you should use the Wilcoxon signed-rank test for comparing EFFSAFE1, EFFSAFE2, EFFSAFE3, and EFFSAFE4
I didn't see the wilcoxon signed-rank test in the code. I noticed you did a paired comparison of EFFSAFE1, EFFSAFE2, EFFSAFE3 and EFFSAFE4 in the first plot, so I am assuming the wilcoxon signed-rank test should have been used.
Show the code
The end of this document should include a text summary of the results and discussions.
Shapiro-Wilk normality test
I would possibly add which variable the test corresponds too in each of these labels to make it more clear.
EFFSAFE1
I recommend changing the all of the x-axis labels for each variable to a short name that represent what the variable is measuring. This helps the reader understand what the graph is representing. I would also change the variable name in the title of each plot.
## note to self: shapiro-wilk norm. test should use the raw variables (not composite scores, etc.)
I would delete this since it is a "note to self"
library("ggpubr")
Make sure to include sources and explanations for all code chunks to make it easier for readers to understand what the code is doing.
#
Make sure to add figure captions to both figures to give the reader a quick description of the figure
Table of contents
I would recommend creating headings. Headings will increase the organization of your code and make it easier to understand the flow of the project. Headings will also display in the table of contents, which will provide readers with a quick overview of your analysis.
1 Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see https://quarto.org. 2 Running Code When you click the Render button a document will be generated that includes both content and the output of embedded code. You can embed code like this: Show the code 1 + 1 [1] 2 You can add options to executable code like this [1] 4 The echo: false option disables the printing of code (only output is displayed).
I would delete this section because it does not pertain to your work. It also displays as the only headings on your table of contents.
#
This is a very large code chunk. I would recommend splitting this code chunk into smaller chunks to help organize the code better. You could have one code chunk for mutating the variables. One code chunk for reshaping the data and a different code chunk for the box plot code.
Create boxplot
For the box plot you could assign each variable a short name that summarizes the variable so that when people look at the box plot x-axis they know what the variable represents, instead of just looking at EFFSAFE1, etc.