Skip to content

Latest commit

 

History

History
547 lines (468 loc) · 22.6 KB

index.md

File metadata and controls

547 lines (468 loc) · 22.6 KB
layout carpentry venue address country language latlng humandate humantime startdate enddate instructor helper email collaborative_notes eventbrite
workshop
dc
School of Clinical Medicine
E-Learning1, Level 2, School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge CB2 0SP
gb
en
52.186900,0.137400
Mar 11-12, 2020
9:30 - 17:30
2020-03-11
2020-03-12
Mark Fernandes
Chandra Sekhar Reddy Chilamakuri

{% comment %} See instructions in the comments below for how to edit specific sections of this workshop template. {% endcomment %}

{% comment %} HEADER

Edit the values in the block above to be appropriate for your workshop. If the value is not 'true', 'false', 'null', or a number, please use double quotation marks around the value, unless specified otherwise. And run 'make workshop-check' before committing to make sure that changes are good. {% endcomment %}

{% comment %} EVENTBRITE

This block includes the Eventbrite registration widget if 'eventbrite' has been set in the header. You can delete it if you are not using Eventbrite, or leave it in, since it will not be displayed if the 'eventbrite' field in the header is not set. {% endcomment %} {% if page.eventbrite %}

<iframe src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt" frameborder="0" width="100%" height="248px" scrolling="auto"> </iframe> {% endif %}

General Information

{% comment %} INTRODUCTION

Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %} {% if page.carpentry == "swc" %} {% include sc/intro.html %} {% elsif page.carpentry == "dc" %} {% include dc/intro.html %} {% elsif page.carpentry == "lc" %} {% include lc/intro.html %} {% endif %}

{% comment %} AUDIENCE

Explain who your audience is. (In particular, tell readers if the workshop is only open to people from a particular institution. {% endcomment %} {% if page.carpentry == "swc" %} {% include sc/who.html %} {% elsif page.carpentry == "dc" %} {% include dc/who.html %} {% elsif page.carpentry == "lc" %} {% include lc/who.html %} {% endif %}

{% comment %} LOCATION

This block displays the address and links to maps showing directions if the latitude and longitude of the workshop have been set. You can use http://itouchmap.com/latlong.html to find the lat/long of an address. {% endcomment %} {% if page.latlng %}

Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.

{% endif %}

{% comment %} DATE

This block displays the date and links to Google Calendar. {% endcomment %} {% if page.humandate %}

When: {{page.humandate}}. {% include workshop_calendar.html %}

{% endif %}

{% comment %} SPECIAL REQUIREMENTS

Modify the block below if there are any special requirements. {% endcomment %}

Requirements: We will be using pre-configured computers in the Schools E-Learning Suite. Participants can bring their own laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below) or by using Docker and relevant containers see here. This can also be done after the course to re-engage with the materials.

They are also required to abide by {% if page.carpentry == "swc" %} Software Carpentry's {% elsif page.carpentry == "dc" %} Data Carpentry's {% elsif page.carpentry == "lc" %} Library Carpentry's {% endif %} Code of Conduct.

{% comment %} ACCESSIBILITY

Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}

Accessibility: We are committed to making this workshop accessible to everybody. Please get in touch (using contact details below) if you have any special requirements.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

{% comment %} CONTACT EMAIL ADDRESS

Display the contact email address set in the configuration file. {% endcomment %}

Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.

{% comment %} SCHEDULE

Show the workshop's schedule. Edit the items and times in the table to match your plans. You may also want to change 'Day 1' and 'Day 2' to be actual dates or days of the week. {% endcomment %}

{% comment %} DO NOT EDIT SURVEY LINKS {% endcomment %}

Surveys

{% if page.carpentry == "swc" %}

Please be sure to complete these surveys before and after the workshop.

(% comment %)

Pre-workshop Survey

Post-workshop Survey

{% elsif page.carpentry == "dc" %}

Please be sure to complete this survey after the workshop: Cambridge training survey

We would also appreciate if you filled in these surveys for the Data Carpentry community:

Data carpentry pre-workshop Survey

Data carpentry post-workshop Survey

{% elsif page.carpentry == "lc" %}

Ask your instructor about pre- and post-workshop Survey details.

