Update 55 packages

[epiverse-trace-bot]

🤖 This is an automated build

This will update 55 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- boot        [required by spdep]
- class       [required by classInt, e1071]
- KernSmooth  [required by classInt]
- MASS        [required by fitdistrplus, ggforce, ggplot2, and 3 others]
- Matrix      [required by expm, igraph, MatrixModels, and 1 other]
- mgcv        [required by ggplot2]
- survival    [required by fitdistrplus, quantreg, vaccineff]
- boot         [1.3-31 -> *]
- class        [7.3-23 -> *]
- KernSmooth   [2.23-26 -> *]
- MASS         [7.3-65 -> *]
- Matrix       [1.7-3 -> *]
- mgcv         [1.9-1 -> *]
- nlme         [3.1-168 -> *]
- survival     [3.8-3 -> *]
- R            [4.4.3 -> 4.5.1]

# CRAN -----------------------------------------------------------------------
- bayesplot         [repo: RSPM -> CRAN; ver: 1.11.1 -> 1.13.0]
- cli               [3.6.4 -> 3.6.5]
- coarseDataTools   [repo: RSPM -> CRAN; ver: 0.6-6 -> 0.7.2]
- curl              [6.2.2 -> 6.4.0]
- data.table        [1.17.0 -> 1.17.6]
- EpiEstim          [repo: RSPM -> CRAN; ver: 2.2-4 -> 2.2-5]
- evaluate          [1.0.3 -> 1.0.4]
- fs                [repo: RSPM -> CRAN; ver: 1.6.5 -> 1.6.6]
- generics          [repo: RSPM -> CRAN; ver: 0.1.3 -> 0.1.4]
- ggforce           [repo: RSPM -> CRAN; ver: 0.4.2 -> 0.5.0]
- ggplot2           [repo: RSPM -> CRAN; ver: 3.5.1 -> 3.5.2]
- haven             [repo: RSPM -> CRAN; ver: 2.5.4 -> 2.5.5]
- incidence         [repo: RSPM -> CRAN; ver: 1.7.5 -> 1.7.6]
- lattice           [repo: RSPM -> CRAN; ver: 0.22-6 -> 0.22-7]
- linelist          [repo: RSPM -> CRAN; ver: 1.1.4 -> 2.0.1]
- litedown          [repo: RSPM -> CRAN; ver: 0.6 -> 0.7]
- MatchIt           [4.7.1 -> 4.7.2]
- openssl           [2.3.2 -> 2.3.3]
- pak               [0.8.0.1 -> 0.9.0]
- patchwork         [repo: RSPM -> CRAN; ver: 1.3.0 -> 1.3.1]
- pillar            [1.10.1 -> 1.10.2]
- pkgbuild          [1.4.7 -> 1.4.8]
- ps                [1.9.0 -> 1.9.1]
- QuickJSR          [1.7.0 -> 1.8.0]
- ragg              [repo: RSPM -> CRAN; ver: 1.3.3 -> 1.4.0]
- RcppArmadillo     [repo: RSPM -> CRAN; ver: 14.4.1-1 -> 14.4.3-1]
- RcppParallel      [repo: RSPM -> CRAN; ver: 5.1.7 -> 5.1.10]
- rlang             [1.1.5 -> 1.1.6]
- s2                [repo: RSPM -> CRAN; ver: 1.1.7 -> 1.1.9]
- sass              [repo: RSPM -> CRAN; ver: 0.4.9 -> 0.4.10]
- scales            [repo: RSPM -> CRAN; ver: 1.3.0 -> 1.4.0]
- sf                [1.0-20 -> 1.0-21]
- spdep             [1.3-10 -> 1.3-13]
- svglite           [repo: RSPM -> CRAN; ver: 2.1.3 -> 2.2.1]
- systemfonts       [1.2.1 -> 1.2.3]
- terra             [1.8-29 -> 1.8-54]
- textshaping       [1.0.0 -> 1.0.1]
- threejs           [repo: RSPM -> CRAN; ver: 0.3.3 -> 0.3.4]
- tibble            [repo: RSPM -> CRAN; ver: 3.2.1 -> 3.3.0]
- tinytex           [0.56 -> 0.57]
- utf8              [repo: RSPM -> CRAN; ver: 1.2.4 -> 1.2.6]
- xfun              [0.51 -> 0.52]
- boot              [* -> 1.3-31]
- class             [* -> 7.3-23]
- KernSmooth        [* -> 2.23-26]
- MASS              [* -> 7.3-65]
- Matrix            [* -> 1.7-3]
- mgcv              [* -> 1.9-1]
- nlme              [* -> 3.1-168]
- survival          [* -> 3.8-3]

# GitHub ---------------------------------------------------------------------
- sivirep           [epiverse-trace/sivirep: d4f1cf99 -> 2de51ca8]
- vaccineff         [epiverse-trace/vaccineff: cb7e27fa -> 9f58f61f]

# RSPM -----------------------------------------------------------------------
- colorspace        [2.1-1 -> *]
- fansi             [1.0.6 -> *]
- munsell           [0.5.1 -> *]

⏱️ 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

• Auto-generated by create-pull-request on 2025-07-01

[github-actions]

🆗 Pre-flight checks passed 😃

This pull request has been checked and contains no modified workflow files or spoofing.

It should be safe to Approve and Run the workflows that need maintainer approval.