Initial add

01_Files.Rmd

@@ -0,0 +1,30 @@
+# Files
+
+You need to make sure that a) you have access to all of your files and b) that
+these are somewhat backed up so it is not entirely reliant on a single device.
+The simplest and recommended way to do this at Liverpool is to keep all your
+files and data on your university account at OneDrive. This is part of the
+Office 365 Suite available from the university, you can find more info at:
+
+> [`https://www.liverpool.ac.uk/csd/working-from-home/`](https://www.liverpool.ac.uk/csd/working-from-home/)
+
+There are Windows and Mac clients that work relatively well (equivalent to
+Dropbox client).
+
+Once you are set up, copy all your files onto your OneDrive account, which
+will create a copy of them in Microsoft's secure cloud. The exception is
+where you have data that has requirements to be managed in particular ways - e.g.
+only from a single machine etc; not in the cloud.
+
+Please, be sure to speak with your PhD supervisor if you access data that
+may pose some challenges when moving from local machines or within the university
+network (remember OneDrive is in the Cloud, not the university servers!).
+
+If you need to move large and/or many files from a local machine to a remote
+server (e.g. from your laptop to a Linux machine at the lab), you will
+probably want to use something like FTP. For that, have a look at the guide
+at:
+
+> [`setup_ftp.md`](setup_ftp.md)
+
+

setup_vpn.md → 02_VPN.Rmd

@@ -1,21 +1,36 @@
-# Set up a VPN connection
-
-This document describes how to set up a VPN. The text below has been copied from CSD website.
-
-To access the VPN service:
-
-1. Register
-
-Submit a request to register for the VPN service via CSD. You will need to explain why you require VPN access and what you intend to do with it. It may be that other services offer the solution you require instead of the VPN.
-
-2. Download the VPN Client
-
-Once your registration is confirmed you will need to download and install the GlobalProtect VPN Client if you are using Windows 10.
-
-You will need admin rights in order to download the GlobalProtect VPN Client. This is how to access admin rights on your MWS PC. Please access admin rights before attempting to download the VPN Client. 
-
-The GlobalProtect VPN Client is also compatible with MacOS. Mobile and tablet devices cannot connect using this client. If you are using a Linux distribution, such as Ubuntu, you may be able to connect to the University network using VPNc.
-
-3. Open the client and connect
-
-Click here for instructions on how to use the GlobalProtect VPN Client to access the University network from your PC or Mac. 
+# VPN
+
+## *What is a VPN?*
+
+A VPN (virtual private network) connects a machine that lies outside of the university (ie. outside the firewall) to the internal network. When the VPN is running, your network traffic (e.g. Internet) is routed through the university in the same way as if the computer was on your work desk. This enables you to:
+
+* Access journal websites like you would inside the university
+* Access network drives (e.g. M Drive etc) - but be careful when transferring big files
+* Access servers (e.g. over the terminal / command line / ftp)
+
+## *How can I setup the VPN for Liverpool?*
+
+You can find a more comprehensive guide to setup your VPN on the
+[`setup_vpn.md`](setup_vpn.md) document of this repository.
+
+## Set up a VPN connection
+
+This document describes how to set up a VPN. The text below has been copied from CSD website.
+
+To access the VPN service:
+
+1. Register
+
+Submit a request to register for the VPN service via CSD. You will need to explain why you require VPN access and what you intend to do with it. It may be that other services offer the solution you require instead of the VPN.
+
+2. Download the VPN Client
+
+Once your registration is confirmed you will need to download and install the GlobalProtect VPN Client if you are using Windows 10.
+
+You will need admin rights in order to download the GlobalProtect VPN Client. This is how to access admin rights on your MWS PC. Please access admin rights before attempting to download the VPN Client. 
+
+The GlobalProtect VPN Client is also compatible with MacOS. Mobile and tablet devices cannot connect using this client. If you are using a Linux distribution, such as Ubuntu, you may be able to connect to the University network using VPNc.
+
+3. Open the client and connect
+
+Click here for instructions on how to use the GlobalProtect VPN Client to access the University network from your PC or Mac. 

