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Late task tutorials #34

Merged
merged 90 commits into from
Oct 31, 2023
Merged

Late task tutorials #34

merged 90 commits into from
Oct 31, 2023

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amanda-minter
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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.

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github-actions bot commented Oct 23, 2023

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

  • 🎯 correct output
  • 🖼️ correct figures
  • ❓ new warnings
  • ‼️ new errors

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
 ...mulating-transmission-rendered-traj-1.png (new) | Bin 0 -> 37015 bytes
 ...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(-)
What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

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

@pratikunterwegs
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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
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
github-actions bot pushed a commit that referenced this pull request Oct 30, 2023
@pratikunterwegs
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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
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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
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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
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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

  1. Could you please format and lint the code, and also run a spellcheck on the episodes to catch typos
  2. I try to have each sentence in the vignettes/episodes on a new line, so that it's easier to comment on specific sentences.
  3. 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.
  4. It would be good to number the figures in each lesson for easier reference.

Simulating transmission

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

  2. In An epidemic model for pandemic influenza:

    1. A message appears which seems to be from {DiagrammeR} - could this be removed?
    2. Could the text on the contact matrix C be moved further up?
  3. 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

  1. 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
  2. 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?

github-actions bot pushed a commit that referenced this pull request Oct 31, 2023
@pratikunterwegs
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Thanks @amanda-minter, looks alright to me, but would be worth running it by Roz or others to sign off on it

@rozeggo
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rozeggo commented Oct 31, 2023

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

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

@amanda-minter amanda-minter merged commit 969a11b into main Oct 31, 2023
3 checks passed
@amanda-minter amanda-minter deleted the late_task_1 branch October 31, 2023 15:37
github-actions bot pushed a commit that referenced this pull request Oct 31, 2023
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]>
github-actions bot pushed a commit that referenced this pull request Oct 31, 2023
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]>
github-actions bot pushed a commit that referenced this pull request Nov 7, 2023
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]>
github-actions bot pushed a commit that referenced this pull request Nov 7, 2023
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]>
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5 participants