+ infrastructure

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

CITATION.cff

@@ -0,0 +1,11 @@
+cff-version: 1.2.0
+message: "Please cite these materials as below."
+authors:
+- family-names: "Rand"
+  given-names: "Emma"
+  orcid: "https://orcid.org/0000-0002-1358-8275"
+title: "Data Analysis for Group Project"
+version: 0.1
+doi: 
+date-released: 2023-08-01
+url: "https://3mmarand.github.io/BIO00088H-data/"

_quarto.yml

@@ -1,19 +1,147 @@
 project:
   type: website
+  output-dir: _site
 
 website:
-  title: "BIO00088H-data"
+  title: "Data Analysis for Group Project"
+  page-footer:
+    left: '`r cffr::cff_to_bibtex("CITATION.cff")`'
+    right:
+      - icon: twitter
+        href: https://twitter.com/er_13
+        aria-label: Twitter
+      - icon: github
+        href: https://github.com/3mmaRand/BIO00088H-data
+        aria-label: BIO00088H-data GitHub
   navbar:
+    background: light
+    twitter-card: true
+    site-url: https://3mmarand.github.io/BIO00088H-data/
+    repo-url: https://github.com/3mmaRand/BIO00088H-data
+    issue-url: https://github.com/3mmaRand/BIO00088H-data/issues/new/choose
+    repo-actions: [edit, issue]
+    page-navigation: true
+    search: true
     left:
-      - href: index.qmd
-        text: Home
-      - about.qmd
+      - text: "Welcome!"
+        file: index.qmd
+      - text: "Core"
+        file:  core/core.qmd
+      - text: "Omics"
+        file:  omics/omics.qmd
+    tools:
+      - icon: twitter
+        href: https://twitter.com/er_13
+        text: Emma's Twitter
+      - icon: github
+        href: https://github.com/3mmaRand/BIO00088H-data
+        text: BIO00088H-data GitHub
+
+  sidebar:
+    - title: "Core"
+      style: "floating"
+      contents: 
+          - href: core/core.qmd
+          - text: ---
+          - text: ---
+          - section: "Week 1: xxx"
+            contents: 
+             - href: core/week-1/overview.qmd
+               text: About  
+             - href: core/week-1/study_before_workshop.qmd
+               text: Prepare! 
+             - href: core/week-1/workshop.qmd
+               text: Workshop
+             - href: core/week-1/study_after_workshop.qmd
+               text: Consolidate!  
+          - text: ---
+          - section: "Week 2: xxx"
+            contents: 
+             - href: core/week-2/overview.qmd
+               text: About  
+             - href: core/week-2/study_before_workshop.qmd
+               text: Prepare! 
+             - href: core/week-2/workshop.qmd
+               text: Workshop
+             - href: core/week-2/study_after_workshop.qmd
+               text: Consolidate!  
+          - text: ---
+          - section: "Week 6: Quarto"
+            contents: 
+             - href: core/week-6/overview.qmd
+               text: About  
+             - href: core/week-6/study_before_workshop.qmd
+               text: Prepare! 
+             - href: core/week-6/workshop.qmd
+               text: Workshop
+             - href: core/week-6/study_after_workshop.qmd
+               text: Consolidate!  
+    - title: "Omics"
+      style: "floating"
+      contents: 
+          - href: omics/omics.qmd
+          - text: ---
+          - text: ---
+          - section: "Week 3: xx"
+            contents: 
+             - href: omics/week-3/overview.qmd
+               text: About  
+             - href: omics/week-3/study_before_workshop.qmd
+               text: Prepare! 
+             - href: omics/week-3/workshop.qmd
+               text: Workshop
+             - href: omics/week-3/study_after_workshop.qmd
+               text: Consolidate!  
+          - text: ---
+          - section: "Week 4: xxx"
+            contents: 
+             - href: omics/week-4/overview.qmd
+               text: About  
+             - href: omics/week-4/study_before_workshop.qmd
+               text: Prepare! 
+             - href: omics/week-4/workshop.qmd
+               text: Workshop
+             - href: omics/week-4/study_after_workshop.qmd
+               text: Consolidate!  
+          - text: ---
+          - section: "Week 5: xxx"
+            contents: libray/week-5/overview.qmd
+               text: About  
+             - href: omics/week-5/study_before_workshop.qmd
+               text: Prepare! 
+             - href: omics/week-5/workshop.qmd
+               text: Workshop
+             - href: omics/week-5/study_after_workshop.qmd
+               text: Consolidate!  
+execute:
+  echo: true
+  warning: false
+  output: true
+  error: true
+  collapse: true
+
 
 format:
   html:
-    theme: cosmo
-    css: styles.css
-    toc: true
+    link-external-newwindow: true
+    link-external-filter: '^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data'
+    theme:
+      light: [cosmo, custom.scss]
+    code-copy: true
+    code-link: true
+    code-overflow: wrap
+    code-line-numbers: false
+    grid:
+      sidebar-width: 250px
+      body-width: 900px
+      margin-width: 300px
+
+    author-meta: Emma Rand
+
+bibliography: references.bib
+
+
+editor: source
+
 