{% endif %}

{% comment %} Collaborative Notes

If you want to use an Etherpad, go to

  http://pad.software-carpentry.org/YYYY-MM-DD-site

where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'. {% endcomment %} {% if page.collaborative_notes %}

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

{% endif %}

Course Overview

overview

Schedule

Timetable.

Day 1

Data organization in spreadsheets ( )

Data files for the lesson are available here.

  1. Introduction (18 mins)
  2. Formatting data (35 mins)
  3. Common formatting problems (20 mins)
  4. Dates as data (13 mins)
  5. Quality control (20 mins)
  6. Exporting data (10 mins)

Data cleaning with OpenRefine ( )

Data files for the lesson are available here

.

  1. Introduction (10 mins)
  2. Basics of OpenRefine (35 mins)
  3. Filtering and sorting (20 mins)
  4. Examining numeric data (20 mins)
  5. Generating scripts (15 mins)
  6. Exporting data (15 mins)
  7. Other resources (10 mins)

Data analysis with R ( )

  1. Overview of R and Rstudio ( mins)
  2. Introduction to R ( mins)
  3. Working with tabular data in R ( mins)

Recap of R materials from Day 1 ( mins)

Day 2

Data analysis with R

  1. Data manipulation using the R package dplyr ( mins)
  2. Data visualisation using the R package ggplot2 ( mins)
  3. Interacting with databases from R ( mins)

CSV data files for the final part of Database lesson are available from here

.

Learn more about SQL from the SQL data lessons.

Should you finish earlier than others and want some more challenges please have a go. at this material from the R Software Carpentry course (They could also be done post-course as a revision exercise): Gapmider R materials

Useful reference sheets

  1. Base R cheatsheet
  2. Dplyr cheatsheet
  3. ggplot2 cheatsheet
  4. Tidyverse cheatsheet
  5. Animations of joins, spread & gather

{% comment %} SYLLABUS

Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside the div's with class="row" to balance the multi-column layout.

This is one of the places where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well.

Syllabus

{% if page.carpentry == "swc" %} {% include sc/syllabus.html %} {% elsif page.carpentry == "dc" %} {% include dc/syllabus.html %} {% elsif page.carpentry == "lc" %} {% include lc/syllabus.html %} {% endif %} {% endcomment %}

{% comment %} SETUP

Delete irrelevant sections from the setup instructions. Each section is inside a 'div' without any classes to make the beginning and end easier to find.

This is the other place where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}

Setup

To participate in a {% if page.carpentry == "swc" %} Software Carpentry {% elsif page.carpentry == "dc" %} Data Carpentry {% elsif page.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

{% comment %} Start of 'R' section. {% endcomment %}

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

{% comment %} End of 'R' section. {% endcomment %}
{% comment %} Start of 'OpenRefine' section. {% endcomment %}

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

Windows

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.

Download software from http://openrefine.org/

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".

Go to your newly created OpenRefine directory.

Launch OpenRefine by clicking google-refine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Mac

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.

Download software from http://openrefine.org/.

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by double-clicking it.

Go to your newly created OpenRefine directory.

Launch OpenRefine by dragging the icon into the Applications folder.

Use Ctrl-click/Open ... to launch it.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Linux

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.

Download software from http://openrefine.org/.

Make a directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory.

Go to your newly created OpenRefine directory.

Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

{% comment %} End of 'OpenRefine' section. {% endcomment %}

{% comment %}

Virtual Machine

Some instructors prefer to have learners use a virtual machine (VM) rather than install software on their own computers. If your instructors have chosen to do this, please:

  1. Install VirtualBox.
  2. Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your workshop.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.
{% endcomment %}
{% comment %} Start of 'SQLite' section. {% endcomment %}

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

macOS

SQLite comes pre-installed on macOS.

Linux

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.

{% comment %} End of 'SQLite' section. {% endcomment %}