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Auto-generated via {sandpaper} Source : 579b726 Branch : main Author : Amanda Minter <[email protected]> Time : 2023-11-09 13:12:10 +0000 Message : Edit to how to guide text Per suggestion from @avallecam
epiverse-trace · Nov 9, 2023 · 87f1348 · 87f1348
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diff --git a/compare-interventions.md b/compare-interventions.md
@@ -23,7 +23,7 @@ exercises: 30 # exercise time in minutes
 ::::::::::::::::::::::::::::::::::::: prereq
 
 ## Prerequisites
-+ Complete tutorials 'Simulating transmission' and 'Modelling interventions'
++ Complete tutorials [Simulating transmission](../episodes/simulating-transmission.md) and [Modelling interventions](../episodes/modelling-interventions.md)
 
 This tutorial has the following concept dependencies:
 
@@ -62,7 +62,8 @@ The Vacamole model is a deterministic model based on a system of ODEs in [Ainsli
 
 The diagram below describes the flow of individuals through the different compartments. 
 
-<img src="fig/compare-interventions-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" />
+<!--html_preserve--><div class="grViz html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-ca6af240f574fa8839fc" style="width:504px;height:504px;"></div>
+<script type="application/json" data-for="htmlwidget-ca6af240f574fa8839fc">{"x":{"diagram":"digraph{\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       Ev [label = <E<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>>, style = filled, fillcolour = \"gray\"]\n       I\n       Iv [label = <I<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>>, style = filled, fillcolour = \"gray\"]\n       H\n       Hv [label = <H<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>>, style = filled, fillcolour = \"gray\"]\n       D\n       R\n       V1 [label = <V<FONT POINT-SIZE=\"8\"><SUB>1<\/SUB><\/FONT>>, style = filled, fillcolour = \"gray\"]\n       V2 [label = <V<FONT POINT-SIZE=\"8\"><SUB>2<\/SUB><\/FONT>>, style = filled, fillcolour = \"gray\"]\n\n\n  # edges\n  #######\n  S -> E [label = \" infection (&beta;) \"]\n  S -> V1 [label = \" vaccination (&nu;1)\"]\n  V1 -> E [label = \" infection (&beta;)\"]\n  V1 -> V2 [label = \" vaccination\n(second dose) (&nu;2)\"]\n  V2 -> Ev [label = \" infection (&beta;)\"]\n  Ev -> Iv [label = \" onset of \ninfectiousness (&alpha;) \"]\n  E -> I [label = \" onset of \ninfectiousness (&alpha;) \"]\n  I -> H [label = \" hospitalisation (&eta;)\"]\n  Iv -> Hv [label = < hospitalisation (&eta;<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>)>]\n  I -> D [label = \" death (&omega;)\"]\n  I -> R [label = \" recovery (&gamma;)\"]\n  Iv -> D [label = < death (&omega;<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>)>]\n  Iv -> R [label = \" recovery (&gamma;)\"]\n  Hv -> D [label = < death (&omega;<FONT POINT-SIZE=\"8\"><SUB>V<\/SUB><\/FONT>)>]\n  Hv -> R [label = \" recovery (&gamma;)\"]\n  H -> D [label = \" death (&omega;)\"]\n  H -> R [label = \" recovery (&gamma;)\"]\n\n  subgraph {\n  rank = same; S; V1;V2;\n  }\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
 
 See `?epidemics::epidemic_vacamole` for detail on how to run the model. 
 

diff --git a/index.md b/index.md
@@ -25,7 +25,7 @@ Also check out the [glossary](../reference.md) for any terms you may be unfamili
 ## Related projects
 
 + R package vignettes : for R package `{package}` find the vignette located at `https://epiverse-trace.github.io/{package}/`. [Look at all Epiverse-TRACE packages in our developer space](https://epiverse-trace.github.io/).
-+ [howto](https://epiverse-trace.github.io/howto/) : reproducible how-to guides of outbreak data analysis tasks using R packages.
++ [How-to guides](https://epiverse-trace.github.io/howto/) : reproducible recipes with concrete steps to solve specific Outbreak Analysis questions.
 + [The Epidemiologist R Handbook](https://www.epirhandbook.com/en/index.html) : Quick R code reference manual with task-centered examples that address common epidemiological problems.
 + *COMING SOON* case studies : reproducible case-studies of outbreak data analysis tasks using R packages.
 

diff --git a/md5sum.txt b/md5sum.txt
@@ -2,12 +2,12 @@
 "CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2023-10-31"
 "LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2023-10-31"
 "config.yaml" "ba8182fefb4b3a156058872157fb2d7d" "site/built/config.yaml" "2023-10-31"
-"index.md" "5cc044519762eb63cc1875e330d3ad1d" "site/built/index.md" "2023-11-09"
+"index.md" "adfca1a79e0106ee8b3f7731d0678b59" "site/built/index.md" "2023-11-09"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2023-10-31"
 "episodes/simulating-transmission.Rmd" "a09170bca196d6a7ba714ddf159e2e2a" "site/built/simulating-transmission.md" "2023-11-09"
-"episodes/model-choices.Rmd" "38e8e793daeee48caf58e50e88518f0a" "site/built/model-choices.md" "2023-11-09"
-"episodes/modelling-interventions.Rmd" "01eff78117bf3f53015154ca9b961651" "site/built/modelling-interventions.md" "2023-10-31"
-"episodes/compare-interventions.Rmd" "d594dc0466f735d14ccbcc7b2a9d56ef" "site/built/compare-interventions.md" "2023-10-31"
+"episodes/model-choices.Rmd" "4e9de6f75c88cfbe0c265a55ea61345f" "site/built/model-choices.md" "2023-11-09"
+"episodes/modelling-interventions.Rmd" "dff06995ab8d9c4b7b73f162dbf52590" "site/built/modelling-interventions.md" "2023-11-09"
+"episodes/compare-interventions.Rmd" "32da6fa2116d62a3d783e397a2908c15" "site/built/compare-interventions.md" "2023-11-09"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2023-10-31"
 "learners/reference.md" "334277298b83c92dd98c28de895d43cb" "site/built/reference.md" "2023-11-09"
 "learners/setup.md" "b3c6bfa13fd687f926bb1a3e772a2516" "site/built/setup.md" "2023-10-31"

