,
Luke Rasmussen [aut] ,
David Mayer [cre, aut] ,
The Wiley Lab [cph, fnd]| Title: | A Light-Weight, Portable Tool for Reviewing Individual Patient Records |
|---|---|
| Description: | A portable Shiny tool to explore patient-level electronic health record data and perform chart review in a single integrated framework. This tool supports browsing clinical data in many different formats including multiple versions of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In addition, chart review information is captured and stored securely via the Shiny interface in a 'REDCap' (Research Electronic Data Capture) project using the 'REDCap' API. See the 'ReviewR' website for additional information, documentation, and examples. |
| Authors: | Laura Wiley [aut] ,
Luke Rasmussen [aut] ,
David Mayer [cre, aut] ,
The Wiley Lab [cph, fnd] |
| Maintainer: | David Mayer <[email protected]> |
| License: | BSD_3_clause + file LICENSE |
| Version: | 2.3.10 |
| Built: | 2024-11-12 05:28:04 UTC |
| Source: | https://github.com/thewileylab/reviewr |
A character vector containing a function template for creating the 'All Patients' table as displayed on the "Patient Search" Tab
db_function_all_patients_table_templatedb_function_all_patients_table_template
A character vector with 22 elements
Other Development Templates:
db_function_subject_table_template,
db_module_template
A character vector containing a function template for creating the 'Subject Filtered' tables as displayed on the "Chart Review" Tab
db_function_subject_table_templatedb_function_subject_table_template
A character vector with 15 elements
Other Development Templates:
db_function_all_patients_table_template,
db_module_template
A character vector containing a database module template
db_module_templatedb_module_template
A character vector with 52 elements
Other Development Templates:
db_function_all_patients_table_template,
db_function_subject_table_template
This function will assist in adding support for a new data model to ReviewR. A schema file, supplied as a CSV, will be added to the package namespace such that upon connection to a database containing the new data model, ReviewR can identify and display it through the database detection module.
Users will be prompted to identify which table in the new data model contains a list of all patients. Additionally, users will be asked to select which field uniquely identifies each patient. This field must be present across all tables in the new data model for best results.
Once selections are captured, a database_tables.R file will be populated and opened for editing in RStudio. Basic table skeletons are created based on the provided schema and user selections.
Note: If the identifier field is not present across all tables, care must be taken to adjust the database_tables.R file to appropriately represent the new data model structure.
dev_add_data_model(csv)dev_add_data_model(csv)
csv |
Required. The file path of a CSV file containing a data model schema |
A .R file populated with basic database table functions
Other Development Functions:
dev_add_database_module()
This function will create a database module skeleton with required elements already populated, based on user inputs. Common database module packages are imported automatically, but developers should add imports to the roxygen skeleton as necessary to both the UI and server functions to collect user info and create a DBI connection object, respectively.
dev_add_database_module(mod_name = NULL, display_name = NULL)dev_add_database_module(mod_name = NULL, display_name = NULL)
mod_name |
Required. A string, denoting the module suffix eg: 'mariadb' |
display_name |
Required. A string, denoting the module display name eg: 'MariaDB Server'. This is the 'user viewable' name that will appear in the database module selector dropdown. |
A .R file populated with a database module skeleton
Other Development Functions:
dev_add_data_model()
A dataset containing valid REDCap "Survey Complete" Values.
redcap_survey_completeredcap_survey_complete
A data frame with 2 rows and 2 variables:
The human readable "Survey Complete" Responses
REDCap API values for "Survey Complete" Responses
...
A dataset that maps REDCap question types and common validations to native shiny widgets through custom functions.
redcap_widget_mapredcap_widget_map
A data frame with 9 rows and 3 variables:
A REDCap Question Type
Custom REDCap Question Type Validation
shinyREDCap function to use when mapping to native Shiny widget
...
Start the ReviewR Application in a browser on port 1410.
__________ .__ __________
\______ \ _______ _|__| ______ _ _\______ \
| _// __ \ \/ / |/ __ \ \/ \/ /| _/
| | \ ___/\ /| \ ___/\ / | | \
|____|_ /\___ >\_/ |__|\___ >\/\_/ |____|_ /
\/ \/ \/ \/
by WileyLab
Making manual record review fun since 2019!
authors: Laura Wiley, Luke Rasmussen, David Mayer
run_app(...)run_app(...)
... |
A list of options to pass to the app including:
|
No return value, called to start the ReviewR Shiny Application!
A dataset containing data model information along with the corresponding version and nested schema information.
supported_data_modelssupported_data_models
A data frame with 12 rows and 4 variables:
Data model name
Version of the data model
Nested database schemas, including included table and field mappings
Where schema was imported from
...
https://github.com/OHDSI/CommonDataModel/
https://github.com/MIT-LCP/mimic-code