differences for PR #113

Author: actions-user

.DS_Store

@@ -0,0 +1,86 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'epiverse-trace'
+
+# Overall title for pages.
+title: 'Scenario modelling for outbreak analytics with R'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: 
+
+# Comma-separated list of keywords for the lesson
+keywords: 'epidemic models, interventions'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'pre-alpha'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/epiverse-trace/tutorials-late'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: 'andree.valle-campos@lshtm.ac.uk'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+- contact-matrices.Rmd
+- simulating-transmission.Rmd
+- model-choices.Rmd
+- modelling-interventions.Rmd
+- compare-interventions.Rmd
+- vaccine-comparisons.Rmd
+- disease-burden.Rmd
+
+# Information for Learners
+learners: 
+
+# Information for Instructors
+instructors: 
+
+# Learner Profiles
+profiles: 
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+
+varnish: epiverse-trace/varnish@epiversetheme
+sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug

config.yaml

@@ -64,7 +64,7 @@ associated with the lessons. They appear in the "Instructor View".
 
 ## A burden model
 
-We will extend the influenza example from the [Simulating transmission](../episodes/simulating-transmission.md) tutorial to calculate hospitalizations over time. Our approach has two main components:
+We will extend the influenza example from the [Simulating transmission](../episodes/simulating-transmission.md) tutorial by using the `output` object to calculate hospitalizations over time. Our approach has two main components:
 
 1. **Transmission model**: An SEIR model that generates new infections over time
 2. **Burden model**: Converts new infections to hospitalizations by accounting for delays between infection and hospitalization
@@ -81,11 +81,77 @@ We'll use `{epiparameter}` to define these delay distributions. The Gamma distri
 - It's bounded at zero (negative delays don't make sense)
 - It's supported by empirical data for many infectious diseases
 
+:::::::::::::::: instructor
 
 
+``` r
+# load contact and population data from socialmixr::polymod
+polymod <- socialmixr::polymod
+contact_data <- socialmixr::contact_matrix(
+  polymod,
+  countries = "United Kingdom",
+  age.limits = c(0, 20, 40),
+  symmetric = TRUE
+)
+
+# prepare contact matrix
+contact_matrix <- t(contact_data$matrix)
+
+# prepare the demography vector
+demography_vector <- contact_data$demography$population
+names(demography_vector) <- rownames(contact_matrix)
+
+# initial conditions: one in every 1 million is infected
+initial_i <- 1e-6
+initial_conditions_inf <- c(
+  S = 1 - initial_i, E = 0, I = initial_i, R = 0, V = 0
+)
+
+initial_conditions_free <- c(
+  S = 1, E = 0, I = 0, R = 0, V = 0
+)
+
+# build for all age groups
+initial_conditions <- rbind(
+  initial_conditions_inf,
+  initial_conditions_free,
+  initial_conditions_free
+)
+rownames(initial_conditions) <- rownames(contact_matrix)
+
+# prepare the population to model as affected by the epidemic
+uk_population <- epidemics::population(
+  name = "UK",
+  contact_matrix = contact_matrix,
+  demography_vector = demography_vector,
+  initial_conditions = initial_conditions
+)
+
+# time periods
+preinfectious_period <- 3.0
+infectious_period <- 7.0
+basic_reproduction <- 1.46
+
+# rates
+infectiousness_rate <- 1.0 / preinfectious_period
+recovery_rate <- 1.0 / infectious_period
+transmission_rate <- basic_reproduction / infectious_period
+
+# run an epidemic model using `epidemic()`
+output <- epidemics::model_default(
+  population = uk_population,
+  transmission_rate = transmission_rate,
+  infectiousness_rate = infectiousness_rate,
+  recovery_rate = recovery_rate,
+  time_end = 600, increment = 1.0
+)
+```
+
+::::::::::::::::
+
 
 ``` r
-new_cases <- new_infections(output_plot, by_group = FALSE)
+new_cases <- new_infections(output, by_group = FALSE)
 head(new_cases)
 ```
 

disease-burden.md

@@ -10,7 +10,7 @@
 "episodes/modelling-interventions.Rmd" "4ddf2a3e860dc11ba7a29ad20228eb3a" "site/built/modelling-interventions.md" "2025-08-19"
 "episodes/compare-interventions.Rmd" "2ef6697bbad9bcfb843ab9d50469123b" "site/built/compare-interventions.md" "2025-08-19"
 "episodes/vaccine-comparisons.Rmd" "bb9110b17b2b5cdc915df3f17eae15df" "site/built/vaccine-comparisons.md" "2025-08-19"
-"episodes/disease-burden.Rmd" "05199c08e0f4394b341dd67b00f7a130" "site/built/disease-burden.md" "2025-08-19"
+"episodes/disease-burden.Rmd" "9deead362349c98be8f1d9380a7b975a" "site/built/disease-burden.md" "2025-08-19"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2025-08-19"
 "learners/BF_measles.Rmd" "5725a25d664730bbce3736a3243c2182" "site/built/BF_measles.md" "2025-08-19"
 "learners/reference.md" "9e836f1ec999f95f55135cdd2c78d2e6" "site/built/reference.md" "2025-08-19"