replacing text in 52M where it refers to babs

_quarto.yml

@@ -255,7 +255,7 @@ website:
              - href: pgt52m/week-8/study_after_workshop.qmd
                text: Consolidate!
           - text: ---
-          - section: "Week 9: Inyroduction to the Assessment"
+          - section: "Week 9: Introduction to the Assessment"
             contents:
              - href:
                text: About

pgt52m/week-2/workshop.qmd

@@ -50,9 +50,9 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ![](images/do_in_R.png) Go the Files tab in the lower right pane and click on the `...` on the right. This will open a "Go to folder" window. Navigate to a place on your computer where you keep your work. Click Open.
 
-![](images/do_in_R.png) Also on the Files tab click on `New Folder`. Type "data-analysis-in-r-1" in to the box. This will be the folder that we work in throughout the Data Analysis in R part BABS1.
+![](images/do_in_R.png) Also on the Files tab click on `New Folder`. Type "data-analysis-in-r-1" in to the box. This will be the folder that we work in throughout.
 
-![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Name the RStudio Project 'week-7'.
+![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Name the RStudio Project 'week-2'.
 
 ![](images/do_in_R.png) Make a new script then save it with a name like analysis.R to carry out the rest of the work.
 
@@ -467,7 +467,7 @@ You're finished!
 
 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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/r4babs1/week-7/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/pgt52m/week-2/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
 

pgt52m/week-3/workshop.qmd

@@ -48,7 +48,7 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ![](images/do_on_your_computer.png) Start RStudio from the Start menu.
 
-![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-1` folder and name the RStudio Project 'week-8'.
+![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-1` folder and name the RStudio Project 'week-3'.
 
 ![](images/do_in_R.png) Make a new script then save it with a name like `analysis.R` to carry out the rest of the work.
 
@@ -58,7 +58,7 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ## Importing data from files
 
-Last week we created data [by typing the values in to R](../week-7/workshop.html#creating-the-data). This is not practical when you have added a lot of data to a spreadsheet, or you are using data file that has been supplied to you by a person or a machine. Far more commonly, we import data from a file into R. This requires you know two pieces of information.
+Last week we created data [by typing the values in to R](../week-2/workshop.html#creating-the-data). This is not practical when you have added a lot of data to a spreadsheet, or you are using data file that has been supplied to you by a person or a machine. Far more commonly, we import data from a file into R. This requires you know two pieces of information.
 
 1.  What format the data are in
 
@@ -228,7 +228,7 @@ This sort of data might be represented with a barchart. You have two options for
 
 2.  plot the raw data using `geom_bar()`
 
-We did the first of these [last week](../week-7/workshop.html#plotting-the-data-with-ggplot). The `geom_col()` function uses the numbers in a second column to determine how high the bars are. However, the `geom_bar()` function will do the tabulating for you.
+We did the first of these [last week](../week-2/workshop.html#plotting-the-data-with-ggplot). The `geom_col()` function uses the numbers in a second column to determine how high the bars are. However, the `geom_bar()` function will do the tabulating for you.
 
 ![](images/do_in_R.png) Plot the coat data using `geom_bar`:
 
@@ -453,7 +453,7 @@ You're finished!
 
 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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/r4babs1/week-8/workshop.qmd). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/pgt52m/week-3/workshop.qmd). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
 

pgt52m/week-4/workshop.qmd

@@ -47,7 +47,7 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ![](images/do_on_your_computer.png) Start RStudio from the Start menu.
 
-![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-1` folder and name the RStudio Project 'week-9'.
+![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-1` folder and name the RStudio Project 'week-4'.
 
 ![](images/do_in_R.png) Make a new folder called `data-raw`. You can do this on the Files Pane by clicking New Folder and typing into the box that appears.
 
@@ -81,7 +81,7 @@ The myoglobin concentration of skeletal muscle of three species of seal in grams
 
 ![](images/do_on_your_computer.png) Save [seal.csv](data-raw/seal.csv) to your `data-raw` folder
 
