From 95e813753ff4a9acd86821640706dd1a9121d6d1 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 12 Mar 2026 12:40:40 +0100 Subject: [PATCH] merge --- R/sysdata.rda | Bin 2668 -> 2671 bytes SESSION.md | 33 ++++---- app_docker/app.R | 33 ++++---- inst/apps/FreesearchR/app.R | 33 ++++---- renv.lock | 148 +++++++++++++++++++----------------- renv/activate.R | 4 +- 6 files changed, 130 insertions(+), 121 deletions(-) diff --git a/R/sysdata.rda b/R/sysdata.rda index bf735f2dcec4f96eb89c18b40a68635bbf4208b7..7ab55e91eff8121f1805d27dc695bbd323b19233 100644 GIT binary patch literal 2671 zcmV-#3Xt_eT4*^jL0KkKS$IOLcmNpnf5iX)Xaz!l|LA{j-@w2B|L{Nn0ssgB;0wPO zI?Ef60prY5M?jH4@DCz|>I}D6Vjig)Ou=qjST_mHq{t4JfPK2 z^a4qw^-m~b4UkNY000dD13&;8162JoB9!$HQM8*RHjwgw000000001!Nf8x2Q}s5c zME0oA8hVdvfuLx~lLQS713&;A4F;JFG-zQ1A)$gaG|8htG7LZfXd+4}>Uu=|O;1qC z=zwTw02%<$0}uen44IP088Q@Sp^UZF^RJjz>?Ymp`cyVor|(|t<6QgAObQYySeny!*l(Mcei)v{_MbhQt;E(e`SG` 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|CRAN (R 4.5.2) | |easystats |0.7.5 |2025-07-11 |CRAN (R 4.5.0) | |ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.5.0) | -|emmeans |2.0.1 |2025-12-16 |CRAN (R 4.5.2) | +|emmeans |2.0.2 |2026-03-05 |CRAN (R 4.5.2) | |esquisse |2.1.0 |2025-02-21 |CRAN (R 4.5.0) | |estimability |1.5.1 |2024-05-12 |CRAN (R 4.5.0) | |eulerr |7.0.4 |2025-09-24 |CRAN (R 4.5.0) | @@ -75,7 +74,6 @@ |farver |2.1.2 |2024-05-13 |CRAN (R 4.5.0) | |fastmap |1.2.0 |2024-05-15 |CRAN (R 4.5.0) | |flextable |0.9.11 |2026-02-13 |CRAN (R 4.5.2) | -|fontawesome |0.5.3 |2024-11-16 |CRAN (R 4.5.0) | |fontBitstreamVera |0.1.1 |2017-02-01 |CRAN (R 4.5.0) | |fontLiberation |0.1.0 |2016-10-15 |CRAN (R 4.5.0) | |fontquiver |0.2.1 |2017-02-01 |CRAN (R 4.5.0) | @@ -84,15 +82,15 @@ |foreign |0.8-90 |2025-03-31 |CRAN (R 4.5.2) | |Formula |1.2-5 |2023-02-24 |CRAN (R 4.5.0) | |FreesearchR |26.3.3 |NA |NA | -|fs |1.6.6 |2025-04-12 |CRAN (R 4.5.0) | +|fs |1.6.7 |2026-03-06 |CRAN (R 4.5.2) | |gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) | |generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) | -|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.5.0) | +|ggalluvial |0.12.6 |2026-02-22 |CRAN (R 4.5.2) | |ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.5.0) | |ggforce |0.5.0 |2025-06-18 |CRAN (R 4.5.0) | |ggplot2 |4.0.2 |2026-02-03 |CRAN (R 4.5.2) | |ggridges |0.5.7 |2025-08-27 |CRAN (R 4.5.0) | -|ggstats |0.12.0 |2025-12-22 |CRAN (R 4.5.2) | +|ggstats |0.13.0 |2026-03-06 |CRAN (R 4.5.2) | |glue |1.8.0 |2024-09-30 |CRAN (R 4.5.0) | |gridExtra |2.3 |2017-09-09 |CRAN (R 4.5.0) | |gt |1.3.0 |2026-01-22 |CRAN (R 4.5.2) | @@ -114,10 +112,10 @@ |KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.2) | |keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) | |knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) | -|later |1.4.6 |2026-02-13 |CRAN (R 4.5.2) | +|later |1.4.6 |2026-03-05 |CRAN (R 4.5.2) | |lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) | |lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) | -|lme4 |1.1-38 |2025-12-02 |CRAN (R 4.5.2) | +|lme4 |2.0-1 |2026-03-05 |CRAN (R 4.5.2) | |lubridate |1.9.5 |2026-02-04 |CRAN (R 4.5.2) | |magrittr |2.0.4 |2025-09-12 |CRAN (R 4.5.0) | |MASS |7.3-65 |2025-02-28 |CRAN (R 4.5.0) | @@ -125,15 +123,15 @@ |memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) | |mime |0.13 |2025-03-17 |CRAN (R 4.5.0) | |minqa |1.2.8 |2024-08-17 |CRAN (R 4.5.0) | -|mvtnorm |1.3-3 |2025-01-10 |CRAN (R 4.5.0) | +|mvtnorm |1.3-5 |2026-03-11 |CRAN (R 4.5.2) | |NHANES |2.1.0 |2015-07-02 |CRAN (R 4.5.0) | |nlme |3.1-168 |2025-03-31 |CRAN (R 4.5.2) | |nloptr |2.2.1 |2025-03-17 |CRAN (R 4.5.0) | |nnet |7.3-20 |2025-01-01 |CRAN (R 4.5.2) | |officer |0.7.3 |2026-01-16 |CRAN (R 4.5.2) | |opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.5.0) | -|openssl |2.3.4 |2025-09-30 |CRAN (R 4.5.0) | -|openxlsx2 |1.23.1 |2026-01-19 |CRAN (R 4.5.2) | +|openssl |2.3.5 |2026-02-26 |CRAN (R 4.5.2) | +|openxlsx2 |1.25 |2026-03-07 |CRAN (R 4.5.2) | |otel |0.2.0 |2025-08-29 |CRAN (R 4.5.0) | |parameters |0.28.3 |2025-11-25 |CRAN (R 4.5.2) | |patchwork |1.3.2 |2025-08-25 |CRAN (R 4.5.0) | @@ -156,7 +154,7 @@ |qqplotr |0.0.7 |2025-09-05 |CRAN (R 4.5.0) | |quarto |1.5.1 |2025-09-04 |CRAN (R 4.5.0) | |R6 |2.6.1 |2025-02-15 |CRAN (R 4.5.0) | -|ragg |1.5.0 |2025-09-02 |CRAN (R 4.5.0) | +|ragg |1.5.1 |2026-03-06 |CRAN (R 4.5.2) | |rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.5.0) | |rbibutils |2.4.1 |2026-01-21 |CRAN (R 4.5.2) | |RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.5.0) | @@ -172,7 +170,7 @@ |reformulas |0.4.4 |2026-02-02 |CRAN (R 4.5.2) | |remotes |2.5.0 |2024-03-17 |CRAN (R 4.5.0) | |rempsyc |0.2.0 |2025-09-15 |CRAN (R 4.5.0) | -|renv |1.1.7 |2026-01-27 |CRAN (R 4.5.2) | +|renv |1.1.7 |2026-03-05 |CRAN (R 4.5.2) | |reshape2 |1.4.5 |2025-11-12 |CRAN (R 4.5.0) | |rio |1.2.4 |2025-09-26 |CRAN (R 4.5.0) | |rlang |1.1.7 |2026-01-09 |CRAN (R 4.5.2) | @@ -193,14 +191,13 @@ |shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.5.0) | |shinyjs |2.1.1 |2026-01-15 |CRAN (R 4.5.2) | |shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.5.0) | -|shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.5.0) | +|shinyWidgets |0.9.1 |2026-03-09 |CRAN (R 4.5.2) | |smd |0.8.0 |2025-02-12 |CRAN (R 4.5.0) | |stringi |1.8.7 |2025-03-27 |CRAN (R 4.5.0) | |stringr |1.6.0 |2025-11-04 |CRAN (R 4.5.0) | |stRoke |25.9.2 |2025-09-30 |CRAN (R 4.5.0) | -|systemfonts |1.3.1 |2025-10-01 |CRAN (R 4.5.0) | -|testthat |3.3.2 |2026-01-11 |CRAN (R 4.5.2) | -|textshaping |1.0.4 |2025-10-10 |CRAN (R 4.5.0) | +|systemfonts |1.3.2 |2026-03-05 |CRAN (R 4.5.2) | +|textshaping |1.0.5 |2026-03-06 |CRAN (R 4.5.2) | |thematic |0.1.8 |2025-09-29 |CRAN (R 4.5.0) | |tibble |3.3.1 |2026-01-11 |CRAN (R 4.5.2) | |tidyr |1.3.2 |2025-12-19 |CRAN (R 4.5.2) | @@ -220,6 +217,6 @@ |writexl |1.5.4 |2025-04-15 |CRAN (R 4.5.0) | |xfun |0.56 |2026-01-18 |CRAN (R 4.5.2) | |xml2 |1.5.2 |2026-01-17 |CRAN (R 4.5.2) | -|xtable |1.8-4 |2019-04-21 |CRAN (R 4.5.0) | +|xtable |1.8-4 |2026-02-22 |CRAN (R 4.5.2) | |yaml |2.3.12 |2025-12-10 |CRAN (R 4.5.2) | |zip |2.3.3 |2025-05-13 |CRAN (R 4.5.0) | diff --git a/app_docker/app.R b/app_docker/app.R index 72d8290a..004466c5 100644 --- a/app_docker/app.R +++ b/app_docker/app.R @@ -1,7 +1,7 @@ ######## -#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmprp4Sq1/fileb602d982aa3.R +#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpmhqokQ/file1a146f4d002a.R ######## i18n_path <- here::here("translations") @@ -2957,7 +2957,7 @@ add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.s type <- "line" ds <- data.frame(x = NA, y = NA) horizontal <- FALSE - } else if (identical(data_cl, "factor")) { + } else if ("factor" %in% data_cl) { type <- "column" s <- summary(data) ds <- data.frame(x = names(s), y = s) @@ -3887,20 +3887,23 @@ file_export <- function(data, #' head(5) |> #' str() default_parsing <- function(data) { - name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) + # name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) # browser() - out <- data |> - setNames(make.names(names(data), unique = TRUE)) |> - ## Temporary step to avoid nested list and crashing - remove_nested_list() |> - REDCapCAST::parse_data() |> - REDCapCAST::as_factor() |> - REDCapCAST::numchar2fct(numeric.threshold = 8, - character.throshold = 10) |> - REDCapCAST::as_logical() |> - REDCapCAST::fct_drop() - - set_column_label(out, setNames(name_labels, names(out)), overwrite = FALSE) + with_labels(data,{ + data |> + setNames(make.names(names(data), unique = TRUE)) |> + ## Temporary step to avoid nested list and crashing + remove_nested_list() |> + REDCapCAST::parse_data() |> + REDCapCAST::as_factor() |> + REDCapCAST::numchar2fct(numeric.threshold = 8, + character.throshold = 10) |> + REDCapCAST::as_logical() |> + REDCapCAST::fct_drop() + }) + # out <- + # + # set_column_label(out, setNames(name_labels, names(out)), overwrite = FALSE) # purrr::map2( # out, diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index de5e9f11..ad0da02a 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -1,7 +1,7 @@ ######## -#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmprp4Sq1/fileb60491b0ce8.R +#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpmhqokQ/file1a14715fd082.R ######## i18n_path <- system.file("translations", package = "FreesearchR") @@ -2957,7 +2957,7 @@ add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.s type <- "line" ds <- data.frame(x = NA, y = NA) horizontal <- FALSE - } else if (identical(data_cl, "factor")) { + } else if ("factor" %in% data_cl) { type <- "column" s <- summary(data) ds <- data.frame(x = names(s), y = s) @@ -3887,20 +3887,23 @@ file_export <- function(data, #' head(5) |> #' str() default_parsing <- function(data) { - name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) + # name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) # browser() - out <- data |> - setNames(make.names(names(data), unique = TRUE)) |> - ## Temporary step to avoid nested list and crashing - remove_nested_list() |> - REDCapCAST::parse_data() |> - REDCapCAST::as_factor() |> - REDCapCAST::numchar2fct(numeric.threshold = 8, - character.throshold = 10) |> - REDCapCAST::as_logical() |> - REDCapCAST::fct_drop() - - set_column_label(out, setNames(name_labels, names(out)), overwrite = FALSE) + with_labels(data,{ + data |> + setNames(make.names(names(data), unique = TRUE)) |> + ## Temporary step to avoid nested list and crashing + remove_nested_list() |> + REDCapCAST::parse_data() |> + REDCapCAST::as_factor() |> + REDCapCAST::numchar2fct(numeric.threshold = 8, + character.throshold = 10) |> + REDCapCAST::as_logical() |> + REDCapCAST::fct_drop() + }) + # out <- + # + # set_column_label(out, setNames(name_labels, names(out)), overwrite = FALSE) # purrr::map2( # out, diff --git a/renv.lock b/renv.lock index dfbaf8cd..11ae7b52 100644 --- a/renv.lock +++ b/renv.lock @@ -2761,7 +2761,7 @@ }, "effectsize": { "Package": "effectsize", - "Version": "1.0.1", + "Version": "1.0.2", "Source": "Repository", "Type": "Package", "Title": "Indices of Effect Size", @@ -2775,11 +2775,11 @@ "R (>= 4.0)" ], "Imports": [ - "bayestestR (>= 0.16.0)", - "insight (>= 