add template features and authorship

epiverse-trace · Oct 3, 2024 · 32aee1c · 32aee1c
1 parent 3ec490a
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diff --git 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
@@ -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
@@ -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