Middle task tutorials

[amanda-minter]

Tutorials for middle tasks 1 (Quantifying transmissibility) and 2 (Create a short-term forecast )

[github-actions]

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-58

The following changes were observed in the rendered markdown documents:

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 create-forecast.md (new)                           |  375 ++++
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 quantify-transmissibility.md (new)                 |  531 ++++++
 reference.md                                       |   16 +-
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 17 files changed, 933 insertions(+), 1947 deletions(-)

What does this mean?

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⏱️ Updated at 2024-02-02 20:02:03 +0000

[sbfnk]

Really nice tutorials! I've left some comments in specific places.

Some of the syntax is currently undergoing some breaking changes with a target of version 2.0.0 - we'll have to decide whether to publish these as 1.4.0 specific tutorials or wait until the new version and then make any necessary changes.

[amanda-minter]

@sbfnk thank you for the previous comments, I've added two further sections to the second tutorial "Create a short-term forecast"

1. Forecast secondary observations : illustrates using esitimate_secondary() and forecast_secondary(). However, when plotting the forecast, there is an error about removing NAs - I think this arises because there are no secondary observations in cases_to_forecast - which I thought would be OK? There may be an error with my implementation

2. Challenge : Ebola outbreak analysis : this is a challenge for learners to complete as part of an Ebola challenge that will be present across all tutorials

If you have time to look at these new sections before Christmas I can any make necessary changes, I will leave these changes as a draft PR regardless so that the tutorials can be updated for EpiNow2 2.0.0 before being made public

[avallecam]

FYI yesterday I change this to ready to review since all workbench gh-actions passed and md-output-PR-58 was generated with pre-rendered readable .md files of each episode in:

• quantify-transmisibility.md
• create-forecast.md

[sbfnk]

This looks great - just a few minor text changes.

Only question that remains is why we don't run the code in the solution - not doing this seems to open ourselves for issues if there are any bugs in the code.

[avallecam]

why we don't run the code in the solution - not doing this seems to open ourselves for issues if there are any bugs in the code.

Good question. Days ago, I had issues making that section pass the workbench gh-actions, although running correctly locally. But I didn't consider that potential vulnerability. I'll open it again and look further if issues appear.

[sbfnk]

why we don't run the code in the solution - not doing this seems to open ourselves for issues if there are any bugs in the code.

Good question. Days ago, I had issues making that section pass the workbench gh-actions, although running correctly locally. But I didn't consider that potential vulnerability. I'll open it again and look further if issues appear.

Great - yes, I noticed some issues with version from a weeks ago that I managed to fix locally (but things had moved on since then). Feel free to ping me for a second pair of eyes if you run into any issues.

[avallecam]

@sbfnk changes incorporated and all checks passed. Thank you for your feedback. Re-requesting review for approval and proceed.

[sbfnk]

Super!