1.3.0)", - "parameters (>= 0.26.0)", - "performance (>= 0.14.0)", - "datawizard (>= 1.1.0)", + "bayestestR (>= 0.17.0)", + "insight (>= 1.4.5)", + "parameters (>= 0.28.3)", + "performance (>= 0.15.3)", + "datawizard (>= 1.3.0)", "stats", "utils" ], @@ -2809,7 +2809,7 @@ "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/Needs/website": "rstudio/bslib, r-lib/pkgdown, easystats/easystatstemplate", @@ -2819,11 +2819,11 @@ }, "emmeans": { "Package": "emmeans", - "Version": "2.0.1", + "Version": "2.0.2", "Source": "Repository", "Type": "Package", "Title": "Estimated Marginal Means, aka Least-Squares Means", - "Date": "2025-12-10", + "Date": "2026-02-20", "Authors@R": "c(person(\"Russell V.\", \"Lenth\", role = c(\"aut\", \"cph\"), email = \"russell-lenth@uiowa.edu\"), person(\"Julia\", \"Piaskowski\", role = c(\"cre\", \"aut\"), email = \"julia.piask@gmail.com\"), person(\"Balazs\", \"Banfai\", role = \"ctb\"), person(\"Ben\", \"Bolker\", role = \"ctb\"), person(\"Paul\", \"Buerkner\", role = \"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role = \"ctb\"), person(\"Maxime\", \"Hervé\", role = \"ctb\"), person(\"Maarten\", \"Jung\", role = \"ctb\"), person(\"Jonathon\", \"Love\", role = \"ctb\"), person(\"Fernando\", \"Miguez\", role = \"ctb\"), person(\"Hannes\", \"Riebl\", role = \"ctb\"), person(\"Henrik\", \"Singmann\", role = \"ctb\"))", "Maintainer": "Julia Piaskowski ", "Depends": [ @@ -2886,7 +2886,7 @@ "sommer", "survival" ], - "URL": "https://rvlenth.github.io/emmeans/,https://rvlenth.github.io/emmeans/", + "URL": "https://rvlenth.github.io/emmeans/, https://github.com/rvlenth/emmeans/", "BugReports": "https://github.com/rvlenth/emmeans/issues", "LazyData": "yes", "ByteCompile": "yes", @@ -3435,16 +3435,16 @@ }, "fs": { "Package": "fs", - "Version": "1.6.6", + "Version": "1.6.7", "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\")) )", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", , \"jeroenooms@gmail.com\", role = \"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\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.", "License": "MIT + file LICENSE", "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs", "BugReports": "https://github.com/r-lib/fs/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1)" ], "Imports": [ "methods" @@ -3465,14 +3465,15 @@ "ByteCompile": "true", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", "Copyright": "file COPYRIGHTS", "Encoding": "UTF-8", "Language": "en-US", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "SystemRequirements": "GNU make", "NeedsCompilation": "yes", - "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd]", - "Maintainer": "Gábor Csárdi ", + "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut], Jeroen Ooms [cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, "gap": { @@ -3642,7 +3643,7 @@ }, "ggalluvial": { "Package": "ggalluvial", - "Version": "0.12.5", + "Version": "0.12.6", "Source": "Repository", "Type": "Package", "Title": "Alluvial Plots in 'ggplot2'", @@ -3889,7 +3890,7 @@ }, "ggstats": { "Package": "ggstats", - "Version": "0.12.0", + "Version": "0.13.0", "Source": "Repository", "Type": "Package", "Title": "Extension to 'ggplot2' for Plotting Stats", @@ -4288,7 +4289,7 @@ }, "highr": { "Package": "highr", - "Version": "0.11", + "Version": "0.12", "Source": "Repository", "Type": "Package", "Title": "Syntax Highlighting for R Source