From 32aee1cf664fdeefa164c4cdcc3050886fa5de76 Mon Sep 17 00:00:00 2001
From: Andree Valle Campos <avallecam@gmail.com>
Date: Thu, 3 Oct 2024 17:50:09 +0100
Subject: [PATCH] add template features and authorship

---
 .../reproduction_number_cluster_size.qmd          | 10 ++++++++++
 .../reproduction_number_serological_data.qmd      | 10 ++++++++++
 .../estimate_infections.qmd                       | 15 +++++++++++++++
 3 files changed, 35 insertions(+)

diff --git a/analyses/quantify_transmission/reproduction_number_cluster_size.qmd b/analyses/quantify_transmission/reproduction_number_cluster_size.qmd
index d374799..a3a5b92 100644
--- a/analyses/quantify_transmission/reproduction_number_cluster_size.qmd
+++ b/analyses/quantify_transmission/reproduction_number_cluster_size.qmd
@@ -9,8 +9,18 @@ editor_options:
 date: last-modified
 toc: true
 toc_float: true
+author: 
+  - name: "Adam Kucharski"
+    orcid: "0000-0001-8814-9421"
 ---
 
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
 ## Ingredients
 
 - Use Bayesian estimation methods to estimate the reproduction number ($R$) and extent of superspreading, represented by the dispersion of a negative binomial distribution for individual-level seconday cases ($k$), from data on MERS-CoV- outbreak clusters.
diff --git a/analyses/quantify_transmission/reproduction_number_serological_data.qmd b/analyses/quantify_transmission/reproduction_number_serological_data.qmd
index f6ecb3a..eaba079 100644
--- a/analyses/quantify_transmission/reproduction_number_serological_data.qmd
+++ b/analyses/quantify_transmission/reproduction_number_serological_data.qmd
@@ -9,8 +9,18 @@ editor_options:
 date: last-modified
 toc: true
 toc_float: true
+author: 
+  - name: "Adam Kucharski"
+    orcid: "0000-0001-8814-9421"
 ---
 
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
 ## Ingredients
 
 - Social mixing data from `socialmixr`
diff --git a/analyses/reconstruct_transmission/estimate_infections.qmd b/analyses/reconstruct_transmission/estimate_infections.qmd
index 7999791..82d6de7 100644
--- a/analyses/reconstruct_transmission/estimate_infections.qmd
+++ b/analyses/reconstruct_transmission/estimate_infections.qmd
@@ -9,8 +9,18 @@ editor_options:
 date: last-modified
 toc: true
 toc_float: true
+author: 
+  - name: "Adam Kucharski"
+    orcid: "0000-0001-8814-9421"
 ---
 
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
 ## Ingredients
 
 - We want to estimate infection dynamics from incidence data on delayed outcomes such as hospitalisations or deaths.
@@ -21,6 +31,11 @@ toc_float: true
 
 
 ## Steps in code
+
+### Example 1
+
+Reconstruct SARS-CoV-2 infection dynamics in the UK from daily data on deaths, 2020
+
 ```{r}
 #| warning: false