Update 24 packages

[epiverse-trace-bot]

🤖 This is an automated build

This will update 24 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS      [required by fitdistrplus]
- Matrix    [required by igraph]
- survival  [required by fitdistrplus]
- MASS       [7.3-65 -> *]
- Matrix     [1.7-4 -> *]
- survival   [3.8-6 -> *]
- lattice    [0.22-7 -> *]

# CRAN -----------------------------------------------------------------------
- base64enc         [0.1-3 -> 0.1-6]
- checkmate         [2.3.3 -> 2.3.4]
- countrycode       [1.6.1 -> 1.7.0]
- DBI               [1.2.3 -> 1.3.0]
- dbplyr            [2.5.1 -> 2.5.2]
- dplyr             [1.1.4 -> 1.2.0]
- dtplyr            [1.3.2 -> 1.3.3]
- EpiNow2           [1.7.1 -> 1.8.0]
- fastymd           [0.1.4 -> 0.1.5]
- ggplot2           [4.0.1 -> 4.0.2]
- grates            [1.7.1 -> 1.7.2]
- httr              [1.4.7 -> 1.4.8]
- igraph            [2.2.1 -> 2.2.2]
- lubridate         [1.9.4 -> 1.9.5]
- openssl           [2.3.4 -> 2.3.5]
- readr             [2.1.6 -> 2.2.0]
- socialmixr        [0.5.0 -> 0.5.1]
- viridisLite       [0.4.2 -> 0.4.3]
- lattice           [* -> 0.22-9]
- MASS              [* -> 7.3-65]
- Matrix            [* -> 1.7-4]
- pracma            [* -> 2.4.6]
- primarycensored   [* -> 1.3.0]
- survival          [* -> 3.8-6]

⏱️ 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 2026-03-03

[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-middle/compare/md-outputs..md-outputs-PR-259

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   92 -
 create-forecast.md                                 |   24 +-
 delays-functions.md                                |    4 +-
 ...create-forecast-rendered-unnamed-chunk-10-1.png |  Bin 9577 -> 9569 bytes
 ...create-forecast-rendered-unnamed-chunk-12-1.png |  Bin 8273 -> 8816 bytes
 fig/create-forecast-rendered-unnamed-chunk-4-1.png |  Bin 47032 -> 46382 bytes
 ...elays-functions-rendered-unnamed-chunk-18-1.png |  Bin 13815 -> 13836 bytes
 ...elays-functions-rendered-unnamed-chunk-19-1.png |  Bin 51011 -> 50289 bytes
 ...elays-functions-rendered-unnamed-chunk-22-1.png |  Bin 49759 -> 50491 bytes
 ...elays-functions-rendered-unnamed-chunk-23-1.png |  Bin 30113 -> 30136 bytes
 ...ransmissibility-rendered-unnamed-chunk-10-1.png |  Bin 60389 -> 59586 bytes
 ...ransmissibility-rendered-unnamed-chunk-19-1.png |  Bin 28855 -> 28575 bytes
 ...ransmissibility-rendered-unnamed-chunk-20-1.png |  Bin 32553 -> 32108 bytes
 ...transmissibility-rendered-unnamed-chunk-8-1.png |  Bin 13223 -> 13367 bytes
 ...reading-estimate-rendered-unnamed-chunk-5-1.png |  Bin 6404924 -> 6750811 bytes
 intro-cfr-adjust-delays.md                         |  110 +-
 md5sum.txt                                         |   38 +-
 network.html                                       |    6 +-
 quantify-transmissibility.md                       |   34 +-
 renv.lock (gone)                                   | 6604 --------------------
 webshot.png                                        |  Bin 6404924 -> 6750811 bytes
 21 files changed, 108 insertions(+), 6804 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 2026-03-20 19:25:02 +0000