Code", @@ -4310,9 +4311,9 @@ "BugReports": "https://github.com/yihui/highr/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Author": "Yihui Xie [aut, cre] (ORCID: ), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, @@ -5041,7 +5042,7 @@ }, "later": { "Package": "later", - "Version": "1.4.6", + "Version": "1.4.8", "Source": "Repository", "Type": "Package", "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", @@ -5217,72 +5218,74 @@ }, "lme4": { "Package": "lme4", - "Version": "1.1-38", + "Version": "2.0-1", "Source": "Repository", "Title": "Linear Mixed-Effects Models using 'Eigen' and S4", - "Authors@R": "c( person(\"Douglas\",\"Bates\", role=\"aut\", comment=c(ORCID=\"0000-0001-8316-9503\")), person(\"Martin\",\"Maechler\", role=\"aut\", comment=c(ORCID=\"0000-0002-8685-9910\")), person(\"Ben\",\"Bolker\",email=\"bbolker+lme4@gmail.com\", role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Steven\",\"Walker\",role=\"aut\", comment=c(ORCID=\"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\",\"Christensen\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4494-3399\")), person(\"Henrik\",\"Singmann\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role=\"ctb\"), person(\"Fabian\", \"Scheipl\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role=\"ctb\"), person(\"Peter\", \"Green\", role=\"ctb\", comment=c(ORCID=\"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role=\"ctb\"), person(\"Alexander\", \"Bauer\", role=\"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role=c(\"ctb\",\"cph\"), comment=c(ORCID=\"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID=\"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"ctb\", comment = c(ORCID=\"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", email=\"ross.boylan@ucsf.edu\", role=(\"ctb\"), comment = c(ORCID=\"0009-0003-4123-8090\")), person(\"Anna\", \"Ly\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0210-0342\")) )", - "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Ben\", \"Bolker\", role = c(\"cre\", \"aut\"), email = \"bbolker+lme4@gmail.com\", comment = c(ORCID = \"0000-0002-2127-0443\")), person(\"Steven\", \"Walker\", role = \"aut\", comment = c(ORCID = \"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\", \"Christensen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4494-3399\")), person(\"Henrik\", \"Singmann\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role = \"ctb\"), person(\"Fabian\", \"Scheipl\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role = \"ctb\"), person(\"Peter\", \"Green\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role = \"ctb\"), person(\"Alexander\", \"Bauer\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = c(\"ctb\", \"cph\"), comment = c(ORCID = \"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", role = \"ctb\", comment = c(ORCID = \"0009-0003-4123-8090\")), person(\"Anna\", \"Ly\", role = \"aut\", comment = c(ORCID = \"0000-0002-0210-0342\")))", + "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", "Depends": [ - "R (>= 3.6.0)", + "R (>= 3.6)", "Matrix", "methods", "stats" ], "LinkingTo": [ + "Matrix (>= 1.5-0)", "Rcpp (>= 0.10.5)", - "RcppEigen (>= 0.3.3.9.4)", - "Matrix (>= 1.5-0)" + "RcppEigen (>= 0.3.3.9.4)" ], "Imports": [ + "MASS", + "Rdpack", + "boot", "graphics", "grid", - "splines", - "utils", - "parallel", - "MASS", "lattice", - "boot", - "nlme (>= 