Update 26 packages

[Bisaloo]

🤖 This is an automated build

This will update 26 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS      [required by fitdistrplus, ggplot2]
- mgcv      [required by ggplot2]
- survival  [required by fitdistrplus]
- MASS           [7.3-65 -> *]
- mgcv           [1.9-1 -> *]
- nlme           [3.1-167 -> *]
- survival       [3.8-3 -> *]
- cffr           [* -> 1.2.0]
- jsonvalidate   [* -> 1.5.0]
- V8             [* -> 6.0.3]
- R              [4.4.2 -> 4.4.3]

# CRAN -----------------------------------------------------------------------
- bit            [4.5.0.1 -> 4.6.0]
- broom          [1.0.7 -> 1.0.8]
- countrycode    [repo: RSPM -> CRAN; ver: 1.6.0 -> 1.6.1]
- curl           [6.2.1 -> 6.2.2]
- grates         [1.4.1 -> 1.4.3]
- incidence2     [2.6.0 -> 2.6.1]
- jsonlite       [1.9.1 -> 2.0.0]
- knitr          [1.49 -> 1.50]
- Matrix         [1.7-2 -> 1.7-3]
- mime           [repo: RSPM -> CRAN; ver: 0.12 -> 0.13]
- pkgbuild       [1.4.6 -> 1.4.7]
- QuickJSR       [1.6.0 -> 1.7.0]
- RcppParallel   [repo: RSPM -> CRAN; ver: 5.1.7 -> 5.1.10]
- readxl         [1.4.4 -> 1.4.5]
- renv           [1.1.2 -> 1.1.4]
- rstan          [repo: RSPM -> CRAN; ver: 2.32.6 -> 2.32.7]
- stringi        [repo: RSPM -> CRAN; ver: 1.8.4 -> 1.8.7]
- tzdb           [repo: RSPM -> CRAN; ver: 0.4.0 -> 0.5.0]
- xml2           [1.3.7 -> 1.3.8]
- MASS           [* -> 7.3-65]
- mgcv           [* -> 1.9-1]
- nlme           [* -> 3.1-167]
- survival       [* -> 3.8-3]

⏱️ 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 2025-04-01

[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-163

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   86 -
 create-forecast.md                                 |   55 +-
 delays-functions.md                                |   34 +-
 ...create-forecast-rendered-unnamed-chunk-10-1.png |  Bin 19258 -> 19260 bytes
 ...create-forecast-rendered-unnamed-chunk-12-1.png |  Bin 18705 -> 18615 bytes
 fig/create-forecast-rendered-unnamed-chunk-4-1.png |  Bin 52720 -> 52421 bytes
 ...elays-functions-rendered-unnamed-chunk-16-1.png |  Bin 54257 -> 54712 bytes
 ...elays-functions-rendered-unnamed-chunk-17-1.png |  Bin 51289 -> 55441 bytes
 ...elays-functions-rendered-unnamed-chunk-20-1.png |  Bin 56520 -> 56676 bytes
 ...elays-functions-rendered-unnamed-chunk-21-1.png |  Bin 34587 -> 35148 bytes
 ...ransmissibility-rendered-unnamed-chunk-10-1.png |  Bin 73442 -> 69236 bytes
 ...ransmissibility-rendered-unnamed-chunk-17-1.png |  Bin 33702 -> 33622 bytes
 ...ransmissibility-rendered-unnamed-chunk-18-1.png |  Bin 38849 -> 38953 bytes
 ...reading-estimate-rendered-unnamed-chunk-4-1.png |  Bin 6139379 -> 5471400 bytes
 md5sum.txt                                         |   34 +-
 network.html                                       |    6 +-
 quantify-transmissibility.md                       |   30 +-
 renv.lock (gone)                                   | 6227 --------------------
 webshot.png                                        |  Bin 6139379 -> 5471400 bytes
 19 files changed, 70 insertions(+), 6402 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 2025-04-01 07:32:12 +0000

[Bisaloo]

The CI on the plot fig/delays-functions-rendered-unnamed-chunk-17-1.png have changed quite dramatically. Is this expected?

b2ec9db#diff-c8ccb4af4f83edac20865ecd44127afcd1986c35efb7c98399c6684abccc0897

[avallecam]

The CI on the plot fig/delays-functions-rendered-unnamed-chunk-17-1.png have changed quite dramatically. Is this expected?

b2ec9db#diff-c8ccb4af4f83edac20865ecd44127afcd1986c35efb7c98399c6684abccc0897

Yes, it is something that I found in the most recent PR md outputs from the last month, but could not reproduce it to report to package maintainers. Even if I got an expected output in one workflow, after many other repetitions, after merging a PR, I got unexpectedly wider CIs at main.

The output message from the previous run suggest that we can stabilize it by setting a fixed set of stan parameters (samples and chains), as in the quantify-transmission episode.

EpiNow2::epinow(
  ...,
  stan = EpiNow2::stan_opts(samples = 1000, chains = 3)
)

@jamesmbaazam from the epinow() output warning message below, we get the figure on the left (unexpected wide CIs), but we get the expected output (figure on the right) without any output message. Should we expect to make this output stable by setting fixed stan samples and chains only? From the warning message, would you suggest that we fix another set of parameters?

WARN [2025-03-28 11:17:41] epinow: There were 500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 12. See
https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded -
WARN [2025-03-28 11:17:41] epinow: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
https://mc-stan.org/misc/warnings.html#bfmi-low -
WARN [2025-03-28 11:17:41] epinow: Examine the pairs() plot to diagnose sampling problems
 -
WARN [2025-03-28 11:17:42] epinow: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat -
WARN [2025-03-28 11:17:43] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess -
WARN [2025-03-28 11:17:44] epinow: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess - 

[jamesmbaazam]

Thanks for tagging @avallecam. I'll take a closer look next week. We have a similar issue in our scheduled rendering of vignettes in https://github.com/epiforecasts/EpiNow2/pull/1060/files. Looks quite strange.