From f981d2680b205d53d7c9e35f8148b40a21d75a87 Mon Sep 17 00:00:00 2001
From: Emma Rand <emma.rand@york.ac.uk>
Date: Tue, 3 Oct 2023 18:08:09 +0100
Subject: [PATCH] outline for core 2 workshop

---
 core/week-2/workshop.qmd | 51 ++++++++++++++++++++++++++++------------
 1 file changed, 36 insertions(+), 15 deletions(-)

diff --git a/core/week-2/workshop.qmd b/core/week-2/workshop.qmd
index 91a3dcc..667465a 100644
--- a/core/week-2/workshop.qmd
+++ b/core/week-2/workshop.qmd
@@ -24,7 +24,7 @@ In this workshop you will
 
 
 
-# File formats
+# File types
 
 
 Types of Data files. 
@@ -34,56 +34,77 @@ Types of Data files.
 
 Similarities and differences
 
-## Getting started
+# Workflow tips
 
-Make a new RStudio project (use the workflow from in the independent
+🎬 Make a new RStudio project (use the workflow from in the independent
 study
 
-Tips
 
-multiple cursors
+-   multiple cursors
 
-open a file
+-   open a file
 
-the command pallette, 
+-   the command palette, 
 
-segmenting code
+-   segmenting code
 
-to correct indentation CONTROL+i
+-   to correct indentation CONTROL+i
 
-to reformat code CONTROL+SHIFT+A Not perfect but corrects spacing, indentation, multiple commands on lines and assignment with `=`
+-   to reformat code CONTROL+SHIFT+A Not perfect but corrects spacing, indentation, multiple commands on lines and assignment with `=`
+
+-   to comment and uncomment lines CONTROL+SHIFT+C
+
+-   Tools | Global options | Code | Display | Show margin
+
+-   Tools | Global options | Code | Diagnostic | Provide R style diagnostics
+
+-   [GitHub Copilot in RStudio, it’s finally here!](https://colorado.posit.co/rsc/rstudio-copilot/#/TitleSlide)
 
 
-to comment and uncomment lines CONTROL+SHIFT+C
 
-show the margin Tools | Global Options | Code
 
 
 
 
 restart R
 
-# The command line
+# Other tools
+
+## The command line
 
 The command line - or shell - is a text interface for your computer.
 It's a program that takes in commands, which it passes on to the
 computer's operating system to run.
 
-## RStudio terminal
+
+-   Windows PowerShell is a command-line in windows. It uses bash-like commands unlike the Command Prompt which uses dos commands (a sort of windows only language). You can open is by going to Start | Windows PowerShell or by searching for it in the search bar.
+
+- Terminal is the command line in Mac OS X. You can open it by going to Applications | Utilities | Terminal or by searching for it in the Spotlight search bar.
+
+-   git bash. I used the bash shell that comes with [Git](https://git-scm.com/)
+
+### RStudio terminal
 
 The RStudio terminal is a convenient interface to the shell without
 leaving RStudio. It is useful for running commands that are not
 available in R. For example, you can use it to run other programs like
 fasqc, git, ftp, ssh
 
+### Using a command line
+
+We are going to learn some commands navigating your folders from the command line
+
+
 ```{bash}
-pwd
+
 ```
 
+
 ```{bash}
 ls
 ```
 
+
 ```{bash}
 ls -l
 ```