markdown source builds

Auto-generated via {sandpaper}
Source  : 5c76e4e
Branch  : main
Author  : Amanda Minter <[email protected]>
Time    : 2023-12-21 14:05:03 +0000
Message : update late tasks from feedback (#85)

* Extend challenge in 'Choosing an appropriate model'

* Edit to accounting for uncertainty example

Store all results and then extract infectious compartment for plotting

* Add detail to Ebola case study challenge

* update glossary entries

* Add callout on ODE solver

* clarify purpose of concept dependencies

* Updates from review

* Remove infection object

* Update simulating-transmission.Rmd

* Update model-choices.Rmd

* Add exercise to `compare_interventions.Rmd`

* update modelling interventions after review

* Update renv.lock

* update plots

* make uncertainty plots consistent across episodes

* fix broken link

* making plots consistent across tutorials

* update summary and key points

* update plots and add challenge

* update introduction

* move contact matrix callout

and clarify reduction is performed within the model functions

* add callout on intervention types

* update introduction and reorder text in other sections

* update PI section

* style code

* spell check

* Update compare-interventions.Rmd

* Apply suggestions from code review

Co-authored-by: Andree Valle Campos <[email protected]>

* Update episodes/modelling-interventions.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* add dropdown menus to make section more interactive

* add reminder about transmissibility calculation

* link to latent period

* update model terms

* add note on flow diagram

* add callout on model rates

* Update episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* Update episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* Update episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* Update episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* Update episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

* update tutorial objectives

* distinguish parameter definitions from process descriptions in flow diagram

* Update model-choices.Rmd

* remove pak call from set up

* Update renv.lock

---------

Co-authored-by: Andree Valle Campos <[email protected]>

config.yaml

@@ -0,0 +1,81 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'incubator'
+
+# Overall title for pages.
+title: 'Outbreak analytics with R'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: ~
+
+# Comma-separated list of keywords for the lesson
+keywords: 'forecasts, epidemic models, interventions' #FIXME
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'pre-alpha'
+
+# License of the lesson
+license: 'CC-BY 4.0' #FIXME
+
+# Link to the source repository for this lesson
+source: 'https://github.com/epiverse-trace/tutorials'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: '[email protected]' #FIXME
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+- simulating-transmission.Rmd
+- model-choices.Rmd
+- modelling-interventions.Rmd
+- compare-interventions.Rmd
+
+# Information for Learners
+learners:
+
+# Information for Instructors
+instructors:
+
+# Learner Profiles
+profiles:
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+varnish: epiverse-trace/varnish@epiversetheme
+sandpaper: 'carpentries/sandpaper#533'