From e6326cb4512d681c9498f706ff1f2441176def08 Mon Sep 17 00:00:00 2001 From: hansvancalster Date: Wed, 21 May 2025 07:53:28 +0200 Subject: [PATCH 1/2] upgrade and hydrate renv.lock (R 4.5.0) --- renv.lock | 403 ++++++++++++++++++++---------------------------- renv/activate.R | 97 +++++++----- 2 files changed, 227 insertions(+), 273 deletions(-) diff --git a/renv.lock b/renv.lock index 5093ee4d..aff543a3 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.3", + "Version": "4.5.0", "Repositories": [ { "Name": "CRAN", @@ -420,7 +420,7 @@ }, "bookdown": { "Package": "bookdown", - "Version": "0.42", + "Version": "0.43", "Source": "Repository", "Type": "Package", "Title": "Authoring Books and Technical Documents with R Markdown", @@ -445,6 +445,7 @@ "downlit (>= 0.4.0)", "htmlwidgets", "jsonlite", + "curl", "rstudioapi", "miniUI", "rsconnect (>= 0.4.3)", @@ -731,7 +732,7 @@ "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "SystemRequirements": "Pandoc (>= 1.17.2)", - "Author": "Thierry Onkelinx [aut, cre] (, Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (, Research Institute for Nature and Forest (INBO)), Hans Van Calster [ctb] (, Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", + "Author": "Thierry Onkelinx [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Hans Van Calster [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", "Maintainer": "Thierry Onkelinx ", "RemoteType": "github", "RemoteHost": "api.github.com", @@ -742,7 +743,7 @@ }, "cli": { "Package": "cli", - "Version": "3.6.4", + "Version": "3.6.5", "Source": "Repository", "Title": "Helpers for Developing Command Line Interfaces", "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"gabor@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kirill\", \"Müller\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", , \"salim-b@pm.me\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -929,63 +930,9 @@ "NeedsCompilation": "no", "Repository": "CRAN" }, - "colorspace": { - "Package": "colorspace", - "Version": "2.1-1", - "Source": "Repository", - "Date": "2024-07-26", - "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", - "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", - "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", - "Depends": [ - "R (>= 3.0.0)", - "methods" - ], - "Imports": [ - "graphics", - "grDevices", - "stats" - ], - "Suggests": [ - "datasets", - "utils", - "KernSmooth", - "MASS", - "kernlab", - "mvtnorm", - "vcd", - "tcltk", - "shiny", - "shinyjs", - "ggplot2", - "dplyr", - "scales", - "grid", - "png", - "jpeg", - "knitr", - "rmarkdown", - "RColorBrewer", - "rcartocolor", - "scico", - "viridis", - "wesanderson" - ], - "VignetteBuilder": "knitr", - "License": "BSD_3_clause + file LICENSE", - "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", - "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", - "LazyData": "yes", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "yes", - "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", - "Maintainer": "Achim Zeileis ", - "Repository": "CRAN" - }, "commonmark": { "Package": "commonmark", - "Version": "1.9.2", + "Version": "1.9.5", "Source": "Repository", "Type": "Package", "Title": "High Performance CommonMark and Github Markdown Rendering in R", @@ -999,7 +946,7 @@ "testthat", "xml2" ], - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2", "Language": "en-US", "Encoding": "UTF-8", "NeedsCompilation": "yes", @@ -1157,7 +1104,7 @@ }, "curl": { "Package": "curl", - "Version": "6.2.1", + "Version": "6.2.2", "Source": "Repository", "Type": "Package", "Title": "A Modern and Flexible Web Client for R", @@ -1325,7 +1272,7 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.5", + "Version": "0.3.6", "Source": "Repository", "Type": "Package", "Title": "Diffs for R Objects", @@ -1337,7 +1284,7 @@ "License": "GPL-2 | GPL-3", "URL": "https://github.com/brodieG/diffobj", "BugReports": "https://github.com/brodieG/diffobj/issues", - "RoxygenNote": "7.1.1", + "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Suggests": [ @@ -1666,7 +1613,7 @@ }, "fs": { "Package": "fs", - "Version": "1.6.5", + "Version": "1.6.6", "Source": "Repository", "Title": "Cross-Platform File System Operations Based on 'libuv'", "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -1708,16 +1655,16 @@ }, "generics": { "Package": "generics", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Title": "Common S3 Generics not Provided by Base R Methods Related to Model Fitting", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"Max\", \"Kuhn\", , \"max@rstudio.com\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@rstudio.com\", role = \"aut\"), person(\"RStudio\", role = \"cph\") )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/03wc8by49\")) )", "Description": "In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.", "License": "MIT + file LICENSE", "URL": "https://generics.r-lib.org, https://github.com/r-lib/generics", "BugReports": "https://github.com/r-lib/generics/issues", "Depends": [ - "R (>= 3.2)" + "R (>= 3.6)" ], "Imports": [ "methods" @@ -1732,15 +1679,15 @@ "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.2.0", + "RoxygenNote": "7.3.2", "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre], Max Kuhn [aut], Davis Vaughan [aut], RStudio [cph]", - "Maintainer": "Hadley Wickham ", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Max Kuhn [aut], Davis Vaughan [aut], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "gert": { "Package": "gert", - "Version": "2.1.4", + "Version": "2.1.5", "Source": "Repository", "Type": "Package", "Title": "Simple Git Client for R", @@ -1775,7 +1722,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.5.1", + "Version": "3.5.2", "Source": "Repository", "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -1835,7 +1782,7 @@ "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Collate": "'ggproto.R' 'ggplot-global.R' 'aaa-.R' 'aes-colour-fill-alpha.R' 'aes-evaluation.R' 'aes-group-order.R' 'aes-linetype-size-shape.R' 'aes-position.R' 'compat-plyr.R' 'utilities.R' 'aes.R' 