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JupyterHub Setup

System Setup

Setup Users/Groups/paths

sudo addgroup pythonusers
sudo gpasswd -M sethr,rebullm,tellb,dewittp pythonusers
sudo mkdir /opt/miniconda3

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How to use R, RStudio, and conda

I created a post to try to combine questions/issues people had as well as solutions I found.

See https://forum.posit.co/t/rstudio-and-conda/186130

RStudio Desktop

Key here is to make sure both R and LD_LIBRARY_PATH are coming from the desired conda environment.

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name: hvplot_example
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.10
  - hvplot
  - intake
  - intake-parquet
  - intake-xarray

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function FindProxyForURL(url, host) {

    // the zotero service should only be local
    if ( shExpMatch(url, "http://127.0.0.1:23119/*") ) {
        return "DIRECT";
    }

    // localhost and local stuff should go to through socks proxy
    if (shExpMatch(host, "skylark.ucdenver.pvt") ||
        shExpMatch(host, "rainier.ucdenver.pvt") ||

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Eureka New User Guide

• Eureka New User Guide
  • General Eureka Information
    • Initial Setup
    • Internet Access
  • R Language Specifics
• Installing Packages

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How to hold back or keep specific R version on Ubuntu

See https://askubuntu.com/questions/18654/how-to-prevent-updating-of-a-specific-package for additional details on package holding.

You have all system R packages as you want them:

If so, run the following:

apt-mark hold r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-doc-info r-recommended

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##
# Customized Nginx configuration
##

server {
        root /var/www/html;
        index index.html index.htm index.nginx-debian.html;
        server_name rstudio.learnclinicaldatascience.org; # managed by Certbot

        access_log            /var/log/nginx/rstudio.learnclinicaldatascience.org;

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library(bigrquery)
library(magrittr)
library(dplyr)
library(tidyr)
project <- "gbqproject"
dataset_writeable <- "gbqdataset"
dataset_readonly <- "gbqdataset_source"

# test query to prompt for GBQ Credentials
# RStudio can't just run the whole file at once

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Jupytext setup (for *nix and Windows)

Installation

Run this command to install the jupytext extension:

conda install jupytext -c conda-forge

Start/restart jupyter. In the environment used to launch jupyter notebook you should now see the File > Jupytext menu. In jupyter lab, Jupytext adds a set of commands to the command palette (View / Activate Command Palette, or Ctrl+Shift+C):

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N3C machine learning introduction

This machine learning example was developed for the paper "The National COVID Cohort Collaborative: Clinical Characterization and Early Severity Prediction" currently available as a preprint.

Although the code is available in the N3C Unite Palantir platform, for faster code sharing, I have made the following publically accessible exports of the workbooks:

• Build ML Dataset - Pulls in many variables curated as part of the Cohort paper and does additional curation.
• scikit-ML - Separation of dataset in to input and outcomes and seasonal versions
• xgboost-ML - Grid search over XGBoost hyperparameters
• Unsupervised ML - UMAP and PCA analysis of data