03_Data_Science_stack.Rmd

@@ -0,0 +1,16 @@
+# Data Science Stack
+
+Once you have access from home to all your files and (remote) university computers, next step is easily being able to bootstrap a full data science stack that allows you to carry out scientific work. There are several ways of achieving this, but our preferred strategy is to rely on container technology, in particular on [Docker](https://www.docker.com/). This will allow you to rapidly install the platform and set of libraries you are familiar with in a way that can be easily reproduced and redeployed (e.g. on a remote computer on campus).
+
+Here are a series of pages that will help you get a stack ready to go:
+
+- [`setup_docker.md`](setup_docker.md): instructions to install and get Docker
+  up and running on different platforms
+- [`setup_jupyterlab.md`](setup_jupyterlab.md): instructions to install and
+  run a JupyterLab server both on local (e.g. laptop) and remote (e.g. server)
+  machines
+- [`setup_rstudio.md`](setup_rstudio.md): instructions to install and
+  run a JupyterLab server both on local (e.g. laptop) and remote (e.g. server)
+  machines
+
+

setup_docker.md → 04_Docker.Rmd

@@ -1,4 +1,4 @@
-# Docker containers
+# Docker
 
 This document describes how to install and use Docker on different platforms.
 

setup_jupyterlab.md → 06_JupyterLab.Rmd

@@ -1,4 +1,7 @@
-# Install and run a JupyterLab server
+# JupyterLab
+
+This document shows how to install and run a JupyterLab server locally and
+remotely.
 
 ## Local install
 

Makefile

@@ -0,0 +1,6 @@
+gitbook:
+	Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"
+ pdf:
+	Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')"   
+ epub:
+	Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::epub_book')"   

README.md

@@ -1,82 +1,5 @@
 # The Knowledge
 
-## Introduction
-
-In preparation to be able to stay productive while having to work fully remote, this document presents a few things jotted down in one place to help with setups, etc. 
-
-The first step is a checklist everyone should go through:
-
-1. Do you have a computer to work on at home?
-1. Are *all* your relevant files accessible from home? (see some info
-   [here](#Files))
-1. Do you have a webcam, mic and speakers/headphones?
-1. Are you able to connect to computers on campus? This involves being setup with the University VPN? (if you don't know what a VPN is or how to set it up, see [here](#VPN))
-
-These are the basic elements you will require, so if the answer to any of the above is no, please speak with your PhD supervisor.
-
-This guide includes information on the following topics:
-
-- [Personal file storage and management](#Files)
-- [VPN introduction and install guidance](#VPN)
-- [Data Science Stack](#Data-Science-Stack)
-
-## Files
-
-You need to make sure that a) you have access to all of your files and b) that
-these are somewhat backed up so it is not entirely reliant on a single device.
-The simplest and recommended way to do this at Liverpool is to keep all your
-files and data on your university account at OneDrive. This is part of the
-Office 365 Suite available from the university, you can find more info at:
-
-> [`https://www.liverpool.ac.uk/csd/working-from-home/`](https://www.liverpool.ac.uk/csd/working-from-home/)
-
-There are Windows and Mac clients that work relatively well (equivalent to
-Dropbox client).
-
-Once you are set up, copy all your files onto your OneDrive account, which
-will create a copy of them in Microsoft's secure cloud. The exception is
-where you have data that has requirements to be managed in particular ways - e.g.
-only from a single machine etc; not in the cloud.
-
-Please, be sure to speak with your PhD supervisor if you access data that
-may pose some challenges when moving from local machines or within the university
-network (remember OneDrive is in the Cloud, not the university servers!).
-
-If you need to move large and/or many files from a local machine to a remote
-server (e.g. from your laptop to a Linux machine at the lab), you will
-probably want to use something like FTP. For that, have a look at the guide
-at:
-
-> [`setup_ftp.md`](setup_ftp.md)
-
-## VPN
-
-### *What is a VPN?*
-
-A VPN (virtual private network) connects a machine that lies outside of the university (ie. outside the firewall) to the internal network. When the VPN is running, your network traffic (e.g. Internet) is routed through the university in the same way as if the computer was on your work desk. This enables you to:
-
-* Access journal websites like you would inside the university
-* Access network drives (e.g. M Drive etc) - but be careful when transferring big files
-* Access servers (e.g. over the terminal / command line / ftp)
-
-### *How can I setup the VPN for Liverpool?*
-
-You can find a more comprehensive guide to setup your VPN on the
-[`setup_vpn.md`](setup_vpn.md) document of this repository.
-
-## Data Science Stack
-
-Once you have access from home to all your files and (remote) university computers, next step is easily being able to bootstrap a full data science stack that allows you to carry out scientific work. There are several ways of achieving this, but our preferred strategy is to rely on container technology, in particular on [Docker](https://www.docker.com/). This will allow you to rapidly install the platform and set of libraries you are familiar with in a way that can be easily reproduced and redeployed (e.g. on a remote computer on campus).
-
-Here are a series of pages that will help you get a stack ready to go:
-
-- [`setup_docker.md`](setup_docker.md): instructions to install and get Docker
-  up and running on different platforms
-- [`setup_jupyterlab.md`](setup_jupyterlab.md): instructions to install and
-  run a JupyterLab server both on local (e.g. laptop) and remote (e.g. server)
-  machines
-- [`setup_rstudio.md`](setup_rstudio.md): instructions to install and
-  run a JupyterLab server both on local (e.g. laptop) and remote (e.g. server)
-  machines
-
+This is a repository covering the building blocks of a productive remote
+experience at the GDSL.
 

