draft plans for core 1

core/core.qmd

@@ -6,27 +6,69 @@ toc-location: right
 
 # Content
 
-## Core 1
+Overview
+You are either an integrated masters student doing 88H Group Project or a MSc Bioinformatics student doing 70M
 
-Note no R coding (too early for 70M)
+
+## Week 1 Core 1 Organising Reproducible Data Analyses
+
+Note no R coding (too early for MSc BIN 70M who share the core and omics teaching)
+
+Before
+-   Optional revision: What they forgot to teach you about computers: operating systems, file systems, file types, working directories and paths
+
+-   Why reproducibility (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)
+
+Workshop
 
 -   Project organisation: folders, files
 -   Project oriented workflow
--   Readme
 -   Naming things
--   Keeping notes
--   Data management, google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6
--   file formats
--   Introduction to data in general. Similarities and differences
+-   File formats
+-   Data management
+    -   google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6
+    -   documenting
+    -   organisation within files
+-   Data files. Similarities and differences
     -   Sequences data
     -   Image data
     -   Structure data. 
+-   Keeping notes
+-   Readme
+-   Reference managers: Zotero
+
+After
+
+## Week 2 Core 2 NEEDS A TITLE
+
+Before
+Possibly:
+Code formatting and style, 😎 Cool code Tips, Code 'algorithmically.', Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)
+
+
+
+Workshop
+
+
+
+After
+
+## Week 6 Core 3 Reproducible Reporting
 
+Before
+ (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown and BIO00058M-Data-science-2020/slides/04_advanced_rmarkdown.html)
+Literate programming
+What is quarto
+markdown basics: text, code chunks, headings
+yaml
+automatic numbering of figures and tables
+cross references
+special characters
+citations
 
-## Core 2
 
-rgetgretger
+Workshop
 
-## Core 3: Quarto
+practice doing the above with your project and data
 
-fgzzdfghdfhg
+After

core/week-1/overview.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Overview"
-subtitle: "Core 1"
+subtitle: "Core 1: Organising Data Analyses"
 ---
 
 xxxxx
@@ -16,7 +16,7 @@ xxxxx
 
 1.  [Prepare](study_before_workshop.qmd)
 
-    i.  📖 Read ddd
+    i.  📖 Read [What they forgot to teach you about computers](https://3mmarand.github.io/comp4biosci/what_they_forgot.html)
 
 2.  [Workshop](workshop.qmd)
 

core/week-1/workshop.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Workshop"
-subtitle: "xxx"
+subtitle: "Organising Reproducible Data Analyses"
 toc: true
 toc-location: right
 ---
@@ -15,44 +15,37 @@ library(tidyverse)
 
 ## 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.
+In this workshop you will 
 
-## 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.
+# Exercises
 
-Add code to load the **`tidyverse`** package [@tidyverse]
 
-# Exercises
+🎬 
+-   Project organisation: folders, files
+-   Project oriented workflow
+-   Naming things
+-   File formats
+-   Data management
+    -   google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6
+    -   documenting
+    -   organisation within files
+-   Data files. Similarities and differences
+    -   Sequences data
+    -   Image data
+    -   Structure data. 
+-   Keeping notes
+-   Readme
+-   Reference managers: Zotero
 
 
 You're finished!

core/week-2/overview.qmd

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

core/week-2/study_after_workshop.qmd

@@ -0,0 +1,25 @@
+---
+title: "Independent Study to consolidate this week"
+subtitle: "Core 2"
+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-2/study_before_workshop.qmd

@@ -0,0 +1,6 @@
+---
+title: "Independent Study to prepare for workshop"
+subtitle: "Core 2"
+---
+
+1.  📖 Read xxxx

core/week-2/workshop.qmd

@@ -0,0 +1,55 @@
+---
+title: "Workshop"
+subtitle: "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
+toc: true
+toc-location: right
+---
+
+```{r}
+#| include: false
+library(tidyverse)
+```
+
+# Introduction
+
+
+## Session overview
+
+In this workshop you will 
+
+
+::: callout-note
+## Key
+
+
+:::
+
+# Getting started
+
+
+# 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

core/week-6/overview.qmd

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

core/week-6/study_after_workshop.qmd

@@ -0,0 +1,25 @@
+---
+title: "Independent Study to consolidate this week"
+subtitle: "Core 3 Reproducible Reporting"
+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-6/study_before_workshop.qmd

@@ -0,0 +1,6 @@
+---
+title: "Independent Study to prepare for workshop"
+subtitle: "Core 3 Reproducible Reporting"
+---
+
+1.  📖 Read xxxx