Update 70 packages

[Bisaloo]

🤖 This is an automated build

This will update 70 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- mgcv  [required by ggplot2]
- colourpicker     [1.3.0 -> *]
- commonmark       [1.9.1 -> *]
- ggExtra          [0.10.1 -> *]
- httpuv           [1.6.15 -> *]
- later            [1.3.2 -> *]
- mgcv             [1.9-1 -> *]
- miniUI           [0.1.1.1 -> *]
- promises         [1.3.0 -> *]
- shiny            [1.8.1.1 -> *]
- shinyjs          [2.1.0 -> *]
- sourcetools      [0.1.7-1 -> *]
- xtable           [1.8-4 -> *]
- bpmodels         [epiverse-trace/bpmodels@main: 07c05409 -> 3d892baa]
- epichains        [ref: HEAD -> *]
- superspreading   [ref: HEAD -> *]
- nlme             [3.1-164 -> *]
- R                [4.4.0 -> 4.4.1]

# CRAN -----------------------------------------------------------------------
- abind            [1.4-5 -> 1.4-8]
- askpass          [1.2.0 -> 1.2.1]
- bit              [4.0.5 -> 4.5.0]
- bit64            [4.0.5 -> 4.5.2]
- broom            [1.0.6 -> 1.0.7]
- bslib            [0.7.0 -> 0.8.0]
- cfr              [0.1.1 -> 0.1.2]
- checkmate        [2.3.1 -> 2.3.2]
- cli              [repo: RSPM -> CRAN; ver: 3.6.2 -> 3.6.3]
- codetools        [0.2-20 -> *]
- colorspace       [2.1-0 -> 2.1-1]
- cpp11            [0.4.7 -> 0.5.0]
- crayon           [1.5.2 -> 1.5.3]
- curl             [5.2.1 -> 5.2.3]
- data.table       [1.15.4 -> 1.16.2]
- digest           [0.6.35 -> 0.6.37]
- distributional   [0.4.0 -> 0.5.0]
- dotCall64        [1.1-1 -> *]
- EpiNow2          [1.5.2 -> 1.6.1]
- evaluate         [0.23 -> 1.0.1]
- fields           [15.2 -> *]
- fitdistrplus     [1.1-11 -> 1.2-1]
- fs               [1.6.4 -> 1.6.5]
- future           [1.33.2 -> *]
- future.apply     [1.11.2 -> *]
- globals          [0.16.3 -> *]
- glue             [1.7.0 -> 1.8.0]
- grates           [1.2.1 -> 1.2.2]
- gtable           [0.3.5 -> 0.3.6]
- igraph           [2.0.3 -> 2.1.1]
- incidence2       [2.3.1 -> 2.5.0]
- jsonlite         [repo: RSPM -> CRAN; ver: 1.8.8 -> 1.8.9]
- knitr            [1.47 -> 1.48]
- listenv          [0.9.1 -> *]
- loo              [2.7.0 -> 2.8.0]
- maps             [3.4.2 -> *]
- MASS             [7.3-60.2 -> 7.3-61]
- Matrix           [1.7-0 -> 1.7-1]
- matrixStats      [1.3.0 -> 1.4.1]
- openssl          [2.2.0 -> 2.2.2]
- parallelly       [1.37.1 -> *]
- patchwork        [1.2.0 -> 1.3.0]
- pkgbuild         [1.4.4 -> 1.4.5]
- posterior        [1.5.0 -> 1.6.0]
- progressr        [0.14.0 -> *]
- ps               [1.7.6 -> 1.8.1]
- QuickJSR         [1.2.2 -> 1.4.0]
- R.oo             [1.26.0 -> 1.27.0]
- ragg             [1.3.2 -> 1.3.3]
- Rcpp             [1.0.12 -> 1.0.13-1]
- RcppEigen        [0.3.4.0.0 -> 0.3.4.0.2]
- RcppParallel     [repo: RSPM -> CRAN; ver: 5.1.7 -> 5.1.9]
- renv             [1.0.7 -> 1.0.11]
- reprex           [2.1.0 -> 2.1.1]
- rmarkdown        [2.27 -> 2.29]
- rstudioapi       [0.16.0 -> 0.17.1]
- socialmixr       [0.3.2 -> 0.4.0]
- spam             [2.10-0 -> *]
- StanHeaders      [2.32.9 -> 2.32.10]
- survival         [3.5-8 -> 3.7-0]
- sys              [3.4.2 -> 3.4.3]
- tinytex          [0.51 -> 0.54]
- uuid             [1.2-0 -> 1.2-1]
- withr            [3.0.0 -> 3.0.2]
- xfun             [0.44 -> 0.49]
- yaml             [repo: RSPM -> CRAN; ver: 2.3.8 -> 2.3.10]
- mgcv             [* -> 1.9-1]
- nlme             [* -> 3.1-166]
- ympes            [* -> 1.6.0]

# GitHub ---------------------------------------------------------------------
- epiparameter     [epiverse-trace/epiparameter@main: 0f805b90 -> d3ab3284]

