Update 78 packages

[Bisaloo]

🤖 This is an automated build

This will update 78 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- class       [required by classInt, e1071]
- cluster     [required by Hmisc]
- foreign     [required by Hmisc, maptools]
- KernSmooth  [required by classInt]
- lattice     [required by coda, maptools, Matrix, and 3 others]
- MASS        [required by fitdistrplus, ggplot2, MCMCpack, and 2 others]
- nnet        [required by Hmisc]
- survival    [required by fitdistrplus, quantreg]
- class        [7.3-22 -> *]
- cluster      [2.1.6 -> *]
- desc         [1.4.2 -> 1.4.3]
- foreign      [0.8-86 -> *]
- KernSmooth   [2.23-22 -> *]
- lattice      [0.22-5 -> *]
- MASS         [7.3-60 -> *]
- nnet         [7.3-19 -> *]
- survival     [3.5-7 -> *]
- pak          [* -> 0.7.1]
- vaccineff    [epiverse-trace/vaccineff@main -> *]
- R            [4.2.2 -> 4.3.2]

# CRAN -----------------------------------------------------------------------
- bayesplot     [1.10.0 -> 1.11.0]
- BH            [1.81.0-1 -> 1.84.0-0]
- checkmate     [2.3.0 -> 2.3.1]
- cli           [3.6.1 -> 3.6.2]
- coda          [0.19-4 -> 0.19-4.1]
- commonmark    [1.9.0 -> 1.9.1]
- config        [0.3.1 -> 0.3.2]
- cowplot       [1.1.1 -> 1.1.3]
- data.table    [1.14.8 -> 1.15.0]
- DBI           [1.1.3 -> 1.2.1]
- digest        [0.6.33 -> 0.6.34]
- dplyr         [1.1.2 -> 1.1.4]
- e1071         [1.7-13 -> 1.7-14]
- fansi         [1.0.4 -> 1.0.6]
- ggfittext     [0.10.1 -> 0.10.2]
- ggridges      [0.5.4 -> 0.5.6]
- glue          [1.6.2 -> 1.7.0]
- htmlwidgets   [1.6.3 -> 1.6.4]
- igraph        [1.5.1 -> 2.0.1.1]
- jsonlite      [1.8.7 -> 1.8.8]
- maptools      [1.1-6 -> *]
- markdown      [1.11 -> 1.12]
- Matrix        [1.6-4 -> 1.6-5]
- matrixStats   [1.1.0 -> 1.2.0]
- MCMCpack      [1.6-3 -> 1.7-0]
- mgcv          [1.9-0 -> 1.9-1]
- patchwork     [1.1.3 -> 1.2.0]
- pkgbuild      [1.4.2 -> 1.4.3]
- processx      [3.8.2 -> 3.8.3]
- progress      [1.2.2 -> 1.2.3]
- ps            [1.7.5 -> 1.7.6]
- purrr         [1.0.1 -> 1.0.2]
- QuickJSR      [1.0.8 -> 1.1.3]
- Rcpp          [1.0.11 -> 1.0.12]
- readr         [2.1.4 -> 2.1.5]
- reprex        [2.0.2 -> 2.1.0]
- rgdal         [1.6-5 -> *]
- rlang         [1.1.1 -> 1.1.3]
- rpart         [4.1.21 -> 4.1.23]
- rprojroot     [2.0.4 -> *]
- rstan         [2.32.3 -> 2.32.5]
- rstantools    [2.3.1.1 -> 2.4.0]
- s2            [1.1.4 -> 1.1.6]
- sass          [0.4.7 -> 0.4.8]
- sf            [1.0-14 -> 1.0-15]
- sp            [2.0-0 -> 2.1-3]
- StanHeaders   [2.26.28 -> 2.32.5]
- tensorA       [0.36.2 -> 0.36.2.1]
- terra         [1.7-55 -> 1.7-71]
- tidyr         [1.3.0 -> 1.3.1]
- timechange    [0.2.0 -> 0.3.0]
- utf8          [1.2.3 -> 1.2.4]
- uuid          [repo: RSPM -> CRAN; ver: 1.1-1 -> 1.2-0]
- viridis       [0.6.4 -> 0.6.5]
- vroom         [1.6.4 -> 1.6.5]
- withr         [2.5.2 -> 3.0.0]
- xfun          [0.40 -> 0.41]
- yaml          [2.3.7 -> 2.3.8]
- class         [* -> 7.3-22]
- cluster       [* -> 2.1.6]
- foreign       [* -> 0.8-86]
- KernSmooth    [* -> 2.23-22]
- lattice       [* -> 0.22-5]
- MASS          [* -> 7.3-60.0.1]
- nnet          [* -> 7.3-19]
- survival      [* -> 3.5-7]

# GitHub ---------------------------------------------------------------------
- epiCo         [epiverse-trace/epiCo@HEAD: c9e5bcad -> f85e5d08]
- serofoi       [epiverse-trace/serofoi@HEAD: 4a25b104 -> f3839277]
- sivirep       [epiverse-trace/sivirep@dev: 837948a2 -> f66542c3]

