38 110001 Unscheduled visit - 22-06-2021 09:57:36 233 156 24-06-2021 98.3 112 admission to day-care
survey_instance_id participant_id survey_name survey_package_name survey_package_instance_id created_on created_by sent_on finished_on survey_package_instance_parent_id survey_package_instance_parent_type SF12_12 SF12_2 SF12_1 VAS SF12_3
4FF130AD-274C-4C8F-A4A0-A7816A5A88E9 110001 QOL Survey My first survey package 0761A9BA-9802-483D-8EB3-D07233A56F2B 2021-06-22 10:12:19.000000 B23ABCC4-3A53-FB32-7B78-3960CC907F25 2021-06-22 10:12:19.000000 2021-06-22 10:12:44.000000 0 Rarely Mostly Excellent 85.00 Mostly
B99F0082-1B20-456B-8D4D-47D16867B211 110001 QOL Survey My first survey package 5B3FE56F-89FA-4C6D-A638-E8FA46113EB0 2021-06-22 10:13:01.000000 B23ABCC4-3A53-FB32-7B78-3960CC907F25 2021-06-22 10:13:01.000000 NA 0 NA NA NA NA NA
29FD41EF-46F1-4DEA-A372-F38FC2C0C9C2 110001 QOL Survey My first survey package EBBB77D0-56A2-49C7-9333-A27C17FA5D95 2021-09-24 13:12:45.000000 B23ABCC4-3A53-FB32-7B78-3960CC907F25 2021-09-24 13:12:45.000000 NA 0 NA NA NA NA NA 
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