⏱️ 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 2024-11-05

[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-131

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   86 -
 create-forecast.md                                 |   77 +-
 delays-access.md                                   |   15 +-
 delays-functions.md                                |   62 +-
 ...create-forecast-rendered-unnamed-chunk-10-1.png |  Bin 19228 -> 19300 bytes
 ...create-forecast-rendered-unnamed-chunk-12-1.png |  Bin 18750 -> 18601 bytes
 fig/create-forecast-rendered-unnamed-chunk-4-1.png |  Bin 55480 -> 52795 bytes
 fig/delays-access-rendered-unnamed-chunk-15-1.png  |  Bin 9568 -> 20263 bytes
 ...elays-functions-rendered-unnamed-chunk-13-1.png |  Bin 5088 -> 9786 bytes
 ...elays-functions-rendered-unnamed-chunk-16-1.png |  Bin 50674 -> 54686 bytes
 ...elays-functions-rendered-unnamed-chunk-17-1.png |  Bin 52344 -> 55652 bytes
 ...elays-functions-rendered-unnamed-chunk-20-1.png |  Bin 49864 -> 56244 bytes
 ...elays-functions-rendered-unnamed-chunk-21-1.png |  Bin 33051 -> 35065 bytes
 ...ransmissibility-rendered-unnamed-chunk-10-1.png |  Bin 68600 -> 70895 bytes
 ...ransmissibility-rendered-unnamed-chunk-18-1.png |  Bin 29803 -> 33338 bytes
 ...ransmissibility-rendered-unnamed-chunk-19-1.png |  Bin 30861 -> 38768 bytes
 ...transmissibility-rendered-unnamed-chunk-5-1.png |  Bin 5925 -> 11300 bytes
 ...transmissibility-rendered-unnamed-chunk-9-1.png |  Bin 9543 -> 18389 bytes
 ...eading-estimate-rendered-unnamed-chunk-10-1.png |  Bin 15447 -> 17026 bytes
 ...eading-estimate-rendered-unnamed-chunk-11-1.png |  Bin 4831 -> 9104 bytes
 ...eading-estimate-rendered-unnamed-chunk-14-1.png |  Bin 16689 -> 19283 bytes
 ...reading-estimate-rendered-unnamed-chunk-4-1.png |  Bin 5031577 -> 6263104 bytes
 ...reading-estimate-rendered-unnamed-chunk-9-1.png |  Bin 4745 -> 9426 bytes
 ...reading-simulate-rendered-unnamed-chunk-1-1.png |  Bin 39692 -> 41222 bytes
 ...eading-simulate-rendered-unnamed-chunk-15-1.png |  Bin 37532 -> 39100 bytes
 ...eading-simulate-rendered-unnamed-chunk-19-1.png |  Bin 4596 -> 9574 bytes
 ...eading-simulate-rendered-unnamed-chunk-20-1.png |  Bin 39692 -> 41222 bytes
 ...eading-simulate-rendered-unnamed-chunk-22-1.png |  Bin 10095 -> 16689 bytes
 ...eading-simulate-rendered-unnamed-chunk-25-1.png |  Bin 4052 -> 6896 bytes
 ...eading-simulate-rendered-unnamed-chunk-26-1.png |  Bin 8636 -> 18167 bytes
 ...reading-simulate-rendered-unnamed-chunk-4-1.png |  Bin 9197 -> 19493 bytes
 md5sum.txt                                         |   32 +-
 network.html                                       |    6 +-
 quantify-transmissibility.md                       |   31 +-
 renv.lock (gone)                                   | 6048 --------------------
 superspreading-estimate.md                         |    2 +-
 webshot.png                                        |  Bin 5031577 -> 6263104 bytes
 37 files changed, 91 insertions(+), 6268 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 2025-02-27 19:53:24 +0000

[avallecam]

@Bisaloo, please, can you help me update this PR? I'm interested in assessing if any output is being affected by EpiNow2 latest CRAN version epiforecasts/EpiNow2#989 (also, can you remind me what the specific step you run to do this?)

Also, we are having a similar issue as solved in https://github.com/epiverse-trace/tutorials-late/pull/77/files but I can work on it, as well as looking at the second issue on RcppParallel epiverse-trace/tutorials#111 to generate the md-output.

[Bisaloo]

The RcppParallel issue needs to be resolved first for the preview to be available.

[avallecam]

The RcppParallel issue needs to be resolved first for the preview to be available.

yes, I can try that. But I need your support to update package versions. Can you help me update the EpiNow2 version to the latest CRAN, now 1.7.1? This is the current status:

- EpiNow2          [1.5.2 -> 1.6.1]

[avallecam]

@Bisaloo thanks for the last commit. Should we remove that last one and add it to a separate PR? It'll be useful to let this PR generate the preview b313d19

[avallecam]

note: I just understood that the change of GP prior in EpiNow2 aims to keep a default more appropriate to the renewal equation. We can expect not to have differences since in tutorials we only rely on the renewal equation model, not in the non-mechanistic one as in the howto's.

[avallecam]

thanks, @Bisaloo, for all the commits to solving the workflows! also the epinow2 commits helped me to notice some other new features! I'll push some other commits to solve some error outputs in the md-outputs due to other epinow2 new features.

[avallecam]

now all errors are solved! interesting issue with webshot and the usage the lintr proposed me to apply in d51116f ready to merge 🚀