Remove DiagrammeR in favour of mermaid

CONTRIBUTING.md

@@ -173,7 +173,7 @@ To write a new episode, follow these guidelines
 - Add commonly used links to `links.md`.
 - Add a visible callout for prerequisites at the beginning following the [ETK modules notation](https://github.com/epiverse-trace/tutorials/issues/19). 
 - Add an [introduction section](https://github.com/epiverse-trace/tutorials/issues/17) with the expected summative assessment. 
-- Add diagrams using Diagrammer with greek letters for parameters to [visually represent mathematical models](https://github.com/epiverse-trace/tutorials/issues/21).  
+- Add diagrams using [mermaid flowcharts](https://quarto.org/docs/authoring/diagrams.html) with greek letters for parameters to [visually represent mathematical models](https://github.com/epiverse-trace/tutorials/issues/21).  
 - Use [callouts](https://carpentries.github.io/sandpaper-docs/instructor/component-guide.html) for complementary concepts and function arguments details.  
   - Review how callouts need to be [coded in plain text](https://github.com/carpentries/sandpaper-docs/blob/main/learners/component-guide.md?plain=1). 
   - Review when to use the [spoiler snipped](https://carpentries.github.io/sandpaper-docs/aio.html#use-spoilers-instead-of-floating-solution-blocks). 

episodes/compare-interventions.Rmd

@@ -6,7 +6,6 @@ exercises: 30 # exercise time in minutes
 ---
 
 ```{r setup, echo= FALSE, message = FALSE, warning = FALSE}
-webshot::install_phantomjs(force = TRUE)
 library(epidemics)
 
 # hidden seed for stable stochastic output in lesson

episodes/contact-matrices.Rmd

@@ -4,11 +4,6 @@ teaching: 40
 exercises: 10
 ---
 
-```{r setup, echo= FALSE, message = FALSE, warning = FALSE}
-# we need {webshot} to print {DiagrammeR} outputs
-webshot::install_phantomjs(force = TRUE)
-```
-
 :::::::::::::::::::::::::::::::::::::: questions 
 
 - What is a contact matrix?

episodes/simulating-transmission.Rmd

@@ -4,12 +4,6 @@ teaching: 45 # teaching time in minutes
 exercises: 30 # exercise time in minutes 
 ---
 
-```{r setup, echo= FALSE, message = FALSE, warning = FALSE}
-library(DiagrammeR)
-library(webshot)
-webshot::install_phantomjs(force = TRUE)
-```
-
 :::::::::::::::::::::::::::::::::::::: questions 
 
 - How do I simulate disease spread using a mathematical model?

renv/activate.R

@@ -3,7 +3,7 @@ local({
 
   # the requested version of renv
   version <- "1.2.3"
-  attr(version, "md5") <- "1bd9f58e1cfe27ce035933937c6f03de"
+  attr(version, "md5") <- "59c2d234587132accb321be54c64b7eb"
   attr(version, "sha") <- NULL
 
   # the project directory