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Merged
milanmlft merged 1 commit into from
Jan 7, 2026
Merged

Update 43 packages #79

milanmlft merged 1 commit into from
Jan 7, 2026

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@milanmlft milanmlft commented Jan 6, 2026

🤖 This is an automated build

This will update 43 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- boot      [required by doBy, lme4]
- MASS      [required by car, doBy, lme4, and 3 others]
- Matrix    [required by doBy, igraph, lme4, and 5 others]
- nlme      [required by car, lme4, mgcv]
- nnet      [required by car]
- survival  [required by quantreg]
- boot       [1.3-32 -> *]
- MASS       [7.3-65 -> *]
- Matrix     [1.7-4 -> *]
- nlme       [3.1-168 -> *]
- nnet       [7.3-20 -> *]
- survival   [3.8-3 -> *]
- R          [4.5.1 -> 4.5.2]

# CRAN -----------------------------------------------------------------------
- broom           [1.0.10 -> 1.0.11]
- data.table      [1.17.8 -> 1.18.0]
- digest          [repo: RSPM -> CRAN; ver: 0.6.37 -> 0.6.39]
- doBy            [4.7.0 -> 4.7.1]
- ggplot2         [4.0.0 -> 4.0.1]
- htmltools       [repo: RSPM -> CRAN; ver: 0.5.8.1 -> 0.5.9]
- isoband         [repo: RSPM -> CRAN; ver: 0.2.7 -> 0.3.0]
- knitr           [1.50 -> 1.51]
- lme4            [1.1-37 -> 1.1-38]
- mgcv            [repo: RSPM -> CRAN; ver: 1.9-3 -> 1.9-4]
- purrr           [1.1.0 -> 1.2.0]
- rbibutils       [2.3 -> 2.4]
- readr           [repo: RSPM -> CRAN; ver: 2.1.5 -> 2.1.6]
- reformulas      [0.4.2 -> 0.4.3]
- RSQLite         [2.4.3 -> 2.4.5]
- S7              [repo: RSPM -> CRAN; ver: 0.2.0 -> 0.2.1]
- selectr         [repo: RSPM -> CRAN; ver: 0.4-2 -> 0.5-1]
- shiny           [1.11.1 -> 1.12.1]
- stringr         [1.5.2 -> 1.6.0]
- tidyr           [repo: RSPM -> CRAN; ver: 1.3.1 -> 1.3.2]
- tinytex         [0.57 -> 0.58]
- vroom           [1.6.6 -> 1.6.7]
- xfun            [0.54 -> 0.55]
- xml2            [1.4.1 -> 1.5.1]
- yaml            [repo: RSPM -> CRAN; ver: 2.3.10 -> 2.3.12]
- zoo             [repo: RSPM -> CRAN; ver: 1.8-14 -> 1.8-15]
- boot            [* -> 1.3-32]
- colorspace      [* -> 2.1-2]
- forecast        [* -> 8.24.0]
- fracdiff        [* -> 1.5-3]
- MASS            [* -> 7.3-65]
- Matrix          [* -> 1.7-4]
- nlme            [* -> 3.1-168]
- nnet            [* -> 7.3-20]
- quadprog        [* -> 1.5-8]
- quantmod        [* -> 0.4.28]
- RcppArmadillo   [* -> 15.2.3-1]
- survival        [* -> 3.8-3]
- timeDate        [* -> 4051.111]
- tseries         [* -> 0.10-58]
- TTR             [* -> 0.24.4]
- urca            [* -> 1.3-4]
- xts             [* -> 0.14.1]

⏱️ 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

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github-actions bot commented Jan 6, 2026 •
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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/UCL-ARC/r-amr-epidemiology/compare/md-outputs..md-outputs-PR-79

The following changes were observed in the rendered markdown documents:

 01-rstudio-intro.md                                |    5 +-
 02-project-intro.md                                |    2 +-
 03-seeking-help.md                                 |    4 +-
 04-data-structures-part1.md                        |    9 +-
 05-data-structures-part2.md                        |    6 +-
 14-data-subsetting.md                              |   15 +-
 15-plot-ggplot2.md                                 |   18 +-
 20-dplyr.md                                        |    6 +-
 23-statistics.md                                   |   10 +-
 25-linreg-diagnostics.md                           |   12 +-
 26-log-regression.md                               |    4 +-
 27-sql-r.md                                        |   10 +-
 best-practices-R.md                                |    2 +-
 config.yaml (gone)                                 |  114 -
 epiDB.sqlite                                       |  Bin 1245184 -> 1245184 bytes
 fig/23-statistics-rendered-unnamed-chunk-4-1.png   |  Bin 4389 -> 4533 bytes
 fig/23-statistics-rendered-unnamed-chunk-4-2.png   |  Bin 4209 -> 4647 bytes
 ...nreg-diagnostics-rendered-unnamed-chunk-8-1.png |  Bin 24481 -> 24505 bytes
 md5sum.txt                                         |   82 +-
 renv.lock (gone)                                   | 5817 --------------------
 20 files changed, 98 insertions(+), 6018 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 2026-01-06 00:42:50 +0000

github-actions bot pushed a commit that referenced this pull request Jan 6, 2026
@actions-user
differences for PR #79
be45388
@milanmlft milanmlft merged commit d88ffb6 into main Jan 7, 2026
3 checks passed
@milanmlft milanmlft deleted the update/packages branch January 7, 2026 11:24
github-actions bot pushed a commit that referenced this pull request Jan 7, 2026
@actions-user
markdown source builds
2e08b56 
Auto-generated via `{sandpaper}`
Source  : d88ffb6
Branch  : main
Author  : Milan Malfait <[email protected]>
Time    : 2026-01-07 11:24:41 +0000
Message : [actions] update 43 packages (#79)
github-actions bot pushed a commit that referenced this pull request Jan 7, 2026
@actions-user
site deploy
44b4ffe 
Auto-generated via `{sandpaper}`
Source  : 2e08b56
Branch  : md-outputs
Author  : GitHub Actions <[email protected]>
Time    : 2026-01-07 11:35:57 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : d88ffb6
Branch  : main
Author  : Milan Malfait <[email protected]>
Time    : 2026-01-07 11:24:41 +0000
Message : [actions] update 43 packages (#79)
github-actions bot pushed a commit that referenced this pull request Jan 20, 2026
@actions-user
markdown source builds
166253f 
Auto-generated via `{sandpaper}`
Source  : d88ffb6
Branch  : main
Author  : Milan Malfait <[email protected]>
Time    : 2026-01-07 11:24:41 +0000
Message : [actions] update 43 packages (#79)
github-actions bot pushed a commit that referenced this pull request Jan 20, 2026
@actions-user
site deploy
b8edc4e 
Auto-generated via `{sandpaper}`
Source  : 166253f
Branch  : md-outputs
Author  : GitHub Actions <[email protected]>
Time    : 2026-01-20 00:04:00 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : d88ffb6
Branch  : main
Author  : Milan Malfait <[email protected]>
Time    : 2026-01-07 11:24:41 +0000
Message : [actions] update 43 packages (#79)
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