Update 27 packages

[epiverse-trace-bot]

🤖 This is an automated build

This will update 27 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- boot        [required by spdep]
- class       [required by classInt, e1071]
- KernSmooth  [required by classInt]
- MASS        [required by fitdistrplus, ggforce, ggraph, and 2 others]
- Matrix      [required by expm, igraph, MatrixModels, and 1 other]
- survival    [required by fitdistrplus, quantreg, vaccineff]
- boot         [1.3-32 -> *]
- class        [7.3-23 -> *]
- KernSmooth   [2.23-26 -> *]
- MASS         [7.3-65 -> *]
- Matrix       [1.7-4 -> *]
- survival     [3.8-6 -> *]

# CRAN -----------------------------------------------------------------------
- checkmate      [2.3.3 -> 2.3.4]
- DBI            [repo: RSPM -> CRAN; ver: 1.2.3 -> 1.3.0]
- dbplyr         [2.5.1 -> 2.5.2]
- deSolve        [repo: RSPM -> CRAN; ver: 1.40 -> 1.41]
- dplyr          [repo: RSPM -> CRAN; ver: 1.1.4 -> 1.2.0]
- dtplyr         [1.3.2 -> 1.3.3]
- ggplot2        [4.0.1 -> 4.0.2]
- ggrepel        [repo: RSPM -> CRAN; ver: 0.9.6 -> 0.9.7]
- graphlayouts   [1.2.2 -> 1.2.3]
- gridtext       [repo: RSPM -> CRAN; ver: 0.1.5 -> 0.1.6]
- httr           [repo: RSPM -> CRAN; ver: 1.4.7 -> 1.4.8]
- igraph         [2.2.1 -> 2.2.2]
- lattice        [repo: RSPM -> CRAN; ver: 0.22-7 -> 0.22-9]
- lubridate      [repo: RSPM -> CRAN; ver: 1.9.4 -> 1.9.5]
- openssl        [2.3.4 -> 2.3.5]
- readr          [2.1.6 -> 2.2.0]
- sf             [1.0-24 -> 1.1-0]
- sp             [repo: RSPM -> CRAN; ver: 2.2-0 -> 2.2-1]
- spdep          [1.4-1 -> 1.4-2]
- viridisLite    [repo: RSPM -> CRAN; ver: 0.4.2 -> 0.4.3]
- boot           [* -> 1.3-32]
- class          [* -> 7.3-23]
- KernSmooth     [* -> 2.23-26]
- MASS           [* -> 7.3-65]
- Matrix         [* -> 1.7-4]
- survival       [* -> 3.8-6]

# GitHub ---------------------------------------------------------------------
- sivirep        [epiverse-trace/sivirep@HEAD: 853c0874 -> 3c2051f0]

⏱️ 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/epimodelac/compare/md-outputs..md-outputs-PR-61

The following changes were observed in the rendered markdown documents:

 EnfermedadX.md                                     |   68 +-
 Serofoi-tutorial.md                                |   48 +-
 config.yaml (gone)                                 |   88 -
 epiCo-tutorial.md                                  |    4 +-
 fig/EnfermedadX-rendered-convergence gamma-1.png   |  Bin 62024 -> 61377 bytes
 ...nfermedadX-rendered-convergence lognormal-1.png |  Bin 61065 -> 61682 bytes
 fig/EnfermedadX-rendered-convergence weibull-1.png |  Bin 62209 -> 61413 bytes
 fig/EnfermedadX-rendered-plot ip-1.png             |  Bin 28376 -> 28449 bytes
 fig/Serofoi-tutorial-rendered-chik2015_vis-1.png   |  Bin 27133 -> 26936 bytes
 ...erofoi-tutorial-rendered-unnamed-chunk-10-1.png |  Bin 39051 -> 37519 bytes
 md5sum.txt                                         |   34 +-
 renv.lock (gone)                                   | 7827 --------------------
 12 files changed, 75 insertions(+), 7994 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 2026-03-03 02:21:34 +0000