replace argument to exclude vaccination in new_infections()

episodes/modelling-interventions.Rmd

@@ -440,7 +440,7 @@ 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
 
@@ -449,13 +449,13 @@ 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
 )
 

episodes/vaccine-comparisons.Rmd

@@ -304,14 +304,14 @@ To understand the **indirect** effect of vaccinations, we want to know the effec
 The inputs required are :
 
 + `data` : the model output,
-+ `compartments_from_susceptible` : this is an optional input, but in our case needed. We don't want the number of people vaccinated to be counted as new infections, so we need to specify the name of the model compartment where individuals transition out from `susceptible` (in this example `vaccinated`),
++ `exclude_compartments` : this is an optional input, but in our case needed. We don't want the number of people vaccinated to be counted as new infections, so we need to specify the name of the model compartment where individuals transition out from `susceptible` (in this example `vaccinated`),
 + `by_group` : should the results be calculated for each demographic group separately. 
 
 
 ```{r}
 vaccinate_01_infections <- epidemics::new_infections(
   output_vaccinate_01,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 ```
@@ -325,17 +325,17 @@ vaccinate_01_infections <- epidemics::new_infections(
 # calculate new infections
 baseline_infections <- epidemics::new_infections(
   output_baseline,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_01_infections <- epidemics::new_infections(
   output_vaccinate_01,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_02_infections <- epidemics::new_infections(
   output_vaccinate_02,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 
@@ -385,17 +385,17 @@ infections %>%
 # calculate new infections
 baseline_infections <- epidemics::new_infections(
   output_baseline,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_01_infections <- epidemics::new_infections(
   output_vaccinate_01,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_02_infections <- epidemics::new_infections(
   output_vaccinate_02,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 
@@ -578,17 +578,17 @@ output_vaccinate_group_3 <- epidemics::model_default(
 
 vaccinate_group_1_infections <- epidemics::new_infections(
   output_vaccinate_group_1,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_group_2_infections <- epidemics::new_infections(
   output_vaccinate_group_2,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_group_3_infections <- epidemics::new_infections(
   output_vaccinate_group_3,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 
@@ -702,17 +702,17 @@ output_vaccinate_group_3 <- epidemics::model_default(
 
 vaccinate_group_1_infections <- epidemics::new_infections(
   output_vaccinate_group_1,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_group_2_infections <- epidemics::new_infections(
   output_vaccinate_group_2,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 vaccinate_group_3_infections <- epidemics::new_infections(
   output_vaccinate_group_3,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = FALSE
 )
 
@@ -789,7 +789,7 @@ To convert infections to deaths, we will need new infections by age group, so we
 ```{r}
 vaccinate_group_1_age <- epidemics::new_infections(
   output_vaccinate_group_1,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
 
@@ -808,7 +808,7 @@ vaccinate_group_1_deaths <-
 
 vaccinate_01_age <- epidemics::new_infections(
   output_vaccinate_01,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
 
@@ -823,7 +823,7 @@ vaccinate_01_deaths <-
 
 vaccinate_group_2_age <- epidemics::new_infections(
   output_vaccinate_group_2,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
 
@@ -838,7 +838,7 @@ vaccinate_group_2_deaths <-
 
 vaccinate_group_3_age <- epidemics::new_infections(
   output_vaccinate_group_3,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
 
@@ -854,7 +854,7 @@ vaccinate_group_3_deaths <-
 
 baseline_age <- epidemics::new_infections(
   output_baseline,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )
 

learners/BF_measles.Rmd

@@ -37,13 +37,13 @@
 recovery duration. Upon recovery, they gain lifelong immunity against
 the current infection, meaning they do not become susceptible again, and
 they move to the recovered class ($\mathbf{R}$) (see
 [Figure 1](#fig-seir)). These are some assumptions for modelling purposes and 
 may not particularly reflect the biological underlying processes.  
 
 ![](fig/t0.drawio.png){ref-parent="fig-seir"}
 ![](fig/t1.drawio.png){ref-parent="fig-seir"}
 ![](fig/t2.drawio.png){ref-parent="fig-seir"}
 ![](fig/t3.drawio.png){ref-parent="fig-seir"}
 
 The four S-E-I-R classes considered in the $\mathbf{SEIR}$ model.
  The number of individuals in each 
@@ -568,7 +568,7 @@
 
 
 
 ::: {.alert .alert-secondary}
 
 ### Question
 
@@ -769,7 +769,7 @@
 # Load new infections data for each scenario
 data_vaccine <- epidemics::new_infections(
   output3,
-  compartments_from_susceptible = "vaccinated",
+  exclude_compartments = "vaccinated",
   by_group = TRUE
 )