site deploy

Auto-generated via {sandpaper}
Source  : dd92d5c
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2023-11-07 00:36:38 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 969a11b
Branch  : main
Author  : Amanda Minter <amandalminter@gmail.com>
Time    : 2023-10-31 15:37:33 +0000
Message : Late task tutorials  (#34)

* Created late task 1 episode file

* Draft questions. objectives and section titles

* Added notes on lesson content and provisional model equations

* More lesson content to Model structures section

* Outlines of remaining sections added

* Edits to model structure section

* Minor updates to model structures

* Edits to introduction section

* Add content to and reorder model parameters section

* Added example plot to introduction

* Minor edit to text

* Add initial conditions section

Added text and code to initial conditions section and updated initial plot to have same initial conditions

* Reorder of sections

* Updated text to introduction

* Add generating trajectories section

Added content to generating trajectories, which details specifying the initial conditions, demography vector and running the model

* Added contact matrix section

* Edits to tutorial content

Content edits and reordering of some text

* Changed naming of tutorial

Updated name to simulating_transmission to better reflect tutorial content

* Remove references from Rmd

Citations have been changed to hyperlinks, so references no longer needed in Rmd header

* Add file for `model_choices.Rmd`

* Additions and edits to tutorial objectives

* Update model_choices.Rmd

Added tutorial content on all sections for Choosing a model

* Update model_choices.Rmd

Add 'Coming soon' to incomplete sections

* Add uncertainty section

Added section on how to account for uncertainty in R0 for influenza example

* Fix typo

* Add Comparing interventions tutorial

* Remove default lesson

* Update model_choices.Rmd

Updated challenge outline to address #27 and to include Carpentries hint structure

* Add glossary and add terms to `simulating_transmission`

Glossary added in response to #24, additional transmission types added to `simulating_transmission` tutorial

* Hide messages in output

Fixes #26 for `simulating_transmission` and `compare_scenarios`

* Update package and function notation

Fixes #25 for current tutorials

* Fix typo

* Add function to view model names

Fixes #23

* Add callout for exposed, infected, infectious

Fixes #20

* Add instructor notes to tutorials

Address #17

* Add concept dependencies to tutorials

Addresses #19

* Add flow diagram of model equations

Fixes #21

* Add definitions of outbreak and epidemic

Added to `model_choices` tutorial and relevant definitions added to glossary

* Add challenge to `model_choices` tutorial

Fixes #14

* Remove reference to epidemic versus outbreak

Keep tutorial content on the types of model used for epidemic versus outbreak analysis, but remove exact reference to epidemic and outbreak model types

* Update intervention functions

* Restructure tutorials

Split `compare_interventions` into two tutorials : `modelling_interventions` and  `compare_interventions`

* Update outline of `compare_interventions`

* Fix typo in ODE equations

* Add section on mask wearing and vaccination

Updates to school closure section as well as added sections on mask wearing and vaccination

* typo and minor rephrase

* Add updated ebola model definition

* Update filenames

Updating filenames to be consistent with the default naming of episodes from `create_episode`

* Add to glossary terms

Incubation period and latent period

* Updates to parameter values used in Covid-19 example

* Add greek letters to flow diagrams

Fixes #29

* Remove reference to model library

* Add flow diagrams to challenged answer

* Add section on Vacamole model description

* Add pak installation to setup chunks

* Revert "Remove default lesson"

This reverts commit 6eadba4.

* Update config.yaml

* Update renv.lock

* Revert "Revert "Remove default lesson""

This reverts commit 8089e4c.

* Revert "Update config.yaml"

This reverts commit 4f2a8e1.

* Update config.yaml

* Fix typos

* Fix typos

* Style code

* Improve figures

* Remove {DiagrammeR} error message display

* Move contact matrix definition

* Colour nodes of vaccination classes

* Fix typo

* Rephrase documentation description

* Update episodes/model-choices.Rmd

Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

* Change title

* Fix typo

* Update title `model_choices.Rmd`

* Fix typo

* Add section on outcomes of interest

* Update uncertainty section

Updated code to run multiple model simulations to be the same as vignette and replaced {data.table} functions with `stat_summary()` stay within Tidyverse

* update axis labels size

* Add baseline trajectories to intervention figures

* Minor rephrasing

* Add details to effect of mask wearing calculation

* Add resource links to concept dependencies

* Add further detail to glossary definitions

---------

Co-authored-by: rozeggo <r.eggo@lshtm.ac.uk>
Co-authored-by: Andree Valle Campos <avallecam@gmail.com>
Co-authored-by: Pratik Gupte <pratik.gupte@lshtm.ac.uk>

config.yaml

@@ -59,6 +59,10 @@ contact: 'andree.valle-campos@lshtm.ac.uk' #FIXME
 
 # Order of episodes in your lesson
 episodes:
+- simulating-transmission.Rmd
+- model-choices.Rmd
+- modelling-interventions.Rmd
+- compare-interventions.Rmd
 
 # Information for Learners
 learners:
@@ -74,4 +78,5 @@ profiles:
 # This space below is where custom yaml items (e.g. pinning
 # sandpaper and varnish versions) should live
 
+sandpaper: 'carpentries/sandpaper#533'