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Auto-generated via {sandpaper} Source : 237d7bb Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-10-31 16:15:02 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 969a11b Branch : main Author : Amanda Minter <[email protected]> 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Andree Valle Campos <[email protected]> Co-authored-by: Pratik Gupte <[email protected]>
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