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Setting up an SSH proxy on Windows

No administrative privileges required.

Steps:

1. Download Cygwin setup application from https://cygwin.com

2. Run Cygwin setup file

   • Select “Install For Just Me”

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    # using a data.frame for output results
    # base time 26 seconds with 60k rows

    # this block takes 27 seconds with 100k rows
    # if (sum(df[i,]))
    #   df$ccc_flag[i] <- 1L

    # this one line takes abotut 10 seconds with 60k rows
    # df$ccc_flag[i] <- ccc_flag

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# install.packages('bigrquery')
library('bigrquery')

project <- "sandbox-nlp" # put your project ID here
sql <- "SELECT *
FROM `sandbox-nlp.MIMIC3_V1_4.ADMISSIONS`
LIMIT 100"
gbq_cursor <- bq_project_query(project, sql)
result <- bq_table_download(gbq_cursor)

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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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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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##
# 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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Introduction

Fast Healthcare Interoperability Resources (http://hl7.org/fhir) - FHIR – is a standards framework created by Health Level 7 (HL7). FHIR combines the features of HL7's previous health data interchange standards including HL7 v2 , HL7 v3 and CDA. FHIR improves on previous standards by using more modern web standards for data exchange, supports many programming languages, and promostes human readability.

Documentation

Start by reading through this first: "FHIR Drills" https://fhir-drills.github.io/index.html

• Python Client: http://docs.smarthealthit.org/client-py/
• Java Client: http://hapifhir.io/doc_rest_client.html

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Steps to upgrade r:

From linux command-line remove all existing R packages:

sudo apt-get update
sudo apt-get remove r-base r-base-dev r-base-core 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-recommended

Next, update /etc/apt/sources.list and add these lines (comment out old R version, add new pkg list):