differences for PR #112

Author: actions-user

.DS_Store

@@ -802,15 +802,34 @@ controlling the epidemic.
 # Load new infections data for each scenario
 data_vaccine <- epidemics::new_infections(
   output3,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
+```
+
+``` error
+Error in epidemics::new_infections(output3, exclude_compartments = "vaccinated", : unused argument (exclude_compartments = "vaccinated")
+```
 
+``` r
 # Assign scenario names
 data_vaccine$scenario <- "Vaccination"
+```
+
+``` error
+Error: object 'data_vaccine' not found
+```
 
+``` r
 # Combine the data from both scenarios (baseline and vaccination)
 data_combined2 <- bind_rows(data_baseline, data_vaccine)
+```
+
+``` error
+Error: object 'data_vaccine' not found
+```
+
+``` r
 # Plot new infections over time by scenario and demographic groups
 ggplot(data_combined2) +
   # Plot new infections with lines for each demographic group and scenario
@@ -867,7 +886,9 @@ ggplot(data_combined2) +
   )
 ```
 
-<img src="fig/BF_measles-rendered-unnamed-chunk-11-1.png" style="display: block; margin: auto;" />
+``` error
+Error: object 'data_combined2' not found
+```
 
 
 ## Combining interventions

BF_measles.md

@@ -7,12 +7,12 @@
 "episodes/contact-matrices.Rmd" "19856620d33f9b7f4e8ee312460494f1" "site/built/contact-matrices.md" "2025-08-06"
 "episodes/simulating-transmission.Rmd" "a416834465425e20bbd0a32afc6c2d32" "site/built/simulating-transmission.md" "2025-08-06"
 "episodes/model-choices.Rmd" "aa195e66455fb6a97b4930fd08c08001" "site/built/model-choices.md" "2025-08-06"
-"episodes/modelling-interventions.Rmd" "3ca4185369a49bdf75828cd5ac43d5af" "site/built/modelling-interventions.md" "2025-08-06"
+"episodes/modelling-interventions.Rmd" "4ddf2a3e860dc11ba7a29ad20228eb3a" "site/built/modelling-interventions.md" "2025-08-19"
 "episodes/compare-interventions.Rmd" "2ef6697bbad9bcfb843ab9d50469123b" "site/built/compare-interventions.md" "2025-08-06"
-"episodes/vaccine-comparisons.Rmd" "a8fc8f333fc466dac9f53c5a17c24760" "site/built/vaccine-comparisons.md" "2025-08-06"
+"episodes/vaccine-comparisons.Rmd" "bb9110b17b2b5cdc915df3f17eae15df" "site/built/vaccine-comparisons.md" "2025-08-19"
 "episodes/disease-burden.Rmd" "05199c08e0f4394b341dd67b00f7a130" "site/built/disease-burden.md" "2025-08-06"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2025-08-06"
-"learners/BF_measles.Rmd" "96bb097b26f09276c095e12f5c9927dc" "site/built/BF_measles.md" "2025-08-06"
+"learners/BF_measles.Rmd" "5725a25d664730bbce3736a3243c2182" "site/built/BF_measles.md" "2025-08-19"
 "learners/reference.md" "9e836f1ec999f95f55135cdd2c78d2e6" "site/built/reference.md" "2025-08-06"
 "learners/setup.md" "ba4314eaa33c1a26c7005999ae684326" "site/built/setup.md" "2025-08-06"
 "profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2025-08-06"

md5sum.txt

@@ -332,7 +332,8 @@ Pharmaceutical interventions (PIs) are measures such as vaccination and mass tre
 
 The diagram below shows the SEIRV model implemented using `model_default()` where susceptible individuals are vaccinated and then move to the $V$ class.
 
-<img src="fig/modelling-interventions-rendered-diagram_SEIRV-1.png" style="display: block; margin: auto;" />
+<!--html_preserve--><div class="grViz html-widget html-fill-item" id="htmlwidget-dc9df32b70b283a80419" style="width:504px;height:504px;"></div>
+<script type="application/json" data-for="htmlwidget-dc9df32b70b283a80419">{"x":{"diagram":"digraph {\n\n  # graph statement\n  ################\n  graph [layout = dot,\n         rankdir = LR,\n         overlap = true,\n         fontsize = 10]\n\n  # nodes\n  #######\n  node [shape = square,\n       fixedsize = true\n       width = 1.3]\n\n       S\n       E\n       I\n       R\n       V\n\n  # edges\n  #######\n  S -> E [label = \" infection (&beta;)\"]\n  S -> V [label = \" vaccination (&nu;)\"]\n  E -> I [label = \" onset of \ninfectiousness (&alpha;)\"]\n  I -> R [label = \" recovery (&gamma;)\"]\n\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
 
 
 
@@ -430,7 +431,7 @@ From the plot, we see that the peak number of total number of infectious individ
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
 Lastly, if you want to plot new infections from an `epidemics::model_default()` that includes a `vaccination` intervention, you need to add one argument to `epidemics::new_infections()`:
-Set `compartments_from_susceptible = "vaccinated"` to tell the function that people moving from "susceptible" to "vaccinated" are not becoming infected. This ensures vaccinated individuals aren't counted as infections.
+Set `exclude_compartments = "vaccinated"` to tell the function that people moving from "susceptible" to "vaccinated" are not becoming infected. This ensures vaccinated individuals aren't counted as infections.
 
 ::::::::::::::::::::: spoiler
 
@@ -440,26 +441,57 @@ Note that if we add `by_group = FALSE` in `epidemics::new_infections()`, we get
 ``` r
 infections_baseline <- epidemics::new_infections(
   data = output_baseline,
-  compartments_from_susceptible = "vaccinated", # if vaccination
+  exclude_compartments = "vaccinated", # if vaccination
   by_group = FALSE
 )
+```
+
+``` error
+Error in epidemics::new_infections(data = output_baseline, exclude_compartments = "vaccinated", : unused argument (exclude_compartments = "vaccinated")
+```
 
+``` r
 infections_intervention <- epidemics::new_infections(
   data = output_vaccinate,
-  compartments_from_susceptible = "vaccinated", # if vaccination
+  exclude_compartments = "vaccinated", # if vaccination
   by_group = FALSE
 )
+```
 
+``` error
+Error in epidemics::new_infections(data = output_vaccinate, exclude_compartments = "vaccinated", : unused argument (exclude_compartments = "vaccinated")
+```
+
+``` r
 # Assign scenario names
 infections_baseline$scenario <- "Baseline"
+```
+
+``` error
+Error: object 'infections_baseline' not found
+```
+
+``` r
 infections_intervention$scenario <- "Vaccination"
+```
 
+``` error
+Error: object 'infections_intervention' not found
+```
+
+``` r
 # Combine the data from both scenarios
 infections_baseline_interv <- dplyr::bind_rows(
   infections_baseline,
   infections_intervention
 )
+```
+
+``` error
+Error: object 'infections_baseline' not found
+```
 
+``` r
 infections_baseline_interv %>%
   ggplot(aes(x = time, y = new_infections, colour = scenario)) +
   geom_line() +
@@ -472,7 +504,9 @@ infections_baseline_interv %>%
   theme_bw()
 ```
 
-<img src="fig/modelling-interventions-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" />
+``` error
+Error: object 'infections_baseline_interv' not found
+```
 
 To get an age-stratified plot, keep the default `by_group = TRUE` and then add `linetype = demography_group` when declaring variables in `ggplot(aes(...))`.