# RSPM -----------------------------------------------------------------------
- httr2         [* -> 1.0.0]
- showtext      [* -> 0.9-6]
- showtextdb    [* -> 3.0]
- sysfonts      [* -> 0.8.8]

# https://carpentries.r-universe.dev -----------------------------------------
- curl          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 5.1.0 -> 5.2.0]
- ragg          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.2.6 -> 1.2.7]
- stringi       [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.8.2 -> 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 2024-02-06

[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-21

The following changes were observed in the rendered markdown documents:

 EnfermedadX.md                                     |  287 +-
 EnfermedadX2.md (gone)                             | 1769 ------------
 Serofoi-tutorial.md                                |   18 +-
 Sivirep-tutorial.md                                |   26 +-
 TallerIntroAnaliticaBrotes.md                      |  120 +-
 Vaccineff-tutorial.md                              |   53 +-
 ZIKAB.md                                           |   28 +-
 config.yaml (gone)                                 |   88 -
 epiCo-tutorial.md                                  | 2674 +++++++++++++++++-
 fig/EnfermedadX-rendered-convergence gamma-1.png   |  Bin 58367 -> 64778 bytes
 ...nfermedadX-rendered-convergence lognormal-1.png |  Bin 58994 -> 61168 bytes
 fig/EnfermedadX-rendered-convergence weibull-1.png |  Bin 62003 -> 62352 bytes
 fig/EnfermedadX-rendered-plot dist-1.png           |  Bin 23133 -> 23182 bytes
 fig/EnfermedadX-rendered-plot ip-1.png             |  Bin 28364 -> 28322 bytes
 ...medadX2-rendered-convergence gamma-1.png (gone) |  Bin 68028 -> 0 bytes
 ...dX2-rendered-convergence lognormal-1.png (gone) |  Bin 63234 -> 0 bytes
 ...dadX2-rendered-convergence weibull-1.png (gone) |  Bin 61675 -> 0 bytes
 fig/EnfermedadX2-rendered-epi curve-1.png (gone)   |  Bin 4374 -> 0 bytes
 fig/EnfermedadX2-rendered-plot dist-1.png (gone)   |  Bin 25228 -> 0 bytes
 fig/EnfermedadX2-rendered-plot ip-1.png (gone)     |  Bin 27312 -> 0 bytes
 fig/EnfermedadX2-rendered-si naive-1.png (gone)    |  Bin 7877 -> 0 bytes
 fig/Serofoi-tutorial-rendered-chik2015_vis-1.png   |  Bin 21178 -> 24520 bytes
 ...AnaliticaBrotes-rendered-unnamed-chunk-15-1.png |  Bin 6924 -> 7055 bytes
 ...AnaliticaBrotes-rendered-unnamed-chunk-19-1.png |  Bin 5512 -> 5667 bytes
 ...AnaliticaBrotes-rendered-unnamed-chunk-40-1.png |  Bin 14154 -> 14148 bytes
 ...cineff-tutorial-rendered-unnamed-chunk-11-1.png |  Bin 20882 -> 15433 bytes
 ...cineff-tutorial-rendered-unnamed-chunk-12-1.png |  Bin 22435 -> 16646 bytes
 ...cineff-tutorial-rendered-unnamed-chunk-13-1.png |  Bin 19552 -> 16256 bytes
 ...ccineff-tutorial-rendered-unnamed-chunk-4-1.png |  Bin 4452 -> 4428 bytes
 ...ccineff-tutorial-rendered-unnamed-chunk-5-1.png |  Bin 13650 -> 13539 bytes
 fig/ZIKAB-rendered-p1-1.png                        |  Bin 34473 -> 34001 bytes
 fig/ZIKAB-rendered-p2-1.png                        |  Bin 24759 -> 24355 bytes
 fig/ZIKAB-rendered-p3-1.png                        |  Bin 30167 -> 29873 bytes
 fig/ZIKAB-rendered-p4-1.png                        |  Bin 21894 -> 21632 bytes
 fig/epiCo-tutorial-rendered-unnamed-chunk-11-1.png |  Bin 51117 -> 45649 bytes
 fig/epiCo-tutorial-rendered-unnamed-chunk-4-1.png  |  Bin 7122 -> 6848 bytes
 fig/epiCo-tutorial-rendered-unnamed-chunk-7-1.png  |  Bin 92557 -> 97749 bytes
 ...o-tutorial-rendered-unnamed-chunk-7-2.png (new) |  Bin 0 -> 97749 bytes
 fig/epiCo-tutorial-rendered-unnamed-chunk-9-1.png  |  Bin 6415 -> 6923 bytes
 md5sum.txt                                         |   35 +-
 renv.lock (gone)                                   | 2904 --------------------
 41 files changed, 2882 insertions(+), 5120 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 2024-07-07 17:54:28 +0000