delete notebook

Author: blenback

55cdf6acf54f7e6e

@@ -44,6 +44,7 @@ Ensure the following are installed:
 Directly using Quarto from the the terminal:
 
 ```{bash}
+#| eval: false
 quarto use template blenback/quarto-eth-phd-thesis
 ```
 
@@ -54,6 +55,7 @@ Once you do that you can render from within the directory.
 Or by cloning the repository
 
 ```{bash}
+#| eval: false
 git clone https://github.com/YOUR_USERNAME/quarto-eth-phd-thesis.git
 cd quarto-eth-phd-thesis
 ```
@@ -67,12 +69,14 @@ Open the `quarto-eth-phd-thesis.Rproj` file in RStudio to access the full projec
 From the RStudio console or terminal:
 
 ```{bash}
+#| eval: false
 quarto render
 ```
 
 ## 🗂️ Project Structure
 
 ```{bash}
+#| eval: false
 quarto-eth-phd-thesis/
   ├── bibliography.bib # BibTeX file for references
   ├── _book/ # Output directory for rendered book
@@ -136,6 +140,7 @@ quarto-eth-phd-thesis/
 I use the `.Rprofile` to load R packages rather than specifying packages within individual `.qmd` files or `.R` scripts as the .Rprofile is called prior to rendering each file. Add any additional packages you require here.
 
 ```{bash}
+#| eval: false
 #load packages
 packs<-c("ggplot2", "knitr", "kableExtra", "ggthemes", "stringr")
 
@@ -150,6 +155,7 @@ Also in the `.Rprofile` are some functions to streamline uniform styling of figu
 For tables the `thesis_tbl()` function sets options for `knitr::kbl()` and `kableExtra::kable_styling()` to produce booktabs style tables, with center aligned content and bold column titles:
 
 ```{bash}
+#| eval: false
 thesis_tbl <- function(x, escape, ltable = FALSE) {
   x %>%
     kbl(digits = 3,
@@ -172,7 +178,7 @@ thesis_tbl <- function(x, escape, ltable = FALSE) {
 An example of applying this function is included in `chapters/paper-01-qmd`:
 
 ```{bash}
-#| tbl-pos: H
+#| eval: false
 
 #load csv of allocation parameter summary statistics
 Calibration_summary <- read.csv("chapters/paper-01/data/Validation_summary.csv")
@@ -189,6 +195,7 @@ Calibration_summary %>%
 For figures the function `theme_publication()` sets a custom `ggplot2` theme:
 
 ```{bash}
+#| eval: false
 #' theme_publication
 #' 
 #' custom ggplot2 theme to apply to all plots
@@ -236,6 +243,7 @@ theme_thesis <- function(
 In addition the `.Rprofile` contains a series of functions for producing custom continuous and discrete color palettes with the base set of colors specified within the function `thesis_color()`:
 
 ```{bash}
+#| eval: false
 thesis_color <- function(...) {
   
   thesis_colors <- c(
@@ -271,6 +279,7 @@ thesis_color <- function(...) {
 These color palettes can be applied using defined `ggplot2::scale_color_*` and `ggplot2::scale_fill_*` methods. An example of applying the `theme_thesis()` and `scale_color_thesis()` functions is provided in `chapters/paper-01/paper-01-figs.R:`
 
 ```{bash}
+#| eval: false
 p <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) +
   geom_point(size = 3) +
   labs(
@@ -287,7 +296,7 @@ p <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) +
 
 The template allows you to add a coverpage using the [`quarto_titlepages`](https://nmfs-opensci.github.io/quarto_titlepages/) extension. The cover page YAML options are set in in `index.qmd`:
 
-``` yaml
+```{yaml}
 ---
 format: 
   pdf:
@@ -326,7 +335,7 @@ Here I have set the title and subtitle using the extension options but you could
 
 The ETH doctoral regulations stipulate that the thesis must include a translation of the summary or abstract into one of the Swiss national languages (following the English version). I have added a seperate `.qmd` file to include this and YAML key for specifying the translation of summary in `_quarto.yml`:
 
-``` yaml
+```{yaml}
 ---
 summarytitle: Zusammenfassung
 ---
@@ -336,7 +345,7 @@ summarytitle: Zusammenfassung
 
 To create the standard ETH title page for thesis I have adapted an [existing LaTeX template](https://github.com/tuxu/ethz-thesis/blob/master/frontbackmatter/titlepage.tex) with the relevant lines included in `ETH-thesis-template.cls`. Rather than directly editing the LaTeX I have defined YAML keys in `partials/title.tex` so that the fields can be filled directly in `_quarto.yml`:
 
-``` yaml
+```{yaml}
 ---
 titlepage-title: "Your thesis title"
 titlepage-author: "Jane Doe"
@@ -362,7 +371,7 @@ Which results in the title page being rendered as:
 
 In the template I have included typical chapters such as the Introduction, State of the Art, Structure, Synthesis and an example of chapter based on a published paper (`chapters/paper-01-qmd`). Each chapter is a separate `.qmd` file and you can include/exclude them, or add additional chapters, using the `chapters` YAML key in `_quarto.yml`:
 
-``` yaml
+```{yaml}
 book: 
   date: last-modified
   chapters:
@@ -394,6 +403,7 @@ The code for this is included in `chapters/paper-01/paper-01.qmd` and it uses th
 My preferred method of preparing figures for Quarto documents is to produce and save them via dedicated R scripts rather than directly within the `.qmd` files themselves. This R script is then sourced directly at the head of the respective `.qmd` file to ensure the most up to date figures are used and the images are then included for each figure as in `paper-01.qmd`:
 
 ```{bash}         
+#| eval: false
 #source the script that prepares all the figures
 source("chapters/paper-01/paper-01-figs.R")
 
@@ -408,7 +418,7 @@ I do this because I find that when I have multiple figures with quite lengthy co
 
 `endmatter/references.qmd` places a div to ensure that all references for all chapters are placed in this section:
 
-``` {bash}        
+``` {bash}    
 ::: {#refs}
 :::
 ```