3.1-123)", "minqa (>= 1.1.15)", + "nlme (>= 3.1-123)", "nloptr (>= 1.0.4)", - "reformulas (>= 0.3.0)", + "parallel", + "reformulas (>= 0.4.3.1)", "rlang", - "Rdpack" + "splines", + "utils" ], - "RdMacros": "Rdpack", "Suggests": [ - "knitr", - "rmarkdown", - "MEMSS", - "testthat (>= 0.8.1)", - "ggplot2", - "mlmRev", - "optimx (>= 2013.8.6)", - "gamm4", - "pbkrtest", "HSAUR3", - "numDeriv", + "MEMSS", "car", "dfoptim", + "gamm4", + "ggplot2", + "glmmTMB", + "knitr", + "merDeriv", "mgcv", - "statmod", + "mlmRev", + "numDeriv", + "optimx (>= 2013.8.6)", + "pbkrtest", + "rmarkdown", "rr2", "semEff", - "tibble", - "merDeriv" + "statmod", + "testthat (>= 0.8.1)", + "tibble" ], "Enhances": [ "DHARMa", "performance" ], + "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "LazyData": "yes", "License": "GPL (>= 2)", "URL": "https://github.com/lme4/lme4/", "BugReports": "https://github.com/lme4/lme4/issues", "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut] (ORCID: ), Ben Bolker [aut, cre] (ORCID: ), Steven Walker [aut] (ORCID: ), Rune Haubo Bojesen Christensen [ctb] (ORCID: ), Henrik Singmann [ctb] (ORCID: ), Bin Dai [ctb], Fabian Scheipl [ctb] (ORCID: ), Gabor Grothendieck [ctb], Peter Green [ctb] (ORCID: ), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (ORCID: , shared copyright on simulate.formula), Emi Tanaka [ctb] (ORCID: ), Mikael Jagan [ctb] (ORCID: ), Ross D. Boylan [ctb] (ORCID: ), Anna Ly [ctb] (ORCID: )", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut] (ORCID: ), Ben Bolker [cre, aut] (ORCID: ), Steven Walker [aut] (ORCID: ), Rune Haubo Bojesen Christensen [ctb] (ORCID: ), Henrik Singmann [ctb] (ORCID: ), Bin Dai [ctb], Fabian Scheipl [ctb] (ORCID: ), Gabor Grothendieck [ctb], Peter Green [ctb] (ORCID: ), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (ORCID: , shared copyright on simulate.formula), Emi Tanaka [ctb] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Ross D. Boylan [ctb] (ORCID: ), Anna Ly [aut] (ORCID: )", "Maintainer": "Ben Bolker ", "Repository": "CRAN" }, @@ -5672,10 +5675,10 @@ }, "mvtnorm": { "Package": "mvtnorm", - "Version": "1.3-3", + "Version": "1.3-5", "Source": "Repository", "Title": "Multivariate Normal and t Distributions", - "Date": "2025-01-09", + "Date": "2026-03-10", "Authors@R": "c(person(\"Alan\", \"Genz\", role = \"aut\"), person(\"Frank\", \"Bretz\", role = \"aut\"), person(\"Tetsuhisa\", \"Miwa\", role = \"aut\"), person(\"Xuefei\", \"Mi\", role = \"aut\"), person(\"Friedrich\", \"Leisch\", role = \"ctb\"), person(\"Fabian\", \"Scheipl\", role = \"ctb\"), person(\"Bjoern\", \"Bornkamp\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6294-8185\")), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")))", "Description": "Computes multivariate normal and t probabilities, quantiles, random deviates, and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.", "Imports": [ @@ -5686,12 +5689,13 @@ ], "Suggests": [ "qrng", - "numDeriv" + "numDeriv", + "bibtex" ], "License": "GPL-2", "URL": "http://mvtnorm.R-forge.R-project.org", "NeedsCompilation": "yes", - "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", + "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (ORCID: ), Martin Maechler [ctb] (ORCID: ), Torsten Hothorn [aut, cre] (ORCID: )", "Maintainer": "Torsten Hothorn ", "Repository": "CRAN" }, @@ -5882,7 +5886,7 @@ }, "openssl": { "Package": "openssl", - "Version": "2.3.4", + "Version": "2.3.5", "Source": "Repository", "Type": "Package", "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", @@ -5915,7 +5919,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.23.1", + "Version": "1.25", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -5942,10 +5946,10 @@ "ggplot2", "knitr", "mschart (>= 0.4)", + "openssl", "rmarkdown", "rvg", "testthat (>= 3.0.0)", - "waldo", "zip" ], "VignetteBuilder": "knitr", @@ -7089,7 +7093,7 @@ }, "ragg": { "Package": "ragg", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Type": "Package", "Title": "Graphic Devices Based on AGG", @@ -7118,7 +7122,7 @@ "Config/testthat/edition": "3", "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), 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 Software, PBC [cph, fnd] (ROR: )", @@ -7541,7 +7545,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.7", + "Version": "1.1.8", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -7585,11 +7589,11 @@ "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", - "NeedsCompilation": "no", "Author": "Kevin Ushey [aut, cre] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Kevin Ushey ", "Repository": "CRAN" @@ -8317,7 +8321,7 @@ }, "shinyWidgets": { "Package": "shinyWidgets", - "Version": "0.9.0", + "Version": "0.9.1", "Source": "Repository", "Title": "Custom Inputs Widgets for Shiny", "Authors@R": "c( person(\"Victor\", \"Perrier\", email = \"victor.perrier@dreamrs.fr\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Fanny\", \"Meyer\", role = \"aut\"), person(\"David\", \"Granjon\", role = \"aut\"), person(\"Ian\", \"Fellows\", role = \"ctb\", comment = \"Methods for mutating vertical tabs & updateMultiInput\"), person(\"Wil\", \"Davis\", role = \"ctb\", comment = \"numericRangeInput function\"), person(\"Spencer\", \"Matthews\", role = \"ctb\", comment = \"autoNumeric methods\"), person(family = \"JavaScript and CSS libraries authors\", role = c(\"ctb\", \"cph\"), comment = \"All authors are listed in LICENSE.md\") )", @@ -8327,7 +8331,7 @@ "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "Depends": [ "R (>= 3.1.0)" ], @@ -8624,7 +8628,7 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Type": "Package", "Title": "System Native Font Finding", @@ -8672,7 +8676,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "1.0.4", + "Version": "1.0.5", "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 Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", @@ -9513,21 +9517,23 @@ }, "xtable": { "Package": "xtable", - "Version": "1.8-4", + "Version": "1.8-8", "Source": "Repository", - "Date": "2019-04-08", + "Date": "2026-02-20", "Title": "Export Tables to LaTeX or HTML", "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", "Maintainer": "David Scott ", "Imports": [ "stats", - "utils" + "utils", + "methods" ], "Suggests": [ "knitr", - "plm", "zoo", - "survival" + "survival", + "glue", + "tinytex" ], "VignetteBuilder": "knitr", "Description": "Coerce data to LaTeX and HTML tables.", diff --git a/renv/activate.R b/renv/activate.R index ef25ef83..6e94798d 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,8 +2,8 @@ local({ # the requested version of renv - version <- "1.1.7" - attr(version, "md5") <- "dd5d60f155dadff4c88c2fc6680504b4" + version <- "1.1.8" + attr(version, "md5") <- "cbffd086c66739a0fdaac7a30b4aa65c" attr(version, "sha") <- NULL # the project directory