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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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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 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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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

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How to get specific rows within a group in generic SQL (SQLite)?

Example scenario: Need to get all encounter rows and summary information about their labs such as min/max, and the value most immediately before and after an event of interest.

The following code will setup an example scenario. Some people have no labs, others only have labs before or only after the event of interest.

SQL Fiddle available at http://sqlfiddle.com/#!5/f80104/1/0

CREATE OR REPLACE TABLE encounter

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How to get specific rows within a group in Google BigQuery?

Example scenario: Need to get all encounter rows and summary information about their labs such as min/max, and the value most immediately before and after an event of interest.

The following code will setup an example scenario. Some people have no labs, others only have labs before or only after the event of interest.

CREATE OR REPLACE TABLE curation.test_encounter
(
  person_id INT64 NOT NULL,