CentOS 7.6.1810 has a very old version of Git (v 1.8.3.1 from ~ 2013). To install a current version of Git, you have a few options:
sudo yum -y install wget perl-CPAN gettext-devel perl-devel openssl-devel zlib-devel
# Test of docker build process | |
# | |
# ctd - Crash Test Dummy. "You can learn a lot from a dummy" | |
# | |
# Sample commnds | |
# date; docker build --tag ctd:1.0 .; date | |
# docker history ctd:1.0 | |
# docker run -i -t ctd:1.0 /bin/bash | |
# this whole thing should take 30 - 35 minutes on first run | |
FROM rocker/r-ver:3.6.3 |
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,
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
Aberdeen | Moore | |
---|---|---|
Advance | Davie | |
Ahoskie | Hertford | |
Alamance | Alamance | |
Albemarle | Stanly | |
Albertson | Duplin | |
Alexander | Buncombe | |
Alexis | Gaston | |
Alliance | Pamlico | |
Almond | Swain |
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:
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
):
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 |
## | |
# 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; |