-![](images/do_in_R.png) Read the data into a dataframe called `seal`. . You might want to look up [data import from last week](../week-8/workshop.html#importing-data-from-files).
+![](images/do_in_R.png) Read the data into a dataframe called `seal`. . You might want to look up [data import from last week](../week-3/workshop.html#importing-data-from-files).
 
 ```{r}
 #| include: false
@@ -510,7 +510,7 @@ You're finished!
 
 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/R4BABS/blob/main/r4babs1/week-9/workshop.qmd). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+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/R4BABS/blob/main/pgt52m/week-4/workshop.qmd). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
 

pgt52m/week-5/study_after_workshop.qmd

@@ -23,7 +23,7 @@ library(tidyverse)
 1.  💻 Adiponectin is exclusively secreted from adipose tissue and modulates a number of metabolic processes. Nicotinic acid can affect adiponectin secretion. 3T3-L1 adipocytes were treated with nicotinic acid or with a control treatment and adiponectin concentration (pg/mL) measured. The data are in [adipocytes.txt](data-raw/adipocytes.txt). Each row represents an independent sample of adipocytes and the first column gives the concentration adiponectin and the second column indicates whether they were treated with nicotinic acid or not. Estimate the mean Adiponectin concentration in each group - this means calculate the sample mean and construct a confidence interval around it for each group. This exercise forces you to bring together ideas from this workshop and from previous workshops
 
 -   How to calculate a confidence intervals (this workshop)  
--   How to summarise variables in more than one group [BABS 1, Week 9: Summarising data in with several variables and the role of variables in analysis](../../r4babs1/week-9/workshop.html#summarise)
+-   How to summarise variables in more than one group (previous workshop)
 
 ```{r}
 #| output: false

pgt52m/week-5/workshop.qmd

@@ -48,23 +48,19 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ![](images/do_on_your_computer.png) Start RStudio from the Start menu.
 
-![](images/do_in_R.png) Go the Files tab in the lower right pane and click on the `...` on the right. This will open a "Go to folder" window. Navigate to a place on your computer where you keep your work. Click Open.
-
-![](images/do_in_R.png) Also on the Files tab click on `New Folder`. Type "data-analysis-in-r-2" in to the box. This will be the folder that we work in throughout the Data Analysis in R part BABS2.
-
-![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Name the RStudio Project 'week-1'.
+![](images/do_in_R.png) Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project.  Navigate to the data-analysis-in-r-1 folder and name the RStudio Project 'week-5'.
 
 ![](images/do_in_R.png) Make a new script then save it with a name like analysis.R to carry out the rest of the work.
 
-![](images/do_in_R.png) Add a comment to the script: `# Introduction to RStudio and your first graph` and load the **`tidyverse`** [@tidyverse] package
+![](images/do_in_R.png) Add a comment to the script: `# The logic of hypothesis testing and confidence intervals` and load the **`tidyverse`** [@tidyverse] package
 
 ![](images/do_in_R.png) Make a new folder called `data-raw`.
 
 # Exercises
 
 ## Remind yourself how to import files!
 
-[Importing data from files](../../r4babs1/week-8/workshop.html#importing-data-from-files) was covered in BABS 1 [@rand2023] if you need to remind yourself.
+[Importing data from files](../week-3/workshop.html#importing-data-from-files) was covered in a previous workshop [@rand2023] if you need to remind yourself.
 
 ## Confidence intervals (large samples)
 
@@ -249,7 +245,7 @@ You're finished!
 
 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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/r4babs2/week-1/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/pgt52m/week-5/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
 

pgt52m/week-6/workshop.qmd

@@ -54,7 +54,7 @@ These four symbols are used at the beginning of each instruction so you know whe
 
 ![](images/do_in_R.png)  Go the Files tab in the lower right pane and click on the `...` on the right. This will open a "Go to folder" window. Navigate to a place on your computer where you keep your work. Click Open.
 
-![](images/do_in_R.png)  Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-2` folder and name the RStudio Project `week-2`.
+![](images/do_in_R.png)  Make an RStudio project for this workshop by clicking on the drop-down menu on top right where it says `Project: (None)` and choosing New Project, then New Directory, then New Project. Navigate to the `data-analysis-in-r-1` folder and name the RStudio Project `week-6`.
 
 ![](images/do_in_R.png)   Make new folders called `data-raw` and `figures`. You can do this on the Files Pane by clicking New Folder and typing into the box that appears.
 
@@ -293,7 +293,7 @@ ggplot(plant, aes(x = day, y = mass)) +
 
 
 ![](images/do_in_R.png) Improve the axes. You may need to refer back 
-[Changing the axes](../../r4babs1/week-7/workshop.html#changing-the-axes) from the Week 7 workshop in BABS1 [@rand2023]
+[Changing the axes](../week-2/workshop.html#changing-the-axes) from the Week 2 workshop
 
 ```{r}
 #| include: false
@@ -379,7 +379,7 @@ You're finished!
 
 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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/r4babs2/week-2/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+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 interweaved 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 Rmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/R4BABS/blob/main/pgt52m/week-6/workshop.qmd).Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
 Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]