'utilities-checks.R' 'legend-draw.R' 'geom-.R' 'annotation-custom.R' 'annotation-logticks.R' 'geom-polygon.R' 'geom-map.R' 'annotation-map.R' 'geom-raster.R' 'annotation-raster.R' 'annotation.R' 'autolayer.R' 'autoplot.R' 'axis-secondary.R' 'backports.R' 'bench.R' 'bin.R' 'coord-.R' 'coord-cartesian-.R' 'coord-fixed.R' 'coord-flip.R' 'coord-map.R' 'coord-munch.R' 'coord-polar.R' 'coord-quickmap.R' 'coord-radial.R' 'coord-sf.R' 'coord-transform.R' 'data.R' 'docs_layer.R' 'facet-.R' 'facet-grid-.R' 'facet-null.R' 'facet-wrap.R' 'fortify-lm.R' 'fortify-map.R' 'fortify-multcomp.R' 'fortify-spatial.R' 'fortify.R' 'stat-.R' 'geom-abline.R' 'geom-rect.R' 'geom-bar.R' 'geom-bin2d.R' 'geom-blank.R' 'geom-boxplot.R' 'geom-col.R' 'geom-path.R' 'geom-contour.R' 'geom-count.R' 'geom-crossbar.R' 'geom-segment.R' 'geom-curve.R' 'geom-defaults.R' 'geom-ribbon.R' 'geom-density.R' 'geom-density2d.R' 'geom-dotplot.R' 'geom-errorbar.R' 'geom-errorbarh.R' 'geom-freqpoly.R' 'geom-function.R' 'geom-hex.R' 'geom-histogram.R' 'geom-hline.R' 'geom-jitter.R' 'geom-label.R' 'geom-linerange.R' 'geom-point.R' 'geom-pointrange.R' 'geom-quantile.R' 'geom-rug.R' 'geom-sf.R' 'geom-smooth.R' 'geom-spoke.R' 'geom-text.R' 'geom-tile.R' 'geom-violin.R' 'geom-vline.R' 'ggplot2-package.R' 'grob-absolute.R' 'grob-dotstack.R' 'grob-null.R' 'grouping.R' 'theme-elements.R' 'guide-.R' 'guide-axis.R' 'guide-axis-logticks.R' 'guide-axis-stack.R' 'guide-axis-theta.R' 'guide-legend.R' 'guide-bins.R' 'guide-colorbar.R' 'guide-colorsteps.R' 'guide-custom.R' 'layer.R' 'guide-none.R' 'guide-old.R' 'guides-.R' 'guides-grid.R' 'hexbin.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'labeller.R' 'labels.R' 'layer-sf.R' 'layout.R' 'limits.R' 'margins.R' 'performance.R' 'plot-build.R' 'plot-construction.R' 'plot-last.R' 'plot.R' 'position-.R' 'position-collide.R' 'position-dodge.R' 'position-dodge2.R' 'position-identity.R' 'position-jitter.R' 'position-jitterdodge.R' 'position-nudge.R' 'position-stack.R' 'quick-plot.R' 'reshape-add-margins.R' 'save.R' 'scale-.R' 'scale-alpha.R' 'scale-binned.R' 'scale-brewer.R' 'scale-colour.R' 'scale-continuous.R' 'scale-date.R' 'scale-discrete-.R' 'scale-expansion.R' 'scale-gradient.R' 'scale-grey.R' 'scale-hue.R' 'scale-identity.R' 'scale-linetype.R' 'scale-linewidth.R' 'scale-manual.R' 'scale-shape.R' 'scale-size.R' 'scale-steps.R' 'scale-type.R' 'scale-view.R' 'scale-viridis.R' 'scales-.R' 'stat-align.R' 'stat-bin.R' 'stat-bin2d.R' 'stat-bindot.R' 'stat-binhex.R' 'stat-boxplot.R' 'stat-contour.R' 'stat-count.R' 'stat-density-2d.R' 'stat-density.R' 'stat-ecdf.R' 'stat-ellipse.R' 'stat-function.R' 'stat-identity.R' 'stat-qq-line.R' 'stat-qq.R' 'stat-quantilemethods.R' 'stat-sf-coordinates.R' 'stat-sf.R' 'stat-smooth-methods.R' 'stat-smooth.R' 'stat-sum.R' 'stat-summary-2d.R' 'stat-summary-bin.R' 'stat-summary-hex.R' 'stat-summary.R' 'stat-unique.R' 'stat-ydensity.R' 'summarise-plot.R' 'summary.R' 'theme.R' 'theme-defaults.R' 'theme-current.R' 'utilities-break.R' 'utilities-grid.R' 'utilities-help.R' 'utilities-matrix.R' 'utilities-patterns.R' 'utilities-resolution.R' 'utilities-tidy-eval.R' 'zxx.R' 'zzz.R'", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut] (), Winston Chang [aut] (), Lionel Henry [aut], Thomas Lin Pedersen [aut, cre] (), Kohske Takahashi [aut], Claus Wilke [aut] (), Kara Woo [aut] (), Hiroaki Yutani [aut] (), Dewey Dunnington [aut] (), Teun van den Brand [aut] (), Posit, PBC [cph, fnd]", @@ -1888,7 +1835,7 @@ }, "git2r": { "Package": "git2r", - "Version": "0.35.0", + "Version": "0.36.2", "Source": "Repository", "Type": "Package", "Title": "Provides Access to Git Repositories", @@ -1908,7 +1855,7 @@ "getPass" ], "NeedsCompilation": "yes", - "SystemRequirements": "libgit2 (>= 1.0): libgit2-devel (rpm) or libgit2-dev (deb)", + "SystemRequirements": "libgit2 (>= 1.0) and its dependencies libssh2 and openssl header and libraries.", "Collate": "'blame.R' 'blob.R' 'branch.R' 'bundle_r_package.R' 'checkout.R' 'commit.R' 'config.R' 'contributions.R' 'credential.R' 'diff.R' 'fetch.R' 'git2r.R' 'index.R' 'libgit2.R' 'merge.R' 'note.R' 'odb.R' 'plot.R' 'pull.R' 'punch_card.R' 'push.R' 'reference.R' 'reflog.R' 'refspec.R' 'remote.R' 'repository.R' 'reset.R' 'revparse.R' 'sha.R' 'signature.R' 'stash.R' 'status.R' 'tag.R' 'time.R' 'tree.R' 'when.R'", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", @@ -2257,7 +2204,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.15", + "Version": "1.6.16", "Source": "Repository", "Type": "Package", "Title": "HTTP and WebSocket Server Library", @@ -2279,6 +2226,7 @@ "Suggests": [ "callr", "curl", + "jsonlite", "testthat", "websocket" ], @@ -2287,7 +2235,7 @@ "Rcpp" ], "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "GNU make, zlib", "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", "NeedsCompilation": "yes", @@ -2337,7 +2285,7 @@ }, "httr2": { "Package": "httr2", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Title": "Perform HTTP Requests and Process the Responses", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Maximilian\", \"Girlich\", role = \"ctb\") )", @@ -2372,6 +2320,7 @@ "jsonlite", "knitr", "later (>= 1.4.0)", + "nanonext", "paws.common", "promises", "rmarkdown", @@ -2394,7 +2343,7 @@ }, "hunspell": { "Package": "hunspell", - "Version": "3.0.5", + "Version": "3.0.6", "Source": "Repository", "Type": "Package", "Title": "High-Performance Stemmer, Tokenizer, and Spell Checker", @@ -2465,7 +2414,7 @@ "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", - "Author": "Els Lommelen [aut, cre] (, Research Institute for Nature and Forest (INBO)), Hans Van Calster [aut] (, Research Institute for Nature and Forest (INBO)), Els De Bie [aut] (, Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (, Research Institute for Nature and Forest (INBO)), Frederic Piesschaert [aut] (, Research Institute for Nature and Forest (INBO)), Toon Westra [aut] (, Research Institute for Nature and Forest (INBO)), Stijn Van Hoey [ctb] (), Research Institute for Nature and Forest (INBO) [cph, fnd]", + "Author": "Els Lommelen [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Hans Van Calster [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els De Bie [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Frederic Piesschaert [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Toon Westra [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Stijn Van Hoey [ctb] (ORCID: ), Research Institute for Nature and Forest (INBO) [cph, fnd]", "Maintainer": "Els Lommelen ", "RemoteType": "github", "RemoteHost": "api.github.com", @@ -2555,7 +2504,7 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.9.1", + "Version": "2.0.0", "Source": "Repository", "Title": "A Simple and Robust JSON Parser and Generator for R", "License": "MIT + file LICENSE", @@ -2577,7 +2526,7 @@ "R.rsp", "sf" ], - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", @@ -2668,7 +2617,7 @@ }, "later": { "Package": "later", - "Version": "1.4.1", + "Version": "1.4.2", "Source": "Repository", "Type": "Package", "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", @@ -2701,9 +2650,9 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-6", + "Version": "0.22-7", "Source": "Repository", - "Date": "2024-03-20", + "Date": "2025-03-31", "Priority": "recommended", "Title": "Trellis Graphics for R", "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", @@ -2968,10 +2917,9 @@ }, "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", @@ -2996,15 +2944,17 @@ "ByteCompile": "yes", "License": "GPL (>= 2)", "NeedsCompilation": "yes", + "Author": "Simon Wood [aut, cre]", + "Maintainer": "Simon Wood ", "Repository": "CRAN" }, "mime": { "Package": "mime", - "Version": "0.12", + "Version": "0.13", "Source": "Repository", "Type": "Package", "Title": "Map Filenames to MIME Types", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )", "Description": "Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.", "Imports": [ "tools" @@ -3012,64 +2962,41 @@ "License": "GPL", "URL": "https://github.com/yihui/mime", "BugReports": "https://github.com/yihui/mime/issues", - "RoxygenNote": "7.1.1", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Yihui Xie [aut, cre] (), Jeffrey Horner [ctb], Beilei Bian [ctb]", + "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Jeffrey Horner [ctb], Beilei Bian [ctb]", "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, "miniUI": { "Package": "miniUI", - "Version": "0.1.1.1", + "Version": "0.1.2", "Source": "Repository", "Type": "Package", "Title": "Shiny UI Widgets for Small Screens", - "Authors@R": "c( person(\"Joe\", \"Cheng\", role = c(\"cre\", \"aut\"), email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\") )", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = c(\"cre\", \"aut\"), email = \"joe@posit.co\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides UI widget and layout functions for writing Shiny apps that work well on small screens.", "License": "GPL-3", - "LazyData": "TRUE", + "URL": "https://github.com/rstudio/miniUI", + "BugReports": "https://github.com/rstudio/miniUI/issues", "Imports": [ "shiny (>= 0.13)", "htmltools (>= 0.3)", "utils" ], - "RoxygenNote": "5.0.1", - "NeedsCompilation": "no", - "Author": "Joe Cheng [cre, aut], RStudio [cph]", - "Maintainer": "Joe Cheng ", - "Repository": "CRAN" - }, - "munsell": { - "Package": "munsell", - "Version": "0.5.1", - "Source": "Repository", - "Type": "Package", - "Title": "Utilities for Using Munsell Colours", - "Author": "Charlotte Wickham ", - "Maintainer": "Charlotte Wickham ", - "Description": "Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. \"5R 5/10\") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.", - "Suggests": [ - "ggplot2", - "testthat" - ], - "Imports": [ - "colorspace", - "methods" - ], - "License": "MIT + file LICENSE", - "URL": "https://cran.r-project.org/package=munsell, https://github.com/cwickham/munsell/", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", - "BugReports": "https://github.com/cwickham/munsell/issues", "NeedsCompilation": "no", + "Author": "Joe Cheng [cre, aut], Posit Software, PBC [cph, fnd] (03wc8by49)", + "Maintainer": "Joe Cheng ", "Repository": "CRAN" }, "nlme": { "Package": "nlme", - "Version": "3.1-167", + "Version": "3.1-168", "Source": "Repository", - "Date": "2025-01-27", + "Date": "2025-03-31", "Priority": "recommended", "Title": "Linear and Nonlinear Mixed Effects Models", "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", @@ -3101,7 +3028,7 @@ }, "odbc": { "Package": "odbc", - "Version": "1.6.0", + "Version": "1.6.1", "Source": "Repository", "Title": "Connect to ODBC Compatible Databases (using the DBI Interface)", "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Oliver\", \"Gjoneski\", role = \"aut\"), person(\"lexicalunit\", role = \"cph\", comment = \"nanodbc library\"), person(\"Google Inc.\", role = \"cph\", comment = \"cctz library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3252,7 +3179,7 @@ }, "pillar": { "Package": "pillar", - "Version": "1.10.1", + "Version": "1.10.2", "Source": "Repository", "Title": "Coloured Formatting for Columns", "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\"), person(given = \"RStudio\", role = \"cph\"))", @@ -3300,7 +3227,7 @@ "Config/testthat/start-first": "format_multi_fuzz, format_multi_fuzz_2, format_multi, ctl_colonnade, ctl_colonnade_1, ctl_colonnade_2", "Config/autostyle/scope": "line_breaks", "Config/autostyle/strict": "true", - "Config/gha/extra-packages": "DiagrammeR=?ignore-before-r=3.5.0", + "Config/gha/extra-packages": "units=?ignore-before-r=4.3.0", "Config/Needs/website": "tidyverse/tidytemplate", "NeedsCompilation": "no", "Author": "Kirill Müller [aut, cre] (), Hadley Wickham [aut], RStudio [cph]", @@ -3341,7 +3268,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.6", + "Version": "1.4.7", "Source": "Repository", "Title": "Find Tools Needed to Build R Packages", "Authors@R": "c( person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3403,10 +3330,10 @@ }, "pkgdown": { "Package": "pkgdown", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Title": "Make Static HTML Documentation for a