Late task tutorials #34

amanda-minter · 2023-10-23T09:27:02Z

Tutorials on late tasks 1 and some of late tasks 2 using the R package epidemics. Merging into main so that @CarmenTamayo can perform a review from the live site.

github-actions · 2023-10-23T09:27:19Z

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-34

The following changes were observed in the rendered markdown documents:

 compare-interventions.md (new)                     | 110 ++++
 config.yaml (gone)                                 |  77 ---
 ...erventions-rendered-unnamed-chunk-1-1.png (new) | Bin 0 -> 65010 bytes
 fig/model-choices-rendered-diagram-1.png (new)     | Bin 0 -> 15404 bytes
 ...el-choices-rendered-unnamed-chunk-1-1.png (new) | Bin 0 -> 26178 bytes
 ...nterventions-rendered-diagram_SEIRV-1.png (new) | Bin 0 -> 23029 bytes
 ...g-interventions-rendered-plot_masks-1.png (new) | Bin 0 -> 16260 bytes
 ...-interventions-rendered-plot_school-1.png (new) | Bin 0 -> 15946 bytes
 ...terventions-rendered-plot_vaccinate-1.png (new) | Bin 0 -> 13565 bytes
 ...ating-transmission-rendered-diagram-1.png (new) | Bin 0 -> 16095 bytes
 ...mulating-transmission-rendered-plot-1.png (new) | Bin 0 -> 15137 bytes
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 ...ing-transmission-rendered-visualise-1.png (new) | Bin 0 -> 37015 bytes
 md5sum.txt                                         |  25 +-
 model-choices.md (new)                             | 153 +++++
 modelling-interventions.md (new)                   | 225 +++++++
 reference.md                                       |  83 ++-
 renv.lock (gone)                                   | 721 ---------------------
 simulating-transmission.md (new)                   | 459 +++++++++++++
 template.md (gone)                                 | 194 ------
 20 files changed, 1042 insertions(+), 1005 deletions(-)

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⏱️ Updated at 2023-10-31 11:44:39 +0000

pratikunterwegs · 2023-10-23T09:35:35Z

Thanks @amanda-minter - I've just merged #31 into main, could you rebase on that? I could take a look on Thursday if that's alright?

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

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

Content edits and reordering of some text

Updated name to simulating_transmission to better reflect tutorial content

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

Added tutorial content on all sections for Choosing a model

Add 'Coming soon' to incomplete sections

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

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

pratikunterwegs · 2023-10-30T16:36:22Z

Hi @avallecam - just looking at this I see that you're merging main into this branch. It's better practice to rebase the feature branches on main, as that helps to keep a linear commit history. You can read more about this in the Blueprints. You'll need to squash-merge this PR, and any other PRs from branches where you've merged main into them.

avallecam · 2023-10-30T17:18:39Z

Hi @avallecam - just looking at this I see that you're merging main into this branch. It's better practice to rebase the feature branches on main, as that helps to keep a linear commit history. You can read more about this in the Blueprints. You'll need to squash-merge this PR, and any other PRs from branches where you've merged main into them.

Thank you for letting me know. I think I misunderstood your suggestion 1 from here #33 (comment) So the specific suggestion is to stop doing this "merge branch main into dev branch" in order to keep linear histories and facilitate the "rebase and merge" option. I interpreted this way because of a button suggesting this step at the end of the PR (in the section of changes requested and checks passed).

pratikunterwegs · 2023-10-31T09:27:57Z

Hi @avallecam - just looking at this I see that you're merging main into this branch. It's better practice to rebase the feature branches on main, as that helps to keep a linear commit history. You can read more about this in the Blueprints. You'll need to squash-merge this PR, and any other PRs from branches where you've merged main into them.

Thank you for letting me know. I think I misunderstood your suggestion 1 from here #33 (comment) So the specific suggestion is to stop doing this "merge branch main into dev branch" in order to keep linear histories and facilitate the "rebase and merge" option. I interpreted this way because of a button suggesting this step at the end of the PR (in the section of changes requested and checks passed).

Yes, that's right. Yes, the button is unfortunately set to have the "wrong" option as the default, so you would need to select the rebase option manually.

amanda-minter · 2023-10-31T11:41:03Z

Thanks for making this PR - I had some general thoughts which I've put down here, with some file-specific comments inline.

Overall I think it might be good to have @rozeggo take a look over this as well.

General

It might be good to start with a some information on who this tutorial is for, e.g. in terms of learner personas? Is that episode-specific, or is there a wider schematic for which episodes are targeted at which learners?

General technical

Could you please format and lint the code, and also run a spellcheck on the episodes to catch typos

I try to have each sentence in the vignettes/episodes on a new line, so that it's easier to comment on specific sentences.

It might be good to choose whether you will be using Tidyverse or data.table for data manipulation in this repo, so as to keep episodes consistent with one another.

It would be good to number the figures in each lesson for easier reference.

Simulating transmission

The figure with the epidemic curve could be modified to have the axis text larger/clearer.

