Update tutorials-late episodes for {epidemics} v0.5.0

[joshwlambert]

• Please check if the PR fulfills these requirements

• I have read the CONTRIBUTING guidelines
• A new item has been added to NEWS.md
• [ ] Tests for the changes have been added (for bug fixes / features) Not applicable
• Docs have been added / updated (for bug fixes / features)
• Checks have been run locally and pass

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

This PR updates the episodes/ in tutorials-late to use the latest version of {epidemics} (v0.5.0).

• What is the current behavior? (You can also link to an open issue here)

The current behaviour was using the previous release of {epidemics} (v0.4.0).

• What is the new behavior (if this is a feature change)?

The episodes/ are updated to use the new {epidemics} functions correctly, e.g. not transposing the contact matrix before running epidemics::model_*() as this is now handled internally in {epidemic} v0.5.0.

• Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

This has breaking changes to the tutorials scripts, but this is required to keep up-to-date with the latest version of the {epidemics} Epivers-TRACE package.

• Other information:

None.

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[joshwlambert]

The {renv} lock file will need to be updated either in this PR or straight afterwards to ensure the tutorials are using {epidemics} v0.5.0. @avallecam please let me know how to proceed as I'm unsure if the package versions used are handled automatically or manually.

[avallecam]

accepting to incorporate the transposition step