Package", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jay\", \"Hesselberth\", role = \"aut\", comment = c(ORCID = \"0000-0002-6299-179X\")), person(\"Maëlle\", \"Salmon\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Olivier\", \"Roy\", role = \"aut\"), person(\"Salim\", \"Brüggemann\", role = \"aut\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jay\", \"Hesselberth\", role = \"aut\", comment = c(ORCID = \"0000-0002-6299-179X\")), person(\"Maëlle\", \"Salmon\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Olivier\", \"Roy\", role = \"aut\"), person(\"Salim\", \"Brüggemann\", role = \"aut\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.", "License": "MIT + file LICENSE", "URL": "https://pkgdown.r-lib.org/, https://github.com/r-lib/pkgdown", @@ -3419,7 +3346,6 @@ "callr (>= 3.7.3)", "cli (>= 3.6.1)", "desc (>= 1.4.0)", - "digest", "downlit (>= 0.4.4)", "fontawesome", "fs (>= 1.4.0)", @@ -3427,8 +3353,8 @@ "jsonlite", "openssl", "purrr (>= 1.0.0)", - "ragg", - "rlang (>= 1.1.0)", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.4)", "rmarkdown (>= 2.27)", "tibble", "whisker", @@ -3444,7 +3370,7 @@ "gt", "htmltools", "htmlwidgets", - "knitr", + "knitr (>= 1.50)", "lifecycle", "magick", "methods", @@ -3464,10 +3390,10 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "build-article, build-quarto-article, build-reference", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.2.9000", "SystemRequirements": "pandoc", "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre] (), Jay Hesselberth [aut] (), Maëlle Salmon [aut] (), Olivier Roy [aut], Salim Brüggemann [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Hadley Wickham [aut, cre] (), Jay Hesselberth [aut] (), Maëlle Salmon [aut] (), Olivier Roy [aut], Salim Brüggemann [aut] (), Posit Software, PBC [cph, fnd] (03wc8by49)", "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, @@ -3792,7 +3718,7 @@ "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "SystemRequirements": "Pandoc (>= 2.0.0)", - "Author": "Hans Van Calster [aut, cre] (, Research Institute for Nature and Forest (INBO)), Thierry Onkelinx [aut] (, Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (, Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (, Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", + "Author": "Hans Van Calster [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Thierry Onkelinx [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", "Maintainer": "Hans Van Calster ", "RemoteType": "github", "RemoteHost": "api.github.com", @@ -3803,7 +3729,7 @@ }, "ps": { "Package": "ps", - "Version": "1.9.0", + "Version": "1.9.1", "Source": "Repository", "Title": "List, Query, Manipulate System Processes", "Authors@R": "c( person(\"Jay\", \"Loden\", role = \"aut\"), person(\"Dave\", \"Daeschler\", role = \"aut\"), person(\"Giampaolo\", \"Rodola'\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3889,7 +3815,7 @@ }, "ragg": { "Package": "ragg", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", "Type": "Package", "Title": "Graphic Devices Based on AGG", @@ -3915,9 +3841,10 @@ ], "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", "Config/testthat/edition": "3", + "Config/build/compilation-database": "true", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", "Repository": "CRAN" @@ -4160,7 +4087,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.2", + "Version": "1.1.4", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -4249,11 +4176,11 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.5", + "Version": "1.1.6", "Source": "Repository", "Title": "Functions for Base Types and Core R and 'Tidyverse' Features", "Description": "A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.", - "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\", role = \"cph\", comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\", comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\", role = \"cph\", comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\", comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", "License": "MIT + file LICENSE", "ByteCompile": "true", "Biarch": "true", @@ -4267,15 +4194,17 @@ "cli (>= 3.1.0)", "covr", "crayon", + "desc", "fs", "glue", "knitr", "magrittr", "methods", "pillar", + "pkgload", "rmarkdown", "stats", - "testthat (>= 3.0.0)", + "testthat (>= 3.2.0)", "tibble", "usethis", "vctrs (>= 0.2.3)", @@ -4288,6 +4217,7 @@ "RoxygenNote": "7.3.2", "URL": "https://rlang.r-lib.org, https://github.com/r-lib/rlang", "BugReports": "https://github.com/r-lib/rlang/issues", + "Config/build/compilation-database": "true", "Config/testthat/edition": "3", "Config/Needs/website": "dplyr, tidyverse/tidytemplate", "NeedsCompilation": "yes", @@ -4519,7 +4449,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.9", + "Version": "0.4.10", "Source": "Repository", "Type": "Package", "Title": "Syntactically Awesome Style Sheets ('Sass')", @@ -4529,7 +4459,7 @@ "URL": "https://rstudio.github.io/sass/, https://github.com/rstudio/sass", "BugReports": "https://github.com/rstudio/sass/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "SystemRequirements": "GNU make", "Imports": [ "fs (>= 1.2.4)", @@ -4555,16 +4485,16 @@ }, "scales": { "Package": "scales", - "Version": "1.3.0", + "Version": "1.4.0", "Source": "Repository", "Title": "Scale Functions for Visualization", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Dana\", \"Seidel\", role = \"aut\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Dana\", \"Seidel\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.", "License": "MIT + file LICENSE", "URL": "https://scales.r-lib.org, https://github.com/r-lib/scales", "BugReports": "https://github.com/r-lib/scales/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1)" ], "Imports": [ "cli", @@ -4572,10 +4502,9 @@ "glue", "labeling", "lifecycle", - "munsell (>= 0.5)", "R6", "RColorBrewer", - "rlang (>= 1.0.0)", + "rlang (>= 1.1.0)", "viridisLite" ], "Suggests": [ @@ -4589,11 +4518,12 @@ ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "LazyLoad": "yes", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit, PBC [cph, fnd]", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (03wc8by49)", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, @@ -4727,25 +4657,25 @@ }, "spatstat": { "Package": "spatstat", - "Version": "3.3-1", + "Version": "3.3-2", "Source": "Repository", - "Date": "2025-01-23", + "Date": "2025-03-22", "Title": "Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", - "spatstat.data (>= 3.1-4)", - "spatstat.univar (>= 3.1-1)", - "spatstat.geom (>= 3.3-5)", - "spatstat.random (>= 3.3-2)", - "spatstat.explore (>= 3.3-4)", - "spatstat.model (>= 3.3-4)", + "spatstat.data (>= 3.1-6)", + "spatstat.univar (>= 3.1-2)", + "spatstat.geom (>= 3.3-6)", + "spatstat.random (>= 3.3-3)", + "spatstat.explore (>= 3.4-2)", + "spatstat.model (>= 3.3-5)", "spatstat.linnet (>= 3.2-5)", "utils" ], "Imports": [ - "spatstat.utils (>= 3.1-2)" + "spatstat.utils (>= 3.1-3)" ], "Suggests": [], "Description": "Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images. Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.", @@ -4759,17 +4689,17 @@ }, "spatstat.data": { "Package": "spatstat.data", - "Version": "3.1-4", + "Version": "3.1-6", "Source": "Repository", - "Date": "2024-11-15", + "Date": "2025-03-17", "Title": "Datasets for 'spatstat' Family", - "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"W\", \"Aherne\", role=\"ctb\"), person(\"Freda\", \"Alexander\", role=\"ctb\"), person(\"Qi Wei\", \"Ang\", role=\"ctb\"), person(\"Sourav\", \"Banerjee\", role=\"ctb\"), person(\"Mark\", \"Berman\", role=\"ctb\"), person(\"R\", \"Bernhardt\", role=\"ctb\"), person(\"Thomas\", \"Berndtsen\", role=\"ctb\"), person(\"Andrew\", \"Bevan\", role=\"ctb\"), person(\"Jeffrey\", \"Betts\", role=\"ctb\"), person(\"Ray\", \"Cartwright\", role=\"ctb\"), person(\"Lucia\", \"Cobo Sanchez\", role=\"ctb\"), person(\"Richard\", \"Condit\", role=\"ctb\"), person(\"Francis\", \"Crick\", role=\"ctb\"), person(\"Marcelino\", \"de la Cruz Rot\", role=\"ctb\"), person(\"Jack\", \"Cuzick\", role=\"ctb\"), person(\"Tilman\", \"Davies\", role=\"ctb\"), person(\"Peter\", \"Diggle\", role=\"ctb\"), person(\"Michael\", \"Drinkwater\", role=\"ctb\"), person(\"Stephen\", \"Eglen\", role=\"ctb\"), person(\"Robert\", \"Edwards\", role=\"ctb\"), person(\"AE\", \"Esler\", role=\"ctb\"), person(\"Gregory\", \"Evans\", role=\"ctb\"), person(\"Bernard\", \"Fingleton\", role=\"ctb\"), person(\"Olivier\", \"Flores\", role=\"ctb\"), person(\"David\", \"Ford\", role=\"ctb\"), person(\"Robin\", \"Foster\", role=\"ctb\"), person(\"Janet\", \"Franklin\", role=\"ctb\"), person(\"Neba\", \"Funwi-Gabga\", role=\"ctb\"), person(\"DJ\", \"Gerrard\", role=\"ctb\"), person(\"Andy\", \"Green\", role=\"ctb\"), person(\"Tim\", \"Griffin\", role=\"ctb\"), person(\"Ute\", \"Hahn\", role=\"ctb\"), person(\"RD\", \"Harkness\", role=\"ctb\"), person(\"Arthur\", \"Hickman\", role=\"ctb\"), person(\"Stephen\", \"Hubbell\", role=\"ctb\"), person(\"Austin\", \"Hughes\", role=\"ctb\"), person(\"Jonathan\", \"Huntington\", role=\"ctb\"), person(\"MJ\", \"Hutchings\", role=\"ctb\"), person(\"Jackie\", \"Inwald\", role=\"ctb\"), person(\"Valerie\", \"Isham\", role=\"ctb\"), person(\"Aruna\", \"Jammalamadaka\", role=\"ctb\"), person(\"Carl\", \"Knox-Robinson\", role=\"ctb\"), person(\"Mahdieh\", \"Khanmohammadi\", role=\"ctb\"), person(\"Tero\", \"Kokkila\", role=\"ctb\"), person(\"Bas\", \"Kooijman\", role=\"ctb\"), person(\"Kenneth\", \"Kosik\", role=\"ctb\"), person(\"Peter\", \"Kovesi\", role=\"ctb\"), person(\"Lily\", \"Kozmian-Ledward\", role=\"ctb\"), person(\"Robert\", \"Lamb\", role=\"ctb\"), person(\"NA\", \"Laskurain\", role=\"ctb\"), person(\"George\", \"Leser\", role=\"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role=\"ctb\"), person(\"AF\", \"Mark\", role=\"ctb\"), person(\"Jorge\", \"Mateu\", role=\"ctb\"), person(\"Annikki\", \"Makela\", role=\"ctb\"), person(\"Enrique\", \"Miranda\", role=\"ctb\"), person(\"Nicoletta\", \"Nava\", role=\"ctb\"), person(\"M\", \"Numata\", role=\"ctb\"), person(\"Matti\", \"Nummelin\", role=\"ctb\"), person(\"Jens Randel\", \"Nyengaard\", role=\"ctb\"), person(\"Yosihiko\", \"Ogata\", role=\"ctb\"), person(\"Si\", \"Palmer\", role=\"ctb\"), person(\"Antti\", \"Penttinen\", role=\"ctb\"), person(\"Sandra\", \"Pereira\", role=\"ctb\"), person(\"Nicolas\", \"Picard\", role=\"ctb\"), person(\"William\", \"Platt\", role=\"ctb\"), person(\"Stephen\", \"Rathbun\", role=\"ctb\"), person(\"Brian\", \"Ripley\", role=\"ctb\"), person(\"Roger\", \"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"W\", \"Aherne\", role=\"ctb\"), person(\"Freda\", \"Alexander\", role=\"ctb\"), person(\"Qi Wei\", \"Ang\", role=\"ctb\"), person(\"Sourav\", \"Banerjee\", role=\"ctb\"), person(\"Mark\", \"Berman\", role=\"ctb\"), person(\"R\", \"Bernhardt\", role=\"ctb\"), person(\"Thomas\", \"Berndtsen\", role=\"ctb\"), person(\"Andrew\", \"Bevan\", role=\"ctb\"), person(\"Jeffrey\", \"Betts\", role=\"ctb\"), person(\"Ray\", \"Cartwright\", role=\"ctb\"), person(\"Lucia\", \"Cobo Sanchez\", role=\"ctb\"), person(\"Richard\", \"Condit\", role=\"ctb\"), person(\"Francis\", \"Crick\", role=\"ctb\"), person(\"Marcelino\", \"de la Cruz