InterHop

Projects

LinkR demo

Plugins

Console

NA

Datatable

NA

Development template

Drug exposure

1) Introduction

The "Drug exposure" plugin allows you to display medication administration data in the form of a timeline.

2) Features

Figure settings

Here are the parameters you can adjust:

• Data to display: choose whether you want to display patient data or stay data

• Concepts to display:

  • All concepts: if you want to display all medications received by the patient during the period
  • Concept classes: if you want to display only one class of concepts. In this case, a dropdown menu allows you to choose which class(es) to display.
  • Selected concepts: if you want to display only certain medications, which you will choose from the concepts dropdown menu

• Synchronize timelines: several plugins work with a timeline (the scroll bar below the timeline where you can choose the period to display). This feature allows you to synchronize the timelines of several widgets on the same tab.

Code

As with all plugins on LinkR, the low-code interface allows you to generate code from the graphical interface.

To do this, go to the "Figure settings" tab, and once you have chosen your parameters, click on "Display figure".

This will:

• generate the code corresponding to the chosen parameters
• then execute the code and display the figure corresponding to the code

You can then modify the code directly and save it.

If you click on "Run code" from the tab with the code editor, it will display the figure corresponding to the code.

However, if you are on the tab corresponding to the figure settings, it will erase the current code and replace it with the code corresponding to the current parameters.

Save files

You can save the figure parameters and code from the save files management page.

To do this, click on the name of the selected file at the top of the widget ("Save File 1" in the screenshot above). You can then add or delete save files.

Then return to the "Figure settings" or "Code" tabs and save your parameters and code.

General settings

The general settings are divided into:

• Display Settings

  • Show save file: show or hide the name of the selected save file
  • Figure and settings/editor side by side: do you want the figure to appear side by side with the figure settings or the figure code? This avoids going back and forth between the different tabs during the widget configuration phase.

• Code Execution

  • Run code when loading a save file: this allows the code to be executed when the selected save file changes, which is useful when loading a project: this allows all widgets with this option to be loaded
  • Run code when data is updated: for this widget, this means that the data is updated when you change patient or visit, depending on the value of the "Data to display" parameter

Hospital stays

NA

Text reader

Timeline {dygraphs}

1) Introduction

The "Timeline {dygraphs}" plugin allows you to display continuous data in the form of a timeline, such as vital signs or laboratory data.

2) Features

Figure settings

Here are the parameters you can adjust:

• Data to display: choose whether you want to display patient data or visit data

• Concepts: which concepts do you want to see on the figure? This list includes the concepts you selected when creating the widget.

• Synchronize timelines: several plugins work with a timeline (the scroll bar below the timeline where you can choose the period to display). This feature allows you to synchronize the timelines of several widgets on the same tab.

Code

As with all plugins on LinkR, the low-code interface allows you to generate code from the graphical interface.

To do this, go to the "Figure settings" tab, and once you have chosen your parameters, click on "Display figure".

This will:

• generate the code corresponding to the chosen parameters
• then execute the code and display the figure corresponding to the code

You can then modify the code directly and save it.

If you click on "Run code" from the tab with the code editor, it will display the figure corresponding to the code.

However, if you are on the tab corresponding to the figure settings, it will erase the current code and replace it with the code corresponding to the current parameters.

Save files

You can save the figure parameters and code from the save files management page.

To do this, click on the name of the selected file at the top of the widget ("Save File 1" in the screenshot above). You can then add or delete save files.

Then return to the "Figure settings" or "Code" tabs and save your parameters and code.

General settings

The general settings are divided into:

• Display Settings

  • Show save file: show or hide the name of the selected save file
  • Figure and settings/editor side by side: do you want the figure to appear side by side with the figure settings or the figure code? This avoids going back and forth between the different tabs during the widget configuration phase.

• Code Execution

  • Run code when loading a save file: this allows the code to be executed when the selected save file changes, which is useful when loading a project: this allows all widgets with this option to be loaded
  • Run code when data is updated: for this widget, this means that the data is updated when you change patient or visit, depending on the value of the "Data to display" parameter

Datasets

MIMIC-IV demo set

The MIMIC database, or Medical Information Mart for Intensive Care, is a North American database containing data from over 50,000 patients admitted to intensive care units. It is one of the most widely used critical care databases due to its free access.

Despite its imperfect data quality, it provides a solid foundation for learning to handle data from health data warehouses (HDW).

The database exists in several versions, with the most recent being MIMIC-IV.

Test Data (Public Access)

The MIMIC database includes test datasets for versions III and IV, containing anonymized data from 100 patients, which are publicly accessible.

You can download the data here:

• MIMIC-III Test: data with the MIMIC data schema
• MIMIC-IV OMOP Test: data with the OMOP data schema

Full Data Access

To access the complete datasets, certain steps need to be completed.

Visit the MIMIC-III database page.

At the bottom of the page, you’ll see this alert:

This is a restricted-access resource. To access the files, you must fulfill all of the following requirements:

• be a credentialed user
• complete required training:
• CITI Data or Specimens Only Research
You may submit your training here.
• sign the data use agreement for the project

You will need to start by registering on the physionet.org website.

Then, you must submit an access request to Physionet, providing some information and the contact details of a supervisor or colleague, who will receive an email.

Next, you must complete the CITI Course, a required training to access data hosted on Physionet. The steps are detailed here.

Once the CITI Course is completed, you can download the certificate and upload it here for validation by the Physionet team.

The final step is to sign the data use agreement.

Data cleaning scripts

No data cleaning scripts available.