Update 49 packages

[Bisaloo]

🤖 This is an automated build

This will update 49 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS  [required by ggplot2]
- mgcv  [required by ggplot2]
- MASS   [7.3-60 -> *]
- mgcv   [1.9-0 -> *]
- nlme   [3.1-163 -> *]
- R      [4.3.1 -> 4.3.2]

# CRAN -----------------------------------------------------------------------
- brio          [1.1.3 -> 1.1.4]
- bslib         [0.5.1 -> 0.6.1]
- checkmate     [2.2.0 -> 2.3.1]
- cli           [3.6.1 -> 3.6.2]
- cpp11         [0.4.6 -> 0.4.7]
- data.table    [1.14.8 -> 1.14.10]
- desc          [1.4.2 -> 1.4.3]
- deSolve       [1.38 -> 1.40]
- dotCall64     [1.1-0 -> 1.1-1]
- dplyr         [1.1.3 -> 1.1.4]
- evaluate      [0.22 -> 0.23]
- fansi         [1.0.5 -> 1.0.6]
- haven         [2.5.3 -> 2.5.4]
- htmltools     [0.5.6.1 -> 0.5.7]
- htmlwidgets   [1.6.2 -> 1.6.4]
- igraph        [1.5.1 -> 1.6.0]
- jsonlite      [1.8.7 -> 1.8.8]
- knitr         [1.44 -> 1.45]
- lattice       [0.22-4 -> 0.22-5]
- lifecycle     [repo: RSPM -> CRAN; ver: 1.0.3 -> 1.0.4]
- maps          [3.4.1 -> 3.4.2]
- Matrix        [1.6-1.1 -> 1.6-4]
- pak           [0.6.0 -> 0.7.1]
- pkgbuild      [1.4.2 -> 1.4.3]
- processx      [3.8.2 -> 3.8.3]
- progress      [1.2.2 -> 1.2.3]
- RcppEigen     [0.3.3.9.3 -> 0.3.3.9.4]
- rlang         [1.1.1 -> 1.1.2]
- rprojroot     [2.0.3 -> 2.0.4]
- sass          [0.4.7 -> 0.4.8]
- scales        [1.2.1 -> 1.3.0]
- socialmixr    [0.3.0 -> 0.3.1]
- stringr       [repo: RSPM -> CRAN; ver: 1.5.0 -> 1.5.1]
- testthat      [3.2.0 -> 3.2.1]
- tinytex       [0.48 -> 0.49]
- vctrs         [0.6.4 -> 0.6.5]
- vroom         [1.6.4 -> 1.6.5]
- waldo         [0.5.1 -> 0.5.2]
- withr         [2.5.1 -> 2.5.2]
- xfun          [0.40 -> 0.41]
- yaml          [2.3.7 -> 2.3.8]
- MASS          [* -> 7.3-60]
- mgcv          [* -> 1.9-0]
- nlme          [* -> 3.1-164]

# GitHub ---------------------------------------------------------------------
- epidemics     [epiverse-trace/epidemics@HEAD: 6004c3a7 -> 5f6825d7]

# https://carpentries.r-universe.dev -----------------------------------------
- curl          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 5.1.0 -> 5.2.0]
- ragg          [repo: RSPM -> https://carpentries.r-universe.dev; ver: 1.2.6 -> 1.2.7]
- stringi       [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.7.12 -> 1.8.3]
- xml2          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.3.5 -> 1.3.6]

⏱️ In a few minutes, a comment will appear that will show you how the output has changed based on these updates.

