Update 100 packages

[carpentries-bot]

:robot: This is an automated build

This will update 100 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- boot      [required by lme4]
- cluster   [required by Hmisc]
- foreign   [required by Hmisc]
- lattice   [required by lme4, Matrix, nlme]
- MASS      [required by car, ggplot2, lme4, and 3 others]
- mgcv      [required by car, ggplot2, grafify]
- nnet      [required by car, Hmisc]
- rpart     [required by Hmisc]
- survival  [required by quantreg]
- lattice         [0.22-5 -> *]
- MASS            [7.3-60 -> *]
- mgcv            [1.9-1 -> *]
- abind           [* -> 1.4-5]
- askpass         [* -> 1.2.0]
- bit             [* -> 4.0.5]
- bit64           [* -> 4.0.5]
- blob            [* -> 1.2.4]
- brio            [* -> 1.1.4]
- broom           [* -> 1.0.5]
- car             [* -> 3.1-2]
- carData         [* -> 3.0-5]
- cellranger      [* -> 1.1.0]
- clipr           [* -> 0.8.0]
- conflicted      [* -> 1.2.0]
- cpp11           [* -> 0.4.7]
- crayon          [* -> 1.5.2]
- data.table      [* -> 1.15.0]
- DBI             [* -> 1.2.1]
- dbplyr          [* -> 2.4.0]
- diffobj         [* -> 0.3.5]
- dplyr           [* -> 1.1.4]
- dtplyr          [* -> 1.3.1]
- emmeans         [* -> 1.10.0]
- estimability    [* -> 1.4.1]
- forcats         [* -> 1.0.0]
- Formula         [* -> 1.2-5]
- gargle          [* -> 1.5.2]
- generics        [* -> 0.1.3]
- googledrive     [* -> 2.1.1]
- googlesheets4   [* -> 1.1.1]
- grafify         [* -> 4.0]
- haven           [* -> 2.5.4]
- Hmisc           [* -> 5.1-1]
- hms             [* -> 1.1.3]
- htmlTable       [* -> 2.4.2]
- htmlwidgets     [* -> 1.6.4]
- httr            [* -> 1.4.7]
- ids             [* -> 1.0.1]
- lme4            [* -> 1.1-35.1]
- lmerTest        [* -> 3.1-3]
- lubridate       [* -> 1.9.3]
- MatrixModels    [* -> 0.5-3]
- minqa           [* -> 1.2.6]
- modelr          [* -> 0.1.11]
- nloptr          [* -> 2.0.3]
- numDeriv        [* -> 2016.8-1.1]
- openssl         [* -> 2.1.1]
- patchwork       [* -> 1.2.0]
- pbkrtest        [* -> 0.5.2]
- pkgload         [* -> 1.3.4]
- praise          [* -> 1.0.0]
- prettyunits     [* -> 1.2.0]
- progress        [* -> 1.2.3]
- purrr           [* -> 1.0.2]
- quantreg        [* -> 5.97]
- readr           [* -> 2.1.5]
- readxl          [* -> 1.4.3]
- rematch         [* -> 2.0.0]
- rematch2        [* -> 2.1.2]
- reprex          [* -> 2.1.0]
- rprojroot       [* -> 2.0.4]
- rstudioapi      [* -> 0.15.0]
- rvest           [* -> 1.0.3]
- selectr         [* -> 0.4-2]
- SparseM         [* -> 1.81]
- sys             [* -> 3.4.2]
- testthat        [* -> 3.2.1]
- tidyr           [* -> 1.3.1]
- tidyselect      [* -> 1.2.0]
- tidyverse       [* -> 2.0.0]
- timechange      [* -> 0.3.0]
- tzdb            [* -> 0.4.0]
- uuid            [* -> 1.2-0]
- viridis         [* -> 0.6.5]
- vroom           [* -> 1.6.5]
- waldo           [* -> 0.5.2]
- curl            [* -> 5.2.0]
- ragg            [* -> 1.2.7]
- systemfonts     [* -> 1.0.5]
- textshaping     [* -> 0.3.7]
- xml2            [* -> 1.3.6]

