From 2cfa2eb10b3070f84896b1bc80f28307fb1b3f64 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 26 Dec 2023 00:33:43 +0000 Subject: [PATCH] markdown source builds Auto-generated via {sandpaper} Source : 5c76e4e7c486be89d6421032172a389c52184099 Branch : main Author : Amanda Minter 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 * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos * 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 * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos * 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 --- config.yaml | 81 +++ renv.lock | 1984 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 2065 insertions(+) create mode 100644 config.yaml create mode 100644 renv.lock diff --git a/config.yaml b/config.yaml new file mode 100644 index 00000000..24f15333 --- /dev/null +++ b/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: 'andree.valle-campos@lshtm.ac.uk' #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' diff --git a/renv.lock b/renv.lock new file mode 100644 index 00000000..09b8a749 --- /dev/null +++ b/renv.lock @@ -0,0 +1,1984 @@ +{ + "R": { + "Version": "4.3.2", + "Repositories": [ + 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