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tableau-status-exporter's Introduction

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
110001 FGV NA 2021-06-22 09:51:49 2021-06-22 FALSE TRUE 2.5 FALSE FALSE
110002 FGV NA 2021-06-22 09:59:01 NA FALSE FALSE NA FALSE FALSE
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

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