-editor: visual
 

core/core.qmd

@@ -0,0 +1,19 @@
+---
+title: "Core Data Analysis for Group Project"
+toc: true
+toc-location: right
+---
+
+# Content
+
+## Core 1
+
+erwtERTERTG
+
+## Core 2
+
+rgetgretger
+
+## Core 3: Quarto
+
+fgzzdfghdfhg

core/week-1/overview.qmd

@@ -0,0 +1,33 @@
+---
+title: "Overview"
+subtitle: "Core 1"
+---
+
+xxxxx
+
+### Learning objectives
+
+-   dd
+-   dd.
+-   dd
+-   d
+
+### Instructions
+
+1.  [Prepare](study_before_workshop.qmd)
+
+    i.  📖 Read ddd
+
+2.  [Workshop](workshop.qmd)
+
+    i.  💻 dd.
+
+    ii. 💻 ddd
+
+    iii. 💻 ddd
+
+3.  [Consolidate](study_after_workshop.qmd)
+
+    i.  💻 dd
+
+    ii. 💻 dd

core/week-1/study_after_workshop.qmd

@@ -0,0 +1,25 @@
+---
+title: "Independent Study to consolidate this week"
+subtitle: "Core 1"
+format:
+  html:
+    code-fold: true
+    code-summary: "Answer - don't look until you have tried!"
+---
+
+# Set up
+
+If you have just opened RStudio you will want to load the packages and import the data.
+
+```{r}
+#| code-fold: false
+library(tidyverse)
+library(readxl)
+```
+
+1.  💻 xx.
+
+```{r}
+
+ 
+```

core/week-1/study_before_workshop.qmd

@@ -0,0 +1,6 @@
+---
+title: "Independent Study to prepare for workshop"
+subtitle: "Core 1"
+---
+
+1.  📖 Read xxxx

core/week-1/workshop.qmd

@@ -0,0 +1,76 @@
+---
+title: "Workshop"
+subtitle: "xxx"
+toc: true
+toc-location: right
+---
+
+```{r}
+#| include: false
+library(tidyverse)
+```
+
+# Introduction
+
+
+## Session overview
+
+In this workshop you will learn to summarise and plot datasets with more than one variable and how to write figures to files. You will also get more practice with working directories, importing data, formatting figures and the pipe.
+
+## Philosophy
+
+Workshops are not a test. It is expected that you often don't know how to start, make a lot of mistakes and need help. It is expected that you are familiar with independent study content before the workshop. However, you need not remember or understand every detail as the workshop should build and consolidate your understanding. Tips
+
+-   don't worry about making mistakes
+-   don't let what you can not do interfere with what you can do
+-   discussing code with your neighbours will help
+-   look things up in the independent study material
+-   look things up in your own code from earlier workshops
+-   there are no stupid questions
+
+::: callout-note
+## Key
+
+These four symbols are used at the beginning of each instruction so you know where to carry out the instruction.
+
+![](images/do_on_your_computer.png) Something you need to do on your computer. It may be opening programs or documents or locating a file.
+
+![](images/do_in_R.png) Something you should do in RStudio. It will often be typing a command or using the menus but might also be creating folders, locating or moving files.
+
+![](images/do_on_internet.png) Something you should do in your browser on the internet. It may be searching for information, going to the VLE or downloading a file.
+
+![](images/answer.png) A question for you to think about and answer. Record your answers in your script for future reference.
+:::
+
+# Getting started
+
+Start RStudio make an RStudio project for this workshop.
+
+Make a new folder called `data-raw`. 
+
+Make a new script then save it to carry out the rest of the work.
+
+Add code to load the **`tidyverse`** package [@tidyverse]
+
+# Exercises
+
+
+You're finished!
+
+# 🥳 Well Done! 🎉
+
+
+
+# Independent study following the workshop
+
+[Consolidate](study_after_workshop.qmd)
+
+# The Code file
+
+These contain all the code needed in the workshop even where it is not visible on the webpage.
+
+The [workshop.qmd](workshop.qmd) file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+
+Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
+
+# References

index.qmd

@@ -1,7 +1,38 @@
 ---
-title: "BIO00088H-data"
+title: "Data Analysis for Group Project"
+toc: true
+toc-location: right
 ---
 
-This is a Quarto website.
+# Overview
+
+blah
+
+## Module Learning Objectives
+
+The BIO00088H Module Learning outcomes that relate this content are
+
+-   ..
+
+-   ..
+
+
+Each week has:
+
+-   An overview on the "About" page which gives the Learning Objectives, a topic summary and the instructions for the week. You should read this first.
+
+-   Some independent study on the "Prepare!" page to prepare you for the workshop. It is designed to take about 30-45 mins on average. You will most likely learn best if you can find people to study with.
+
+-   A two-hour workshop. Talking to other people in the workshop about the exercises and working together will really help you understand more. There will be plenty of help from me and my demonstrators.
+
+-   Some independent study on the "Consolidate!" page to give you more practice. The exercises are usually similar to those in the workshop but with less guidance. It is designed to take about 30-45 mins on average but may be quicker if you understood the workshop very well or slower if you need to revisit the workshop.
+
+
+## What is this site for?
+
+All material is on the VLE so why is this site useful? Well, perhaps more than any other material, you will want to refer back when applying your skills and this site collects everything together in a searchable way. The search icon is on the top right.
+
+Resources.
+
+R4 BABS
 
-To learn more about Quarto websites visit <https://quarto.org/docs/websites>.

omics/omics.qmd

@@ -0,0 +1,19 @@
+---
+title: "Omics Data Analysis for Group Project"
+toc: true
+toc-location: right
+---
+
+# Content
+
+## Omics 1
+
+erwtERTERTG
+
+## Omics 2
+
+rgetgretger
+
+## Omics 3
+
+fgzzdfghdfhg