In An epidemic model for pandemic influenza:

A message appears which seems to be from {DiagrammeR} - could this be removed?

Could the text on the contact matrix C be moved further up?

Model parameters - good to note that the <infection> class will be removed shortly, so the code in this section will have to be updated.

Choosing a model

No comments.

Modelling interventions

The Prerequisites box lists "Outbreak response : Intervention types" - where can readers find some information on these?

Compare interventions

This episode doesn't seem to be complete - is it intended to be part of this PR? In the compartmental diagram, I think it would be nice to clearly mark that the population is split into two arms by vaccination, such as by a colour scheme.

Thanks Pratik for your thorough review. I think I have addressed the majority of your comments, a couple that are not referenced are:

General

The tutorials are aimed at specific learner profiles, this will be added (#6) and discussed in the introductory materials (this is one of the later tutorials in the workflow).

General technical

As the primary purpose of the files is to be educational materials, I think the need for paragraphs outweighs the need for the being able to comment on specific sentences
Unfortunately, Carpentries does not currently support figure numbering, so figure numbers cannot be added at this time

Do you have any further comments on the changes I have made in response to your review?

pratikunterwegs · 2023-10-31T13:27:07Z

Thanks @amanda-minter, looks alright to me, but would be worth running it by Roz or others to sign off on it

rozeggo · 2023-10-31T14:14:09Z

Great. I had a look during the development day and looks good for merging.

amanda-minter · 2023-10-31T14:25:30Z

Hi @avallecam - just looking at this I see that you're merging main into this branch. It's better practice to rebase the feature branches on main, as that helps to keep a linear commit history. You can read more about this in the Blueprints. You'll need to squash-merge this PR, and any other PRs from branches where you've merged main into them.

Thank you for letting me know. I think I misunderstood your suggestion 1 from here #33 (comment) So the specific suggestion is to stop doing this "merge branch main into dev branch" in order to keep linear histories and facilitate the "rebase and merge" option. I interpreted this way because of a button suggesting this step at the end of the PR (in the section of changes requested and checks passed).

Yes, that's right. Yes, the button is unfortunately set to have the "wrong" option as the default, so you would need to select the rebase option manually.

To confirm, I will need to squash and merge this PR as main has been merged into this branch?

pratikunterwegs · 2023-10-31T14:55:14Z

Yes that's right. I don't think you'll be able to rebase and merge as there are merge commits in this branch.

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]>

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]>

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]>

Auto-generated via {sandpaper} Source : dd92d5c Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-11-07 00:36:38 +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]>

amanda-minter requested a review from pratikunterwegs October 23, 2023 09:27

amanda-minter added 27 commits October 23, 2023 10:46

Created late task 1 episode file

2b87659

Draft questions. objectives and section titles

ec99476

Added notes on lesson content and provisional model equations

18eee59

More lesson content to Model structures section

e0c569e

Outlines of remaining sections added

745c9d0

Edits to model structure section

9c2981f

Minor updates to model structures

dd5b69a

Edits to introduction section

a8ae924

Add content to and reorder model parameters section

89bffd7

Added example plot to introduction

8e4605b

Minor edit to text

095e2ef

Add initial conditions section

cc1b9da

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

Reorder of sections

b8e50f1

Updated text to introduction

c71e2e0

Add generating trajectories section

f87db2f

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

Added contact matrix section

3b3afd1

Edits to tutorial content

4a894b6

Content edits and reordering of some text

Changed naming of tutorial

d131cb4

Updated name to simulating_transmission to better reflect tutorial content

Remove references from Rmd

102f50d

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

Add file for model_choices.Rmd

7e46cdd

Additions and edits to tutorial objectives

daa2599

Update model_choices.Rmd

0ea5a62

Added tutorial content on all sections for Choosing a model

Update model_choices.Rmd

34dbd6f

Add 'Coming soon' to incomplete sections

Add uncertainty section

aa755eb

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

Fix typo

b43c56f

Add Comparing interventions tutorial

2f4447c

Remove default lesson

6eadba4

Update uncertainty section

e2c2aeb

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

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Minor rephrasing

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Add details to effect of mask wearing calculation

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Late task tutorials #34

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amanda-minter commented Oct 31, 2023

General

General technical

Simulating transmission

Choosing a model

Modelling interventions

Compare interventions

pratikunterwegs commented Oct 31, 2023

rozeggo commented Oct 31, 2023

amanda-minter commented Oct 31, 2023

pratikunterwegs commented Oct 31, 2023

Late task tutorials #34

Late task tutorials #34

Conversation

amanda-minter commented Oct 23, 2023

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Thank you!

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avallecam commented Oct 30, 2023

pratikunterwegs commented Oct 31, 2023

amanda-minter commented Oct 31, 2023

General

General technical

Simulating transmission

Choosing a model

Modelling interventions

Compare interventions

General

General technical

pratikunterwegs commented Oct 31, 2023

rozeggo commented Oct 31, 2023

amanda-minter commented Oct 31, 2023

pratikunterwegs commented Oct 31, 2023

github-actions bot commented Oct 23, 2023 •

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