Rot\", role=\"ctb\"), person(\"Jack\", \"Cuzick\", role=\"ctb\"), person(\"Tilman\", \"Davies\", role=\"ctb\"), person(\"Peter\", \"Diggle\", role=\"ctb\"), person(\"Michael\", \"Drinkwater\", role=\"ctb\"), person(\"Stephen\", \"Eglen\", role=\"ctb\"), person(\"Robert\", \"Edwards\", role=\"ctb\"), person(\"Johannes\", \"Elias\", role=\"ctb\"), person(\"AE\", \"Esler\", role=\"ctb\"), person(\"Gregory\", \"Evans\", role=\"ctb\"), person(\"Bernard\", \"Fingleton\", role=\"ctb\"), person(\"Olivier\", \"Flores\", role=\"ctb\"), person(\"David\", \"Ford\", role=\"ctb\"), person(\"Robin\", \"Foster\", role=\"ctb\"), person(\"Janet\", \"Franklin\", role=\"ctb\"), person(\"Neba\", \"Funwi-Gabga\", role=\"ctb\"), person(\"DJ\", \"Gerrard\", role=\"ctb\"), person(\"Andy\", \"Green\", role=\"ctb\"), person(\"Tim\", \"Griffin\", role=\"ctb\"), person(\"Ute\", \"Hahn\", role=\"ctb\"), person(\"RD\", \"Harkness\", role=\"ctb\"), person(\"Arthur\", \"Hickman\", role=\"ctb\"), person(\"Stephen\", \"Hubbell\", role=\"ctb\"), person(\"Austin\", \"Hughes\", role=\"ctb\"), person(\"Jonathan\", \"Huntington\", role=\"ctb\"), person(\"MJ\", \"Hutchings\", role=\"ctb\"), person(\"Jackie\", \"Inwald\", role=\"ctb\"), person(\"Valerie\", \"Isham\", role=\"ctb\"), person(\"Aruna\", \"Jammalamadaka\", role=\"ctb\"), person(\"Carl\", \"Knox-Robinson\", role=\"ctb\"), person(\"Mahdieh\", \"Khanmohammadi\", role=\"ctb\"), person(\"Tero\", \"Kokkila\", role=\"ctb\"), person(\"Bas\", \"Kooijman\", role=\"ctb\"), person(\"Kenneth\", \"Kosik\", role=\"ctb\"), person(\"Peter\", \"Kovesi\", role=\"ctb\"), person(\"Lily\", \"Kozmian-Ledward\", role=\"ctb\"), person(\"Robert\", \"Lamb\", role=\"ctb\"), person(\"NA\", \"Laskurain\", role=\"ctb\"), person(\"George\", \"Leser\", role=\"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role=\"ctb\"), person(\"AF\", \"Mark\", role=\"ctb\"), person(\"Sebastian\", \"Meyer\", role=\"ctb\"), person(\"Jorge\", \"Mateu\", role=\"ctb\"), person(\"Annikki\", \"Makela\", role=\"ctb\"), person(\"Enrique\", \"Miranda\", role=\"ctb\"), person(\"Nicoletta\", \"Nava\", role=\"ctb\"), person(\"M\", \"Numata\", role=\"ctb\"), person(\"Matti\", \"Nummelin\", role=\"ctb\"), person(\"Jens Randel\", \"Nyengaard\", role=\"ctb\"), person(\"Yosihiko\", \"Ogata\", role=\"ctb\"), person(\"Si\", \"Palmer\", role=\"ctb\"), person(\"Antti\", \"Penttinen\", role=\"ctb\"), person(\"Sandra\", \"Pereira\", role=\"ctb\"), person(\"Nicolas\", \"Picard\", role=\"ctb\"), person(\"William\", \"Platt\", role=\"ctb\"), person(\"Stephen\", \"Rathbun\", role=\"ctb\"), person(\"Brian\", \"Ripley\", role=\"ctb\"), person(\"Roger\", \"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Ulrich\", \"Vogel\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)" ], "Imports": [ - "spatstat.utils (>= 3.0-5)", + "spatstat.utils (>= 3.1-2)", "Matrix" ], "Suggests": [ @@ -4786,23 +4716,23 @@ "NeedsCompilation": "no", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.data/issues", - "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", + "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], Johannes Elias [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Sebastian Meyer [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Ulrich Vogel [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", "Repository": "CRAN" }, "spatstat.explore": { "Package": "spatstat.explore", - "Version": "3.3-4", + "Version": "3.4-2", "Source": "Repository", - "Date": "2025-01-08", + "Date": "2025-03-20", "Title": "Exploratory Data Analysis for the 'spatstat' Family", - "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"))", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Ya-Mei\", \"Chang\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"), person(\"Tingting\", \"Zhan\", role=\"ctb\"))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1-2)", - "spatstat.univar (>= 3.0-0)", - "spatstat.geom (>= 3.3-2)", - "spatstat.random (>= 3.3-1)", + "spatstat.univar (>= 3.1-2)", + "spatstat.geom (>= 3.3-6)", + "spatstat.random (>= 3.3-2)", "stats", "graphics", "grDevices", @@ -4833,21 +4763,21 @@ "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.explore/issues", - "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] (), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb]", + "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] (), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Ya-Mei Chang [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb], Tingting Zhan [ctb]", "Repository": "CRAN" }, "spatstat.geom": { "Package": "spatstat.geom", - "Version": "3.3-5", + "Version": "3.4-1", "Source": "Repository", - "Date": "2025-01-18", + "Date": "2025-05-20", "Title": "Geometrical Functionality of the 'spatstat' Family", - "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Warick\", \"Brown\" , role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1)", - "spatstat.univar (>= 3.1-0)", + "spatstat.univar (>= 3.1)", "stats", "graphics", "grDevices", @@ -4855,9 +4785,9 @@ "methods" ], "Imports": [ - "spatstat.utils (>= 3.1-2)", + "spatstat.utils (>= 3.1-4)", "deldir (>= 1.0-2)", - "polyclip (>= 1.10-0)" + "polyclip (>= 1.10)" ], "Suggests": [ "spatstat.random (>= 3.3)", @@ -4866,7 +4796,7 @@ "spatstat.linnet (>= 3.2)", "spatial", "fftwtools (>= 0.9-8)", - "spatstat (>= 3.2)" + "spatstat (>= 3.3)" ], "Description": "Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)", "License": "GPL (>= 2)", @@ -4874,7 +4804,7 @@ "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.geom/issues", - "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] (), Tilman Davies [ctb], Ute Hahn [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Warick Brown [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", "Repository": "CRAN" }, "spatstat.linnet": { @@ -4920,9 +4850,9 @@ }, "spatstat.model": { "Package": "spatstat.model", - "Version": "3.3-4", + "Version": "3.3-5", "Source": "Repository", - "Date": "2025-01-20", + "Date": "2025-03-22", "Title": "Parametric Statistical Modelling and Inference for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Achmad\", \"Choiruddin\", role = c(\"ctb\", \"cph\")), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = \"ctb\"), person(\"Bethany\", \"Macdonald\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"))", "Maintainer": "Adrian Baddeley ", @@ -4959,7 +4889,7 @@ "nleqslv", "glmnet", "spatstat.linnet (>= 3.2-2)", - "spatstat (>= 3.2-1)" + "spatstat (>= 3.3)" ], "Description": "Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.", "License": "GPL (>= 2)", @@ -4972,31 +4902,31 @@ }, "spatstat.random": { "Package": "spatstat.random", - "Version": "3.3-2", + "Version": "3.3-3", "Source": "Repository", - "Date": "2024-09-18", + "Date": "2025-03-19", "Title": "Random Generation Functionality for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = c(\"aut\", \"cph\"), comment=c(ORCID=\"0000-0003-0565-1825\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = c(\"ctb\", \"cph\")), person(\"David\", \"Bryant\", role = c(\"ctb\", \"cph\")), person(\"Ya-Mei\", \"Chang\", role = c(\"ctb\", \"cph\"), email = \"yamei628@gmail.com\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = c(\"ctb\", \"cph\")), person(\"Rasmus\", \"Plenge Waagepetersen\", role = c(\"ctb\", \"cph\")))", "Maintainer": "Adrian Baddeley ", "Depends": [ "R (>= 3.5.0)", "spatstat.data (>= 3.1)", - "spatstat.univar (>= 3.0-0)", - "spatstat.geom (>= 3.3-0)", + "spatstat.univar (>= 3.1)", + "spatstat.geom (>= 3.3-6)", "stats", "utils", "methods", "grDevices" ], "Imports": [ - "spatstat.utils (>= 3.1-0)" + "spatstat.utils (>= 3.1-2)" ], "Suggests": [ "spatial", - "spatstat.linnet (>= 3.1-5)", + "spatstat.linnet (>= 3.2)", "spatstat.explore", "spatstat.model", - "spatstat (>= 3.0)", + "spatstat (>= 3.3)", "gsl" ], "Description": "Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.", @@ -5039,9 +4969,9 @@ }, "spatstat.univar": { "Package": "spatstat.univar", - "Version": "3.1-2", + "Version": "3.1-3", "Source": "Repository", - "Date": "2025-03-05", + "Date": "2025-05-07", "Title": "One-Dimensional Probability Distribution Support for the 'spatstat' Family", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(c(\"Tilman\", \"M.\"), \"Davies\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Tilman.Davies@otago.ac.nz\", comment = c(ORCID=\"0000-0003-0565-1825\")), person(c(\"Martin\", \"L.\"), \"Hazelton\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Martin.Hazelton@otago.ac.nz\", comment = c(ORCID=\"0000-0001-7831-725X\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")))", "Maintainer": "Adrian Baddeley ", @@ -5050,7 +4980,8 @@ "stats" ], "Imports": [ - "spatstat.utils (>= 3.1-2)" + "spatstat.utils (>= 3.1-2)", + "graphics" ], "Description": "Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.", "License": "GPL (>= 2)", @@ -5058,14 +4989,14 @@ "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.univar/issues", - "Author": "Adrian Baddeley [aut, cre, cph] (), Tilman M. Davies [aut, ctb, cph] (), Martin L. Hazelton [aut, ctb, cph] (), Ege Rubak [aut, cph] (), Rolf Turner [aut, cph] (), Greg McSwiggan [ctb, cph]", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Tilman M. Davies [aut, ctb, cph] (ORCID: ), Martin L. Hazelton [aut, ctb, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Greg McSwiggan [ctb, cph]", "Repository": "CRAN" }, "spatstat.utils": { "Package": "spatstat.utils", - "Version": "3.1-3", + "Version": "3.1-4", "Source": "Repository", - "Date": "2025-03-15", + "Date": "2025-05-15", "Title": "Utility Functions for 'spatstat'", "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", "Maintainer": "Adrian Baddeley ", @@ -5086,14 +5017,14 @@ "NeedsCompilation": "yes", "ByteCompile": "true", "BugReports": "https://github.com/spatstat/spatstat.utils/issues", - "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] ()", + "Author": "Adrian Baddeley [aut, cre] (ORCID: ), Rolf Turner [aut] (ORCID: ), Ege Rubak [aut] (ORCID: )", "Repository": "CRAN" }, "stringi": { "Package": "stringi", - "Version": "1.8.4", + "Version": "1.8.7", "Source": "Repository", - "Date": "2024-05-06", + "Date": "2025-03-27", "Title": "Fast and Portable Character String Processing Facilities", "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at and the paper by Gagolewski (2022, ).", "URL": "https://stringi.gagolewski.com/, https://github.com/gagolews/stringi, https://icu.unicode.org/", @@ -5110,11 +5041,12 @@ ], "Biarch": "TRUE", "License": "file LICENSE", - "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], and others (stringi source code); Unicode, Inc. and others (ICU4C source code, Unicode Character Database)", - "Maintainer": "Marek Gagolewski ", - "RoxygenNote": "7.2.3", + "Authors@R": "c(person(given = \"Marek\", family = \"Gagolewski\", role = c(\"aut\", \"cre\", \"cph\"), email = \"marek@gagolewski.com\", comment = c(ORCID = \"0000-0003-0637-6028\")), person(given = \"Bartek\", family = \"Tartanus\", role = \"ctb\"), person(\"Unicode, Inc. and others\", role=\"ctb\", comment = \"ICU4C source code, Unicode Character Database\") )", + "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "NeedsCompilation": "yes", + "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], Unicode, Inc. and others [ctb] (ICU4C source code, Unicode Character Database)", + "Maintainer": "Marek Gagolewski ", "License_is_FOSS": "yes", "Repository": "CRAN" }, @@ -5188,11 +5120,11 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.2.1", + "Version": "1.2.3", "Source": "Repository", "Type": "Package", "Title": "System Native Font Finding", - "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Devon\", \"Govett\", role = \"aut\", comment = \"Author of font-manager\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Devon\", \"Govett\", role = \"aut\", comment = \"Author of font-manager\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/systemfonts, https://systemfonts.r-lib.org", @@ -5200,6 +5132,14 @@ "Depends": [ "R (>= 3.2.0)" ], + "Imports": [ + "base64enc", + "grid", + "jsonlite", + "lifecycle", + "tools", + "utils" + ], "Suggests": [ "covr", "farver", @@ -5212,20 +5152,14 @@ "cpp11 (>= 0.2.1)" ], "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "SystemRequirements": "fontconfig, freetype2", - "Config/Needs/website": "tidyverse/tidytemplate", - "Imports": [ - "grid", - "jsonlite", - "lifecycle", - "tools", - "utils" - ], - "Config/build/compilation-database": "true", "NeedsCompilation": "yes", - "Author": "Thomas Lin Pedersen [aut, cre] (), Jeroen Ooms [aut] (), Devon Govett [aut] (Author of font-manager), Posit, PBC [cph, fnd]", + "Author": "Thomas Lin Pedersen [aut, cre] (ORCID: ), Jeroen Ooms [aut] (ORCID: ), Devon Govett [aut] (Author of font-manager), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, @@ -5302,10 +5236,10 @@ }, "textshaping": { "Package": "textshaping", - "Version": "1.0.0", + "Version": "1.0.1", "Source": "Repository", "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", - "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/textshaping", @@ -5333,13 +5267,14 @@ "systemfonts (>= 1.0.0)" ], "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "SystemRequirements": "freetype2, harfbuzz, fribidi", - "Config/build/compilation-database": "true", - "Config/testthat/edition": "3", "NeedsCompilation": "yes", - "Author": "Thomas Lin Pedersen [cre, aut] (), Posit, PBC [cph, fnd]", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, @@ -5485,7 +5420,7 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.56", + "Version": "0.57", "Source": "Repository", "Type": "Package", "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", @@ -5694,7 +5629,7 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.4", + "Version": "1.2.5", "Source": "Repository", "Title": "Unicode Text Processing", "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", @@ -5717,7 +5652,7 @@ "VignetteBuilder": "knitr, rmarkdown", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2.9000", "NeedsCompilation": "yes", "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)", "Maintainer": "Kirill Müller ", @@ -5992,7 +5927,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.51", + "Version": "0.52", "Source": "Repository", "Type": "Package", "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", @@ -6016,18 +5951,15 @@ "mime", "litedown (>= 0.4)", "commonmark", - "knitr (>= 1.47)", + "knitr (>= 1.50)", "remotes", "pak", - "rhub", - "renv", "curl", "xml2", "jsonlite", "magick", "yaml", - "qs", - "rmarkdown" + "qs" ], "License": "MIT + file LICENSE", "URL": "https://github.com/yihui/xfun", @@ -6238,10 +6170,10 @@ }, "zip": { "Package": "zip", - "Version": "2.3.2", + "Version": "2.3.3", "Source": "Repository", "Title": "Cross-Platform 'zip' Compression", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", @@ -6256,10 +6188,11 @@ ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-05-07", "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2.9000", "NeedsCompilation": "yes", - "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" } diff --git a/renv/activate.R b/renv/activate.R index c9f59425..90b251ca 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.1.2" + version <- "1.1.4" attr(version, "sha") <- NULL # the project directory @@ -695,11 +695,19 @@ local({ } - renv_bootstrap_platform_prefix <- function() { + renv_bootstrap_platform_prefix_default <- function() { - # construct version prefix - version <- paste(R.version$major, R.version$minor, sep = ".") - prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) @@ -708,10 +716,19 @@ local({ identical(R.version[["nickname"]], "Unsuffered Consequences") if (devel) - prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() # build list of path components - components <- c(prefix, R.version$platform) + components <- c(version, R.version$platform) # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() @@ -950,14 +967,14 @@ local({ } renv_bootstrap_validate_version_dev <- function(version, description) { - + expected <- description[["RemoteSha"]] if (!is.character(expected)) return(FALSE) - + pattern <- sprintf("^\\Q%s\\E", version) grepl(pattern, expected, perl = TRUE) - + } renv_bootstrap_validate_version_release <- function(version, description) { @@ -1198,86 +1215,89 @@ local({ } renv_json_read_patterns <- function() { - + list( - + # objects - list("{", "\t\n\tobject(\t\n\t"), - list("}", "\t\n\t)\t\n\t"), - + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + # arrays - list("[", "\t\n\tarray(\t\n\t"), - list("]", "\n\t\n)\n\t\n"), - + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + # maps - list(":", "\t\n\t=\t\n\t") - + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + ) - + } renv_json_read_envir <- function() { envir <- new.env(parent = emptyenv()) - + envir[["+"]] <- `+` envir[["-"]] <- `-` - + envir[["object"]] <- function(...) { result <- list(...) names(result) <- as.character(names(result)) result } - + envir[["array"]] <- list - + envir[["true"]] <- TRUE envir[["false"]] <- FALSE envir[["null"]] <- NULL - + envir - + } renv_json_read_remap <- function(object, patterns) { - + # repair names if necessary if (!is.null(names(object))) { - + nms <- names(object) for (pattern in patterns) nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) names(object) <- nms - + } - + # repair strings if necessary if (is.character(object)) { for (pattern in patterns) object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) } - + # recurse for other objects if (is.recursive(object)) for (i in seq_along(object)) object[i] <- list(renv_json_read_remap(object[[i]], patterns)) - + # return remapped object object - + } renv_json_read_default <- function(file = NULL, text = NULL) { # read json text text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - + # convert into something the R parser will understand patterns <- renv_json_read_patterns() transformed <- text for (pattern in patterns) transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) - + # parse it rfile <- tempfile("renv-json-", fileext = ".R") on.exit(unlink(rfile), add = TRUE) @@ -1287,9 +1307,10 @@ local({ # evaluate in safe environment result <- eval(json, envir = renv_json_read_envir()) - # fix up strings if necessary + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) renv_json_read_remap(result, patterns) - + } From 33c1bd3eaeafaf6c786ca28c40027fecca1cf105 Mon Sep 17 00:00:00 2001 From: hansvancalster Date: Wed, 21 May 2025 07:53:57 +0200 Subject: [PATCH 2/2] update pandoc to version 3.4 --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 95412b6a..74c48b39 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,9 +26,9 @@ RUN apt-get update \ && rm -rf /var/lib/apt/lists/* ## Install pandoc -RUN wget https://github.com/jgm/pandoc/releases/download/3.2/pandoc-3.2-1-amd64.deb \ - && dpkg -i pandoc-3.2-1-amd64.deb \ - && rm pandoc-3.2-1-amd64.deb +RUN wget https://github.com/jgm/pandoc/releases/download/3.4/pandoc-3.4-1-amd64.deb \ + && dpkg -i pandoc-3.4-1-amd64.deb \ + && rm pandoc-3.4-1-amd64.deb ## Copy R profile COPY docker/Rprofile.site $R_HOME/etc/Rprofile.site