differences for PR #93

epiverse-trace · Dec 18, 2023 · abce44f · abce44f
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diff --git a/config.yaml b/config.yaml
diff --git a/fig/modelling-interventions-rendered-plot_masks-1.png b/fig/modelling-interventions-rendered-plot_masks-1.png
diff --git a/fig/modelling-interventions-rendered-plot_school-1.png b/fig/modelling-interventions-rendered-plot_school-1.png
diff --git a/fig/modelling-interventions-rendered-plot_vaccinate-1.png b/fig/modelling-interventions-rendered-plot_vaccinate-1.png
diff --git a/fig/simulating-transmission-rendered-plot-1.png b/fig/simulating-transmission-rendered-plot-1.png
diff --git a/fig/simulating-transmission-rendered-traj-1.png b/fig/simulating-transmission-rendered-traj-1.png
diff --git a/fig/simulating-transmission-rendered-visualise-1.png b/fig/simulating-transmission-rendered-visualise-1.png
diff --git a/md5sum.txt b/md5sum.txt
@@ -1,15 +1,15 @@
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diff --git a/modelling-interventions.md b/modelling-interventions.md
@@ -50,6 +50,9 @@ In mathematical modelling, we must make assumptions about how NPIs will affect t
 #### Effect of school closures on COVID-19 spread
 
 
+```{.error}
+Error in infection(r0 = 2.7, preinfectious_period = 4, infectious_period = 5.5): could not find function "infection"
+```
 
 
 We want to investigate the effect of school closures on reducing the number of individuals infectious with COVID-19 through time. We assume that a school closure will reduce the frequency of contacts within and between different age groups. 
@@ -108,6 +111,9 @@ close_schools <- intervention(
 ```
 
 
+```{.error}
+Error in model_default_cpp(population = uk_population, infection = covid, : unused argument (infection = covid)
+```
 
 
 To run the model with an intervention we set ` intervention = list(contacts = close_schools)` as follows:
@@ -122,10 +128,17 @@ output_school <- model_default_cpp(
 )
 ```
 
+```{.error}
+Error in model_default_cpp(population = uk_population, infection = covid, : unused argument (infection = covid)
+```
+
 
 We see that with the intervention (solid line) in place, the infection still spreads through the population, though the epidemic peak is smaller than the baseline with no intervention in place (dashed line).
 
-<img src="fig/modelling-interventions-rendered-plot_school-1.png" style="display: block; margin: auto;" />
+
+```{.error}
+Error in eval(expr, envir, enclos): object 'output_school' not found
+```
 
 #### Effect of mask wearing on COVID-19 spread
 
@@ -158,9 +171,16 @@ output_masks <- model_default_cpp(
 )
 ```
 
+```{.error}
+Error in model_default_cpp(population = uk_population, infection = covid, : unused argument (infection = covid)
+```
+
+
 
 
-<img src="fig/modelling-interventions-rendered-plot_masks-1.png" style="display: block; margin: auto;" />
+```{.error}
+Error in eval(expr, envir, enclos): object 'output_masks' not found
+```
 
 
 ## Pharmaceutical interventions
@@ -208,9 +228,16 @@ output_vaccinate <- model_default_cpp(
 )
 ```
 
+```{.error}
+Error in model_default_cpp(population = uk_population, infection = covid, : unused argument (infection = covid)
+```
+
 Here we see that the total number of infectious individuals when vaccination is in place is much lower compared to school closures and mask wearing interventions. 
 
-<img src="fig/modelling-interventions-rendered-plot_vaccinate-1.png" style="display: block; margin: auto;" />
+
+```{.error}
+Error in eval(expr, envir, enclos): object 'output_vaccinate' not found
+```
 
 
 ## Summary