From 87f13480721bb4903b6cc007a3bcc8dab29893db Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 9 Nov 2023 13:16:09 +0000 Subject: [PATCH] markdown source builds Auto-generated via {sandpaper} Source : 579b7262e6b7ff8512b88c04d81b86cf43e43e47 Branch : main Author : Amanda Minter Time : 2023-11-09 13:12:10 +0000 Message : Edit to how to guide text Per suggestion from @avallecam --- compare-interventions.md | 5 +++-- index.md | 2 +- md5sum.txt | 8 ++++---- model-choices.md | 8 +++++--- modelling-interventions.md | 35 ++++++++++++++++++++++++++++++----- 5 files changed, 43 insertions(+), 15 deletions(-) diff --git a/compare-interventions.md b/compare-interventions.md index 49d9676e..ad547092 100644 --- 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. - +
+ See `?epidemics::epidemic_vacamole` for detail on how to run the model. diff --git a/index.md b/index.md index 51f40cf5..f81c8e37 100644 --- 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 index 699fae0d..d94d4bc6 100644 --- 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 index ab08ba7c..e9273698 100644 --- 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. - +
+ 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. - +
+ diff --git a/modelling-interventions.md b/modelling-interventions.md index 3808a76a..7a82be3f 100644 --- 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). - + +```{.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" +``` - + + +```{.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. - +
+ 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. - + +```{.error} +Error in eval(expr, envir, enclos): object 'output_vaccinate' not found +``` ## Summary