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Andreas Gammelgaard Damsbo 2026-03-12 12:40:40 +01:00
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SESSION.md
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@ -33,7 +33,6 @@
|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.5.0) |
|bitops |1.0-9 |2024-10-03 |CRAN (R 4.5.0) |
|boot |1.3-32 |2025-08-29 |CRAN (R 4.5.2) |
|brio |1.1.5 |2024-04-24 |CRAN (R 4.5.0) |
|broom |1.0.12 |2026-01-27 |CRAN (R 4.5.2) |
|broom.helpers |1.22.0 |2025-09-17 |CRAN (R 4.5.0) |
|bsicons |0.1.2 |2023-11-04 |CRAN (R 4.5.0) |
@ -67,7 +66,7 @@
|e1071 |1.7-17 |2025-12-18 |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) |

33
app_docker/app.R
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@ -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,

33
inst/apps/FreesearchR/app.R
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@ -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,

148
renv.lock
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@ -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 <julia.piask@gmail.com>",
"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 <csardi.gabor@gmail.com>",
"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: <https://ror.org/03wc8by49>)",
"Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
"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] (<https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
"Author": "Yihui Xie [aut, cre] (ORCID: <https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
"Maintainer": "Yihui Xie <xie@yihui.name>",
"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: <https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (ORCID: <https://orcid.org/0000-0002-8685-9910>), Ben Bolker [aut, cre] (ORCID: <https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (ORCID: <https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (ORCID: <https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (ORCID: <https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (ORCID: <https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (ORCID: <https://orcid.org/0000-0002-0238-9852>), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (ORCID: <https://orcid.org/0000-0002-9101-3362>, shared copyright on simulate.formula), Emi Tanaka [ctb] (ORCID: <https://orcid.org/0000-0002-1455-259X>), Mikael Jagan [ctb] (ORCID: <https://orcid.org/0000-0002-3542-2938>), Ross D. Boylan [ctb] (ORCID: <https://orcid.org/0009-0003-4123-8090>), Anna Ly [ctb] (ORCID: <https://orcid.org/0000-0002-0210-0342>)",
"Author": "Douglas Bates [aut] (ORCID: <https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (ORCID: <https://orcid.org/0000-0002-8685-9910>), Ben Bolker [cre, aut] (ORCID: <https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (ORCID: <https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (ORCID: <https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (ORCID: <https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (ORCID: <https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (ORCID: <https://orcid.org/0000-0002-0238-9852>), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (ORCID: <https://orcid.org/0000-0002-9101-3362>, shared copyright on simulate.formula), Emi Tanaka [ctb] (ORCID: <https://orcid.org/0000-0002-1455-259X>), Mikael Jagan [aut] (ORCID: <https://orcid.org/0000-0002-3542-2938>), Ross D. Boylan [ctb] (ORCID: <https://orcid.org/0009-0003-4123-8090>), Anna Ly [aut] (ORCID: <https://orcid.org/0000-0002-0210-0342>)",
"Maintainer": "Ben Bolker <bbolker+lme4@gmail.com>",
"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] (<https://orcid.org/0000-0002-6294-8185>), Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>), Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)",
"Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (ORCID: <https://orcid.org/0000-0002-6294-8185>), Martin Maechler [ctb] (ORCID: <https://orcid.org/0000-0002-8685-9910>), Torsten Hothorn [aut, cre] (ORCID: <https://orcid.org/0000-0001-8301-0471>)",
"Maintainer": "Torsten Hothorn <Torsten.Hothorn@R-project.org>",
"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: <https://orcid.org/0000-0002-5147-4711>), 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: <https://ror.org/03wc8by49>)",
@ -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: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
"Maintainer": "Kevin Ushey <kevin@rstudio.com>",
"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 <d.scott@auckland.ac.nz>",
"Imports": [
"stats",
"utils"
"utils",
"methods"
],
"Suggests": [
"knitr",
"plm",
"zoo",
"survival"
"survival",
"glue",
"tinytex"
],
"VignetteBuilder": "knitr",
"Description": "Coerce data to LaTeX and HTML tables.",

4
renv/activate.R
View file

@ -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