From 579d99b994346f9c1bff8f4545c5d608a81c8116 Mon Sep 17 00:00:00 2001 From: Andree Valle Campos Date: Thu, 24 Jul 2025 16:16:53 +0100 Subject: [PATCH 1/2] test fix --- episodes/modelling-interventions.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/episodes/modelling-interventions.Rmd b/episodes/modelling-interventions.Rmd index 221d79d3..2b7597e1 100644 --- a/episodes/modelling-interventions.Rmd +++ b/episodes/modelling-interventions.Rmd @@ -321,7 +321,7 @@ The diagram below shows the SEIRV model implemented using `model_default()` wher DiagrammeR::grViz("digraph { # graph statement - ################# + ################ graph [layout = dot, rankdir = LR, overlap = true, From eb57293e0c3aba5732a601bdd8efc8704dc00314 Mon Sep 17 00:00:00 2001 From: Andree Valle Campos Date: Thu, 24 Jul 2025 16:44:26 +0100 Subject: [PATCH 2/2] update renv --- renv/profiles/lesson-requirements/renv.lock | 72 +++++++++------------ 1 file changed, 30 insertions(+), 42 deletions(-) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 004be4ec..431c8950 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -24,8 +24,7 @@ "NeedsCompilation": "no", "Author": "Dirk Eddelbuettel [aut, cre] (), John W. Emerson [aut], Michael J. Kane [aut] ()", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "DBI": { "Package": "DBI", @@ -250,8 +249,7 @@ "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", "License": "Apache License 2.0", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "Rcpp": { "Package": "Rcpp", @@ -317,8 +315,7 @@ "NeedsCompilation": "yes", "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "V8": { "Package": "V8", @@ -420,8 +417,7 @@ "License": "GPL-2 | GPL-3", "URL": "http://www.rforge.net/base64enc", "NeedsCompilation": "yes", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "bit": { "Package": "bit", @@ -794,8 +790,7 @@ "NeedsCompilation": "no", "Author": "Jennifer Bryan [cre, aut], Hadley Wickham [ctb]", "Maintainer": "Jennifer Bryan ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "cffr": { "Package": "cffr", @@ -904,7 +899,7 @@ "NeedsCompilation": "yes", "Author": "Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "cli": { "Package": "cli", @@ -1284,8 +1279,7 @@ "URL": "http://desolve.r-forge.r-project.org/", "LazyData": "yes", "NeedsCompilation": "yes", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "desc": { "Package": "desc", @@ -1374,8 +1368,7 @@ "NeedsCompilation": "no", "Author": "Steph Locke [cre], Rich FitzJohn [aut], Anne Cori [aut], Thibaut Jombart [aut]", "Maintainer": "Steph Locke ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "distributional": { "Package": "distributional", @@ -1573,13 +1566,16 @@ "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", - "Author": "Pratik Gupte [aut, cph] (ORCID: ), Rosalind Eggo [aut, cph, cre] (ORCID: ), Edwin Van Leeuwen [aut, cph] (ORCID: ), Adam Kucharski [ctb, rev] (ORCID: ), Tim Taylor [ctb, rev] (ORCID: ), Banky Ahadzie [ctb], Alexis Robert [ctb] (ORCID: ), Hugo Gruson [rev] (ORCID: ), Joshua W. Lambert [rev] (ORCID: ), James M. Azam [rev] (ORCID: ), Alexis Robert [rev] (ORCID: )", + "NeedsCompilation": "yes", + "Author": "Pratik Gupte [aut, cph] (), Rosalind Eggo [aut, cph, cre] (), Edwin Van Leeuwen [aut, cph] (), Adam Kucharski [ctb, rev] (), Tim Taylor [ctb, rev] (), Banky Ahadzie [ctb], Alexis Robert [ctb] (), Hugo Gruson [rev] (), Joshua W. Lambert [rev] (), James M. Azam [rev] (), Alexis Robert [rev] ()", "Maintainer": "Rosalind Eggo ", "RemoteType": "github", - "RemoteUsername": "epiverse-trace", + "RemoteHost": "api.github.com", "RemoteRepo": "epidemics", - "RemoteSha": "f064fc478bf96b75e7891b0583695d98a18a7a0f", - "RemoteHost": "api.github.com" + "RemoteUsername": "epiverse-trace", + "RemotePkgRef": "epiverse-trace/epidemics", + "RemoteRef": "HEAD", + "RemoteSha": "f064fc478bf96b75e7891b0583695d98a18a7a0f" }, "epiparameter": { "Package": "epiparameter", @@ -2503,8 +2499,7 @@ "NeedsCompilation": "no", "Author": "Rich FitzJohn [aut, cre]", "Maintainer": "Rich FitzJohn ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "igraph": { "Package": "igraph", @@ -2770,8 +2765,7 @@ "stats", "graphics" ], - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "lattice": { "Package": "lattice", @@ -2810,8 +2804,7 @@ "NeedsCompilation": "yes", "Author": "Deepayan Sarkar [aut, cre] (), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", "Maintainer": "Deepayan Sarkar ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "lifecycle": { "Package": "lifecycle", @@ -2963,10 +2956,9 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.9-1", + "Version": "1.9-3", "Source": "Repository", - "Author": "Simon Wood ", - "Maintainer": "Simon Wood ", + "Authors@R": "person(given = \"Simon\", family = \"Wood\", role = c(\"aut\", \"cre\"), email = \"simon.wood@r-project.org\")", "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", "Priority": "recommended", @@ -2991,6 +2983,8 @@ "ByteCompile": "yes", "License": "GPL (>= 2)", "NeedsCompilation": "yes", + "Author": "Simon Wood [aut, cre]", + "Maintainer": "Simon Wood ", "Repository": "CRAN" }, "mime": { @@ -3104,8 +3098,7 @@ "Maintainer": "Paul Gilbert ", "URL": "http://optimizer.r-forge.r-project.org/", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "oai": { "Package": "oai", @@ -3180,7 +3173,7 @@ "NeedsCompilation": "no", "Author": "Rich FitzJohn [aut, cre], Thibaut Jombart [ctb], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "openssl": { "Package": "openssl", @@ -3853,7 +3846,7 @@ "NeedsCompilation": "yes", "Author": "Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "rlang": { "Package": "rlang", @@ -4144,8 +4137,7 @@ "NeedsCompilation": "no", "Author": "Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]", "Maintainer": "Simon Potter ", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "socialmixr": { "Package": "socialmixr", @@ -4730,8 +4722,7 @@ "URL": "https://www.rforge.net/uuid", "BugReports": "https://github.com/s-u/uuid/issues", "NeedsCompilation": "yes", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "vctrs": { "Package": "vctrs", @@ -4850,8 +4841,7 @@ "RoxygenNote": "7.1.2", "NeedsCompilation": "no", "Author": "Almende B.V. and Contributors [aut, cph] (vis.js library in htmlwidgets/lib, https://visjs.org/, https://github.com/visjs/vis-network), Benoit Thieurmel [aut, cre] (R interface)", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "vroom": { "Package": "vroom", @@ -5013,8 +5003,7 @@ "License": "GPL (>= 2)", "URL": "http://population.un.org/wpp", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "xfun": { "Package": "xfun", @@ -5121,8 +5110,7 @@ "URL": "https://github.com/vubiostat/r-yaml/", "BugReports": "https://github.com/vubiostat/r-yaml/issues", "NeedsCompilation": "yes", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" } } }