differences for PR #249

Author: actions-user

fig/superspreading-estimate-rendered-unnamed-chunk-10-1.png

@@ -9,7 +9,7 @@
 "episodes/delays-functions.Rmd" "44567c40c9ecf6de5387668753328cf3" "site/built/delays-functions.md" "2025-10-17"
 "episodes/create-forecast.Rmd" "cc408a17d67fd9429a308b723ad17952" "site/built/create-forecast.md" "2025-10-17"
 "episodes/severity-static.Rmd" "22c2a1c522e4bd4a1f4291df17ac38cb" "site/built/severity-static.md" "2025-10-20"
-"episodes/superspreading-estimate.Rmd" "6295d858f39b668451318a5daabafc43" "site/built/superspreading-estimate.md" "2025-10-24"
+"episodes/superspreading-estimate.Rmd" "75f53bcea81f5ff753b95e85b25fa1a7" "site/built/superspreading-estimate.md" "2025-10-24"
 "episodes/superspreading-simulate.Rmd" "e7fedcad27065f7df8465759ab4dd799" "site/built/superspreading-simulate.md" "2025-10-17"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2025-10-17"
 "learners/intro-cfr-adjust-delays.Rmd" "87d00768a1c2daedc4303f0889472349" "site/built/intro-cfr-adjust-delays.md" "2025-10-17"

fig/superspreading-estimate-rendered-unnamed-chunk-11-1.png

@@ -24,16 +24,35 @@ exercises: 2
 
 ::::::::::::::::::::::::::::::::::::: prereq
 
-## Prerequisites
-
 Learners should familiarise themselves with following concept dependencies before working through this tutorial: 
 
 **Statistics**: common probability distributions, particularly Poisson and negative binomial.
 
 **Epidemic theory**: The reproduction number, R.
 
+**R packages installed**: `{epicontacts}`, `{fitdistrplus}`, `{superspreading}`, `{outbreaks}`, `{tidyverse}`.
+
 :::::::::::::::::::::::::::::::::
 
+:::::::::: spoiler
+
+Install packages if their are not already installed
+
+
+``` r
+# if {pak} is not installed, run: install.packages("pak")
+pak::pak("epicontacts")
+pak::pak("fitdistrplus")
+pak::pak("superspreading")
+pak::pak("outbreaks")
+pak::pak("tidyverse")
+```
+
+If you have any error message,
+go to the [main setup page](../learners/setup.md#software-setup).
+
+::::::::::
+
 ## Introduction
 
 <!-- we know -->
@@ -105,7 +124,7 @@ With the argument `directed = TRUE` we configure a directed graph. These directi
 epicontacts::vis_epicontacts(epi_contacts)
 ```
 
-<img src="fig/superspreading-estimate-rendered-unnamed-chunk-4-1.png" style="display: block; margin: auto;" />
+<img src="fig/superspreading-estimate-rendered-unnamed-chunk-5-1.png" style="display: block; margin: auto;" />
 
 ::::::::::::::::::::::::::: spoiler
 
@@ -254,15 +273,15 @@ all_secondary_cases %>%
   )
 ```
 
-<img src="fig/superspreading-estimate-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" />
+<img src="fig/superspreading-estimate-rendered-unnamed-chunk-9-1.png" style="display: block; margin: auto;" />
 
 The number of secondary cases can be used to _empirically_ estimate the **offspring distribution**, which is the number of secondary _infections_ caused by each case. One candidate statistical distribution used to model the offspring distribution is the **negative binomial** distribution with two parameters:
 
 - **Mean**, which represents the $R_{0}$, the average number of (secondary) cases produced by a single individual in an entirely susceptible population, and
 
 - **Dispersion**, expressed as $k$, which represents the individual-level variation in transmission by single individuals.
 
-<img src="fig/superspreading-estimate-rendered-unnamed-chunk-9-1.png" style="display: block; margin: auto;" />
+<img src="fig/superspreading-estimate-rendered-unnamed-chunk-10-1.png" style="display: block; margin: auto;" />
 
 From the histogram and density plot, we can identify that the offspring distribution is highly skewed or **overdispersed**. In this framework, the superspreading events (SSEs) are not arbitrary or exceptional, but simply realizations from the right-hand tail of the offspring distribution, which we can quantify and analyse ([Lloyd-Smith et al., 2005](https://www.nature.com/articles/nature04153)).
 
@@ -335,7 +354,7 @@ ebola_secondary %>%
   )
 ```
 
-<img src="fig/superspreading-estimate-rendered-unnamed-chunk-10-1.png" style="display: block; margin: auto;" />
+<img src="fig/superspreading-estimate-rendered-unnamed-chunk-11-1.png" style="display: block; margin: auto;" />
 
 From a visual inspection, the distribution of secondary cases for the Ebola data set in `ebola_sim_clean` shows an skewed distribution with secondary cases equal or lower than 6. We need to complement this observation with a statistical analysis to evaluate for overdispersion.
 
@@ -388,7 +407,7 @@ From the number secondary cases distribution we estimated a dispersion parameter
 
 We can overlap the estimated density values of the fitted negative binomial distribution and the histogram of the number of secondary cases:
 
-<img src="fig/superspreading-estimate-rendered-unnamed-chunk-13-1.png" style="display: block; margin: auto;" />
+<img src="fig/superspreading-estimate-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" />
 
 :::::::::::::::::::: callout