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PharmAccess / hdc-data-analytics-handbook

https://pharmaccess.github.io/hdc-data-analytics-handbook/
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hdc-data-analytics-handbook

Installation

To be able to run all the code in this handbook, you will need to install and run the following.

Clone this repo

Install quarto
We assume you will be using Visual Studio Code to run this notebook. First you need to install quarto

  1. Navigate to https://quarto.org/docs/get-started/ and install quarto following the instructions on the webpage.
  2. After installation, in vs code, open the market place (extensions) in the left-hand menu and search for Quarto.
  3. Unstall and enable the Quarto extension for vs-code
  4. When you now open a quarto document, you should see a preview button in the right corner of the editor.

install java
Java is required to run the synthea generator and to use the pyspark library. The version and distribution depends on your laptop, but can be found on this webpage. Note that a version of Java JDK 11 or 17 is required to be able to run the synthea patient generator. (I used Java JDK 11)

Install the environment
As we are using a python and r environment together, we recommend you to install anaconda to make sure you have the right python and r distribution.

  1. If you dont have anaconda installed yet install it from anaconda
  2. Open the terminal of vs code
  3. A yml installation file of this project has been added in the main folder, named analytics_handbook_env.yml.
  4. Open the vs code terminal and run the following code to create the anaconda environment: 
conda env create -f analytics_handbook_env.yml

NOTE: If you have a mac and the arm64 version of anaconda installed, anaconda will automatically look into condaforge/osx-arm64 channel for packages, in which some packages like r-duckdb are not available. Therefore you need to specify too look in the conda-forge/osx-64 channel. To do so in the analytics_handbook_env.yml add /osx-64 after conda-forge in the channels.

  1. To activate the environment run: conda activate HDC-handbook-r-python
  2. Set the python interpreter (ctr/cmnd + shift + p, or navigate to settings >> command pallette..) and click on Python: select interpreter. Now select the environment you just installed. Note: for the environment to become visible in the list, it might be required to restart vs code.
  3. Now first run a single code cell in any of the documents, this will ask you to install a kerner for your environment. Click install.
  4. Now all is set, to run the entire handbook, click on the preview button in any of the qmd files.