add reconstruct transmission subtitle in index page

.github/CONTRIBUTING.md

@@ -42,7 +42,7 @@ After following the steps above:
 
 #### 1. Find your folder
 
-Folder names corresponds to each box of the [pipeline roadmap](https://epiverse-trace.github.io/) within the `analyses/` folder:
+Folder names corresponds to each task (box) of the [pipeline roadmap](https://epiverse-trace.github.io/getting-started.html#roadmap) within the `analyses/` folder:
 
   - `read_cases/` → Read case data
   - `describe_cases/` → Describe case data
@@ -92,7 +92,7 @@ Use the [**Render** button](https://quarto.org/docs/get-started/hello/rstudio.ht
 
 To render the whole website, use the **Render Website** button within the [Build pane](https://docs.posit.co/ide/user/ide/guide/ui/ui-panes.html).
 
-If your entry is not listed in the `index.qmd` page, try adding a new entry to the `listing:` section in the YAML on top. In the template below, edit the `id:` and `contents:` with for the corresponding task.
+If the task (folder) of your entry is not listed in the `index.qmd` page, First, add a new task entry to the `listing:` section in the YAML on top. In the template below, edit the `id:` and `contents:` with for the corresponding task (folder name). For example, for the task `"Describe case data"` with used as ID `describe-cases` and detailed the folder path `analyses/describe_cases/*.qmd`:
 
 ```
 listing: 
@@ -102,6 +102,15 @@ listing:
     fields: [title]
 ```
 
+Second, to make the listing visible in the website, add a subtitle with the task name (`Describe case data`) and refer to the ID (`describe-cases`) in the following format:
+
+```
+## Describe case data
+
+:::{#describe-cases}
+:::
+```
+
 #### 6. Add new packages to renv
 
 We use the [{renv} R package](https://rstudio.github.io/renv/) to ensure reproducibility of the how-to guides we are providing. All packages used in this repository are registered in the [`renv.lock`](https://github.com/epiverse-trace/howto/blob/main/renv.lock) file.

analyses/reconstruct_transmission/estimate_infections.qmd

@@ -52,8 +52,6 @@ withr::local_options(list(mc.cores = 4))
 
 # Extract data on UK COVID deaths and format for EpiNow2
 incidence_data <- incidence2::covidregionaldataUK %>% 
-  # convert to tibble format
-  dplyr::as_tibble() %>% # for simpler dataframe output
   # preprocess missing values
   tidyr::replace_na(list(deaths_new = 0)) %>%
   # compute the daily incidence
@@ -64,11 +62,11 @@ incidence_data <- incidence2::covidregionaldataUK %>%
     date_names_to = "date",
     complete_dates = TRUE
   ) %>%
-  dplyr::select(-count_variable)
-
-# Focus on early 2020 period and sort by ascending date
-incidence_data <- incidence_data %>% 
-  dplyr::filter(date<"2020-07-01" & date>="2020-03-01")
+  dplyr::select(-count_variable) %>% 
+  # Focus on early 2020 period and sort by ascending date
+  dplyr::filter(date<"2020-07-01" & date>="2020-03-01") %>% 
+  # convert to tibble format for simpler data frame output
+  dplyr::as_tibble()
 
 # Preview data
 incidence_data

index.qmd

@@ -33,6 +33,11 @@ The Epiverse-TRACE **How-to guides** aim to collect recipe-like reproducible scr
 :::{#describe-cases}
 :::
 
+## Reconstruct transmission
+
+:::{#reconstruct-transmission}
+:::
+
 ## Quantify transmission
 
 :::{#quantify-transmission}