_bookdown.yml

@@ -0,0 +1,8 @@
+book_filename: "gdsl_knowledge"
+language:
+  ui:
+    chapter_name: "Chapter "
+delete_merged_file: true
+new_session: yes
+output_dir: docs
+

_build.sh

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+set -ev
+
+Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"
+Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')"
+Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::epub_book')"
+

_output.yml

@@ -0,0 +1,17 @@
+bookdown::gitbook:
+  css: style.css
+  config:
+    toc:
+      before: |
+        <li><a href="./">A Minimal Book Example</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
+    edit: https://github.com/rstudio/bookdown-demo/edit/master/%s
+    download: ["pdf", "epub"]
+bookdown::pdf_book:
+  includes:
+    in_header: preamble.tex
+  latex_engine: xelatex
+  citation_package: natbib
+  keep_tex: yes
+bookdown::epub_book: default

book.bib

@@ -0,0 +1,10 @@
+@Book{xie2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.name/knitr/},
+}

index.Rmd

@@ -0,0 +1,28 @@
+--- 
+title: "The Knowledge"
+author: "Geographic Data Science Lab"
+date: "`r Sys.Date()`"
+site: bookdown::bookdown_site
+output: bookdown::gitbook
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+github-repo: gdsl-ul/the_knowledge
+description: "What every GDSLer should know to work from anywhere"
+---
+
+# The Knowledge
+
+In preparation to be able to stay productive while having to work fully remote, this document presents a few things jotted down in one place to help with setups, etc. 
+
+The first step is a checklist everyone should go through:
+
+1. Do you have a computer to work on at home?
+1. Are *all* your relevant files accessible from home?
+1. Do you have a webcam, mic and speakers/headphones?
+1. Are you able to connect to computers on campus? This involves being setup with the University VPN?
+
+These are the basic elements you will require, so if the answer to any of the above is no, please speak with your PhD supervisor.
+
+

packages.bib

@@ -0,0 +1,29 @@
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2019},
+  url = {https://www.R-project.org/},
+}
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2020},
+  note = {R package version 0.17},
+  url = {https://CRAN.R-project.org/package=bookdown},
+}
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2019},
+  note = {R package version 1.23},
+  url = {https://CRAN.R-project.org/package=knitr},
+}
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2019},
+  note = {R package version 1.14},
+  url = {https://CRAN.R-project.org/package=rmarkdown},
+}

preamble.tex

@@ -0,0 +1,8 @@
+\usepackage{booktabs}
+\usepackage{amsthm}
+\makeatletter
+\def\thm@space@setup{%
+  \thm@preskip=8pt plus 2pt minus 4pt
+  \thm@postskip=\thm@preskip
+}
+\makeatother

style.css

@@ -0,0 +1,14 @@
+p.caption {
+  color: #777;
+  margin-top: 10px;
+}
+p code {
+  white-space: inherit;
+}
+pre {
+  word-break: normal;
+  word-wrap: normal;
+}
+pre code {
+  white-space: inherit;
+}