tocs to all babs1 and 2

r4babs1/week-6/overview.qmd

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 ---
 title: Overview
 subtitle: "Understanding file systems"
+toc: true
+toc-location: right
 ---
 
 This week you will carry out some independent study to ensure you have some understanding of computer file systems. We will introduce you to the concepts of paths and working directories.

r4babs1/week-6/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Understanding file systems"
+toc: true
+toc-location: right
 ---
 
 

r4babs1/week-6/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Understanding file systems"
+toc: true
+toc-location: right
 ---
 
 1.  Watch an Introduction to Data Analysis in R for BABS 1 - 4

r4babs1/week-7/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: Overview
 subtitle: "Introduction to R, RStudio and project organisation"
+toc: true
+toc-location: right
 ---
 
 This week you will start writing R code in RStudio and will create your first graph! You will learn about data types such as "numerics" and "characters" and some of the different types of objects in R such as "vectors" and "dataframes". These are the building blocks for the rest of your R journey. You will also learn a workflow and about the layout of RStudio and using RStudio Projects.

r4babs1/week-7/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Introduction to R, RStudio and project organisation"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs1/week-7/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Introduction to R, RStudio and project organisation"
+toc: true
+toc-location: right
 ---
 
 1.  **Either** 

r4babs1/week-8/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "Types of variable, the normal distribution and summarising data"
+toc: true
+toc-location: right
 ---
 
 The type of values our data can take is important in how we analyse and visualise it. This week you will learn the difference between continuous and discrete values and how we summarise and visualise them. You will also learn about the "normal distribution" which is the most important continuous distribution. 

r4babs1/week-8/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Types of variable, the normal distribution and summarising data"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs1/week-8/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Types of variable, the normal distribution and summarising data"
+toc: true
+toc-location: right
 ---
 
 1.  📖 Read [Ideas about data](https://3mmarand.github.io/comp4biosci/ideas_about_data.html)

r4babs1/week-9/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "Summarising data in with several variables and the role of variables in analysis"
+toc: true
+toc-location: right
 ---
 
 Last week you summarised and plotted single variables. This week you will start plotting data sets with more than one variable. This means you need to be able determine which variable is the response and which is the explanatory. You will find out what is meant by "tidy" data and how to perform a simple data tidying task. Finally you will discover how to save your figures and place them in documents.

r4babs1/week-9/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Summarising data in with several variables and the role of variables in analysis"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs1/week-9/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Summarising data in with several variables and the role of variables in analysis"
+toc: true
+toc-location: right
 ---
 
 1.  📖 Read [From importing to reporting](https://3mmarand.github.io/comp4biosci/import_to_report.html). The first part of this chapter is about data import which we covered in the last workshop. You may be able to skip that part or you may find it useful to revise. The section on [Summarising data](https://3mmarand.github.io/comp4biosci/import_to_report.html#summarising-data) will be mainly new.

r4babs2/week-1/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "The logic of hypothesis testing and confidence intervals"
+toc: true
+toc-location: right
 ---
 
 This week we will cover the logic of consider the logic of hypothesis testing and type 1 and type 2 errors. We will also find out what the sampling distribution of the mean and the standard error are, and how to calculate confidence intervals.

r4babs2/week-1/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "The logic of hypothesis testing and confidence intervals"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-1/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "The logic of hypothesis testing and confidence intervals"
+toc: true
+toc-location: right
 ---
 
 1. 📖 Read [The logic of hyothesis testing](https://3mmarand.github.io/comp4biosci/logic_hyopthesis_testing.html) 

r4babs2/week-2/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subitle: "Introduction to statistical models: Single linear regression"
+toc: true
+toc-location: right
 ---
 
 This week you will be introduced to the idea of a statistical "model" in general and to general linear model in particular. Our first general linear model will be single linear regression which puts a line of best fit through data so the response can be predicted from the explanatory variable. We will consider the two "parameters" estimated by the model (the slope and the intercept) and whether these differ from zero

r4babs2/week-2/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Introduction to statistical models: Single linear regression"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-2/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Introduction to statistical models: Single linear regression"
+toc: true
+toc-location: right
 ---
 
 1. 📖 Read [What is a statistical model](https://3mmarand.github.io/comp4biosci/what_statistical_model.html)

r4babs2/week-3/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "Two-sample tests"
+toc: true
+toc-location: right
 ---
 
 This week you will how to use and interpret the general linear model when the *x* variable is categorical and has two groups. Just as with single linear regression, the model puts a line of best through data and the model parameters, the intercept and the slope, have the same in interpretation The intercept is one of the group means and the slope is the difference between that, mean and the other group mean. You will also learn about the non-parametric equivalents - the tests we use when the assumptions of the general linear model are not met. 

r4babs2/week-3/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Two-sample tests"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-3/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Two-sample tests"
+toc: true
+toc-location: right
 ---
 
 1.  Prepare

r4babs2/week-4/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
-subtitle: "One-way ANOVA and Kruskal-Wallis"
+subtitle: "One-way ANOVA and Kruskal-Wallis"toc: true
+toc-location: right
+
 ---
 
 Last week you learnt how to use and interpret the general linear model when the *x* variable was categorical with two groups. You will now extend that to situations when there are more than two groups. This is often known as the one-way ANOVA (**an**alysis **o**f **var**iance). You will also learn about the Kruskal- Wallis test which can be used when the assumptions of the general linear model are not met.

r4babs2/week-4/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "One-way ANOVA and Kruskal-Wallis"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-4/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "One-way ANOVA and Kruskal-Wallis"
+toc: true
+toc-location: right
 ---
 
 1.  Prepare

r4babs2/week-5/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "Two-way ANOVA"
+toc: true
+toc-location: right
 ---
 
 This week we will extend of our understanding by learning how to include *two*

r4babs2/week-5/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Two-way ANOVA"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-5/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Two-way ANOVA"
+toc: true
+toc-location: right
 ---
 
 1.  Prepare

r4babs2/week-6/overview.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Overview"
 subtitle: "Chi-squared tests and correlation"
+toc: true
+toc-location: right
 ---
 
 This week you will 

r4babs2/week-6/study_after_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to consolidate this week"
 subtitle: "Chi-squared tests and correlation"
+toc: true
+toc-location: right
 format:
   html:
     code-fold: true

r4babs2/week-6/study_before_workshop.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Independent Study to prepare for workshop"
 subtitle: "Chi-squared tests and correlation"
+toc: true
+toc-location: right
 ---
 
 1.  Prepare