If you want to inspect these changes locally, you can use the following code to check out a new branch:

git fetch origin update/packages
git checkout update/packages

• Auto-generated by create-pull-request on 2023-12-18

[github-actions]

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-93

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   81 -
 ...-interventions-rendered-plot_masks-1.png (gone) |  Bin 16260 -> 0 bytes
 ...interventions-rendered-plot_school-1.png (gone) |  Bin 15946 -> 0 bytes
 ...erventions-rendered-plot_vaccinate-1.png (gone) |  Bin 13565 -> 0 bytes
 ...ulating-transmission-rendered-plot-1.png (gone) |  Bin 16506 -> 0 bytes
 ...ulating-transmission-rendered-traj-1.png (gone) |  Bin 37015 -> 0 bytes
 ...ng-transmission-rendered-visualise-1.png (gone) |  Bin 37015 -> 0 bytes
 md5sum.txt                                         |   28 +-
 modelling-interventions.md                         |   30 +-
 renv.lock (gone)                                   | 1993 --------------------
 simulating-transmission.md                         |   14 +-
 11 files changed, 47 insertions(+), 2099 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 2023-12-20 17:14:22 +0000

[avallecam]

This will partially fix #98

[avallecam]

ready to merge 🚀

[Bisaloo]

Are you going to fix the epidemics version in a separate PR?

[avallecam]

Are you going to fix the epidemics version in a separate PR?

I appreciate that reminder.

I see two paths for this to fix {epidemics} and the errors in the current online version:

(1) Update the episodes to the most recent {epidemics} functions, plus updating the renv.lock (this may be the most time-demanding edit) or

(2) Keep the current version in the renv.lock:

tutorials/renv/profiles/lesson-requirements/renv.lock

Lines 562 to 585 in 215be1a

	"epidemics": {
	"Package": "epidemics",
	"Version": "0.0.0.9000",
	"Source": "GitHub",
	"RemoteType": "github",
	"RemoteHost": "api.github.com",
	"RemoteRepo": "epidemics",
	"RemoteUsername": "epiverse-trace",
	"RemotePkgRef": "epiverse-trace/epidemics",
	"RemoteRef": "HEAD",
	"RemoteSha": "6004c3a7e50be7b127070c4e96a011630307df17",
	"Requirements": [
	"BH",
	"Rcpp",
	"RcppEigen",
	"checkmate",
	"data.table",
	"deSolve",
	"glue",
	"jsonlite",
	"stats",
	"utils"
	],
	"Hash": "96a7b1457b8a5d89f146d0abf3de7eff"

And replace the suggested installation:

tutorials/episodes/simulating-transmission.Rmd

Line 152 in 215be1a

pak::pak("epiverse-trace/epidemics")

Adding the tag version in it:

pak::pak("epiverse-trace/epidemics@96a7b1457")

@Bisaloo, please let me know if there would be any additional (or fewer) steps to take this PR as an opportunity to fix {epidemics}.

@amanda-minter, can you do this fixing? It would depend on your time available.

[Bisaloo]

(2) Keep the current version in the renv.lock:

I would be fine with this in theory and happy to opt for this option in the future so we don't necessarily have to always keep up to date with the very latest version of epidemics.

However, in this case, I suspect that different episodes were written with different versions of epidemics. This is my best guess to explain the error messages we currently have in the "Simulating transmission" episode: https://epiverse-trace.github.io/tutorials/simulating-transmission.html#introduction

So either we table this for now, merge this PR with a note that this needs to be resolved as soon as possible (either by using the epidemics version from renv.lock or the latest, I don't mind) or we tackle it in this PR.

[avallecam]

Let's try doing (2) to solve the website output. If this does not work, we'll proceed with (1) after this PR.

I identified that the maintainer can do (2) and the developer can do (1), so I'll add the version tag.

[avallecam]

@Bisaloo so, this should be ready to merge.

[Bisaloo]

Flagging that as per 60db9e0, this is causing even more errors than previously.

[avallecam]

I'll do the merge.

I expect that removing the installation lines from the .Rmd files in this PR allow using the registered {epidemics} version in the renv.lock.

[avallecam]

Flagging that as per 60db9e0, this is causing even more errors than previously.

@Bisaloo, thank you for flagging this. Errors do persist after merging option (2). This requires to do option (1) in a separate PR
to solve this.