# CRAN -----------------------------------------------------------------------
- BH            [1.81.0-1 -> 1.84.0-0]
- cowplot       [1.1.2 -> 1.1.3]
- digest        [0.6.33 -> 0.6.34]
- glue          [repo: RSPM -> CRAN; ver: 1.6.2 -> 1.7.0]
- Matrix        [1.6-4 -> 1.6-5]
- ps            [1.7.5 -> 1.7.6]
- QuickJSR      [1.0.9 -> 1.1.3]
- Rcpp          [1.0.11 -> 1.0.12]
- rlang         [1.1.2 -> 1.1.3]
- rstan         [2.32.3 -> 2.32.5]
- StanHeaders   [2.26.28 -> 2.32.5]
- withr         [2.5.2 -> 3.0.0]
- boot          [* -> 1.3-28.1]
- cluster       [* -> 2.1.6]
- foreign       [* -> 0.8-86]
- lattice       [* -> 0.22-5]
- MASS          [* -> 7.3-60.0.1]
- mgcv          [* -> 1.9-1]
- nnet          [* -> 7.3-19]
- rpart         [* -> 4.1.23]
- survival      [* -> 3.5-7]

:stopwatch: 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[bot]]

Thank you!

Thank you for your pull request :smiley:

:robot: 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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/statistical-probabilistic-programming-r/compare/md-outputs..md-outputs-PR-4

The following changes were observed in the rendered markdown documents:

 bayesian-statistics.md                             |  36 +-
 ...sian-statistics-rendered-unnamed-chunk-17-1.png | Bin 20429 -> 20343 bytes
 ...esian-statistics-rendered-unnamed-chunk-3-1.png | Bin 29576 -> 29505 bytes
 ...ssian-processes-rendered-unnamed-chunk-10-1.png | Bin 92412 -> 89048 bytes
 ...processes-rendered-unnamed-chunk-13-1.png (new) | Bin 0 -> 6225 bytes
 ...processes-rendered-unnamed-chunk-16-1.png (new) | Bin 0 -> 19995 bytes
 ...processes-rendered-unnamed-chunk-18-1.png (new) | Bin 0 -> 19210 bytes
 ...ussian-processes-rendered-unnamed-chunk-2-1.png | Bin 27755 -> 23243 bytes
 ...ussian-processes-rendered-unnamed-chunk-7-1.png | Bin 79387 -> 89947 bytes
 ...archical-models-rendered-unnamed-chunk-12-1.png | Bin 35503 -> 35856 bytes
 ...archical-models-rendered-unnamed-chunk-13-1.png | Bin 23689 -> 24386 bytes
 ...archical-models-rendered-unnamed-chunk-14-1.png | Bin 17562 -> 19784 bytes
 ...archical-models-rendered-unnamed-chunk-16-1.png | Bin 6116 -> 5989 bytes
 ...rarchical-models-rendered-unnamed-chunk-6-1.png | Bin 10358 -> 10210 bytes
 fig/mcmc-rendered-unnamed-chunk-10-1.png           | Bin 85383 -> 85368 bytes
 fig/mcmc-rendered-unnamed-chunk-9-1.png            | Bin 37952 -> 37956 bytes
 fig/stan-rendered-unnamed-chunk-11-1.png           | Bin 40623 -> 43927 bytes
 fig/stan-rendered-unnamed-chunk-12-1.png           | Bin 4941 -> 5479 bytes
 fig/stan-rendered-unnamed-chunk-7-1.png            | Bin 5323 -> 5392 bytes
 gaussian-processes.md                              | 474 ++++++++++++++++++---
 hierarchical-models.md                             |  61 ++-
 mcmc.md                                            |  18 +-
 md5sum.txt                                         |  36 +-
 model-critisism.md                                 |  40 +-
 stan.md                                            |  86 ++--
 25 files changed, 550 insertions(+), 201 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.

:stopwatch: Updated at 2024-06-04 01:41:46 +0000