diff --git a/model-choices.md b/model-choices.md
@@ -25,7 +25,7 @@ exercises: 20 # exercise time in minutes
 ::::::::::::::::::::::::::::::::::::: prereq
 
 ## Prerequisites
-+ Complete tutorial 'Simulating transmission'
++ Complete tutorial [Simulating transmission](../episodes/simulating-transmission.md)
 :::::::::::::::::::::::::::::::::
 
 
@@ -122,7 +122,8 @@ Consider the following questions:
 
 A deterministic SEIR model with age specific direct transmission. 
 
-<img src="fig/model-choices-rendered-diagram-1.png" style="display: block; margin: auto;" />
+<!--html_preserve--><div class="grViz html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-133f080a5048e6f8c46b" style="width:504px;height:504px;"></div>
+<script type="application/json" data-for="htmlwidget-133f080a5048e6f8c46b">{"x":{"diagram":"digraph {\n  # graph statement\n  #################\n  graph [layout = dot,\n         rankdir = LR,\n         overlap = true,\n         fontsize = 10]\n  # nodes\n  #######\n  node [shape = square,\n       fixedsize = true,\n       width = 1.3]\n       S\n       E\n       I\n       R\n\n  # edges\n  #######\n  S -> E [label = \" infection\"]\n  E -> I [label = \" onset of \ninfectiousness\"]\n  I -> R [label = \" recovery\"]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
 
 
 The model is capable of predicting an Ebola type outbreak, but as the model is deterministic, we are not able to explore stochastic variation in the early stages of the outbreak.
@@ -132,7 +133,8 @@ The model is capable of predicting an Ebola type outbreak, but as the model is d
 
 A stochastic SEIHFR (Susceptible, Exposed, Infectious, Hospitalised, Funeral, Removed) model that was developed specifically for infection with Ebola.
 
-<img src="fig/model-choices-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" />
+<!--html_preserve--><div class="grViz html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-2bce1f548a563a09141f" style="width:504px;height:504px;"></div>
+<script type="application/json" data-for="htmlwidget-2bce1f548a563a09141f">{"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       H\n       F\n       R\n\n  # edges\n  #######\n  S -> E [label = \" infection \"]\n  E -> I [label = \" onset of \ninfectiousness\"]\n  I -> F [label = \" death \n(funeral) \"]\n  F -> R [label = \" safe burial\"]\n  I -> H [label = \" hospitalisation\"]\n  H -> R [label = \" recovery or \nsafe burial\"]\n\n  subgraph {\n    rank = same; I; F;\n  }\n  subgraph {\n    rank = same; H; R;\n  }\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
 
 
 

diff --git a/modelling-interventions.md b/modelling-interventions.md
@@ -23,7 +23,7 @@ exercises: 30 # exercise time in minutes
 ::::::::::::::::::::::::::::::::::::: prereq
 
 ## Prerequisites
-+ Complete tutorial 'Simulating transmission'
++ Complete tutorial [Simulating transmission](../episodes/simulating-transmission.md)
 
 This tutorial has the following concept dependencies:
 
@@ -108,6 +108,9 @@ close_schools <- intervention(
 ```
 
 
+```{.error}
+Error in epidemic_default_cpp(population = uk_population, infection = covid, : could not find function "epidemic_default_cpp"
+```
 
 
 To run the model with an intervention we set ` intervention = list(contacts = close_schools)` as follows:
@@ -122,10 +125,17 @@ output_school <- epidemic_default_cpp(
 )
 ```
 
+```{.error}
+Error in epidemic_default_cpp(population = uk_population, infection = covid, : could not find function "epidemic_default_cpp"
+```
+
 
 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
 
@@ -158,16 +168,24 @@ output_masks <- epidemic_default_cpp(
 )
 ```
 
+```{.error}
+Error in epidemic_default_cpp(population = uk_population, infection = covid, : could not find function "epidemic_default_cpp"
+```
 
 
-<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
 
 Models can be used to investigate the effect of pharmaceutical interventions, such as vaccination. In this case, it is useful to add another disease state to track the number of vaccinated individuals through time. The diagram below shows an SEIRV model 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-overflow-hidden html-fill-item" id="htmlwidget-f0beb0255d025fcdcecd" style="width:504px;height:504px;"></div>
+<script type="application/json" data-for="htmlwidget-f0beb0255d025fcdcecd">{"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-->
 
 The equations describing this model are as follows: 
 
@@ -208,9 +226,16 @@ output_vaccinate <- epidemic_default_cpp(
 )
 ```
 
+```{.error}
+Error in epidemic_default_cpp(population = uk_population, infection = covid, : could not find function "epidemic_default_cpp"
+```
+
 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