differences for PR #112

Author: actions-user

.DS_Store

@@ -802,7 +802,7 @@ 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
 )
 

BF_measles.md

@@ -1,19 +1,19 @@
 "file" "checksum" "built" "date"
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-"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2025-08-06"
-"config.yaml" "a0c04c1d43ce0640c3ea333b140e89c8" "site/built/config.yaml" "2025-08-06"
-"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2025-08-06"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2025-08-06"
-"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"
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-"episodes/modelling-interventions.Rmd" "3ca4185369a49bdf75828cd5ac43d5af" "site/built/modelling-interventions.md" "2025-08-06"
-"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/disease-burden.Rmd" "05199c08e0f4394b341dd67b00f7a130" "site/built/disease-burden.md" "2025-08-06"
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-"renv/profiles/lesson-requirements/renv.lock" "d3ac3b591e433d9d022e6b261165e086" "site/built/renv.lock" "2025-08-06"
+"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2025-08-19"
+"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2025-08-19"
+"config.yaml" "a0c04c1d43ce0640c3ea333b140e89c8" "site/built/config.yaml" "2025-08-19"
+"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2025-08-19"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2025-08-19"
+"episodes/contact-matrices.Rmd" "19856620d33f9b7f4e8ee312460494f1" "site/built/contact-matrices.md" "2025-08-19"
+"episodes/simulating-transmission.Rmd" "a416834465425e20bbd0a32afc6c2d32" "site/built/simulating-transmission.md" "2025-08-19"
+"episodes/model-choices.Rmd" "aa195e66455fb6a97b4930fd08c08001" "site/built/model-choices.md" "2025-08-19"
+"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"
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+"learners/setup.md" "ba4314eaa33c1a26c7005999ae684326" "site/built/setup.md" "2025-08-19"
+"profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2025-08-19"
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config.yaml

@@ -430,7 +430,7 @@ 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
 
@@ -440,13 +440,13 @@ 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
 )
 
 infections_intervention <- epidemics::new_infections(
   data = output_vaccinate,
-  compartments_from_susceptible = "vaccinated", # if vaccination
+  exclude_compartments = "vaccinated", # if vaccination
   by_group = FALSE
 )