From 42cc9e7660e5d7b6493630560ac372bda45324c3 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Wed, 27 Aug 2025 12:45:02 +0200 Subject: [PATCH] ready for docker update --- app_docker/Dockerfile | 2 +- app_docker/app.R | 20 +++++- app_docker/renv.lock | 130 +++++++++++++++++++++++++------------- app_docker/www/scripts.js | 54 ++++++++++++---- 4 files changed, 146 insertions(+), 60 deletions(-) diff --git a/app_docker/Dockerfile b/app_docker/Dockerfile index 877787f..a4f31bc 100644 --- a/app_docker/Dockerfile +++ b/app_docker/Dockerfile @@ -3,7 +3,7 @@ RUN apt-get update -y && apt-get install -y cmake make libcurl4-openssl-dev lib RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/ RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site RUN R -e 'install.packages("remotes")' -RUN R -e 'remotes::install_version("renv", version = "1.1.4")' +RUN R -e 'remotes::install_version("renv", version = "1.1.5")' COPY renv.lock renv.lock RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()' WORKDIR /srv/shiny-server/ diff --git a/app_docker/app.R b/app_docker/app.R index ac51ad5..b57e14a 100644 --- a/app_docker/app.R +++ b/app_docker/app.R @@ -3527,7 +3527,8 @@ dummy_Imports <- function() { cardx::all_of(), parameters::ci(), DT::addRow(), - bslib::accordion() + bslib::accordion(), + NHANES::NHANES() ) # https://github.com/hadley/r-pkgs/issues/828 } @@ -4046,7 +4047,7 @@ simple_snake <- function(data){ #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R ######## -hosted_version <- function()'v25.8.1-250808' +hosted_version <- function()'v25.8.1-250827' ######## @@ -8486,10 +8487,11 @@ ui_elements <- function(selection) { icon = shiny::icon("pen-to-square"), value = "nav_prepare", bslib::nav_panel( - title = "Overview", + title = "Overview and filter", icon = shiny::icon("eye"), value = "nav_prepare_overview", tags$h3("Overview and filtering"), + # validation_ui("validation_col"), fluidRow( shiny::column( width = 9, @@ -10964,6 +10966,18 @@ server <- function(input, output, session) { }) + # validation_server(id = "validation_col", + # data = purrr::map2( + # .x = validation_lib()[1], + # .y = list( + # list( + # x = + # reactive(rv$data), + # y = + # reactive(rv$data_variables) + # )), + # make_validation)) + ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue # Consider using shinyDataFilter, though not on CRAN diff --git a/app_docker/renv.lock b/app_docker/renv.lock index 57077d0..0735cef 100644 --- a/app_docker/renv.lock +++ b/app_docker/renv.lock @@ -4,16 +4,16 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://mirrors.dotsrc.org/cran" } ] }, "Packages": { "DEoptimR": { "Package": "DEoptimR", - "Version": "1.1-3-1", + "Version": "1.1-4", "Source": "Repository", - "Date": "2024-11-23", + "Date": "2025-07-27", "Title": "Differential Evolution Optimization in Pure R", "Authors@R": "c( person(c(\"Eduardo\", \"L. T.\"), \"Conceicao\", role = c(\"aut\", \"cre\"), email = \"mail@eduardoconceicao.org\"), person(\"Martin\", \"Maechler\", role = \"ctb\", email = \"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) )", "URL": "svn://svn.r-forge.r-project.org/svnroot/robustbase/pkg/DEoptimR", @@ -25,12 +25,12 @@ "robustbase" ], "License": "GPL (>= 2)", - "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] ()", + "Author": "Eduardo L. T. Conceicao [aut, cre], Martin Maechler [ctb] (ORCID: )", "Maintainer": "Eduardo L. T. Conceicao ", "Repository": "CRAN", "Repository/R-Forge/Project": "robustbase", - "Repository/R-Forge/Revision": "1008", - "Repository/R-Forge/DateTimeStamp": "2024-11-23 19:13:45", + "Repository/R-Forge/Revision": "1009", + "Repository/R-Forge/DateTimeStamp": "2025-07-27 18:16:52", "NeedsCompilation": "no" }, "DHARMa": { @@ -241,7 +241,7 @@ }, "IDEAFilter": { "Package": "IDEAFilter", - "Version": "0.2.0", + "Version": "0.2.1", "Source": "Repository", "Type": "Package", "Title": "Agnostic, Idiomatic Data Filter Module for Shiny", @@ -251,7 +251,7 @@ "URL": "https://biogen-inc.github.io/IDEAFilter/, https://github.com/Biogen-Inc/IDEAFilter", "BugReports": "https://github.com/Biogen-Inc/IDEAFilter/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.2", "Imports": [ "crayon", "ggplot2", @@ -276,7 +276,7 @@ "R (>= 2.10)" ], "NeedsCompilation": "no", - "Author": "Aaron Clark [aut, cre] (), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", + "Author": "Aaron Clark [aut, cre] (ORCID: ), Jeff Thompson [aut], Doug Kelkhoff [ctb, cph] (Author of shinyDataFilter), Maya Gans [ctb], SortableJS contributors [ctb] (SortableJS library), Biogen [cph]", "Maintainer": "Aaron Clark ", "Repository": "CRAN" }, @@ -386,6 +386,28 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, + "NHANES": { + "Package": "NHANES", + "Version": "2.1.0", + "Source": "Repository", + "Type": "Package", + "Title": "Data from the US National Health and Nutrition Examination Study", + "Date": "2015-07-02", + "Author": "Randall Pruim ", + "Maintainer": "Randall Pruim ", + "Description": "Body Shape and related measurements from the US National Health and Nutrition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/nchs/nhanes.htm for details.", + "Depends": [ + "R (>= 3.0)" + ], + "Suggests": [ + "mosaic" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "LazyData": "yes", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.2", @@ -575,7 +597,7 @@ }, "REDCapR": { "Package": "REDCapR", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Title": "Interaction Between R and REDCap", "Description": "Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.", @@ -583,7 +605,7 @@ "URL": "https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org", "BugReports": "https://github.com/OuhscBbmc/REDCapR/issues", "Depends": [ - "R(>= 3.5.0)" + "R (>= 4.1.0)" ], "Imports": [ "checkmate (>= 2.0)", @@ -618,7 +640,7 @@ "Config/testthat/edition": "3", "Language": "en-US", "NeedsCompilation": "no", - "Author": "Will Beasley [aut, cre] (), David Bard [ctb] (), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (), Benjamin Nutter [ctb], Andrew Peters [ctb] (), Hao Zhu [ctb] (), Janosch Linkersdörfer [ctb] (), Jonathan Mang [ctb] (), Felix Torres [ctb], Philip Chase [ctb] (), Victor Castro [ctb] (), Greg Botwin [ctb], Stephan Kadauke [ctb] (), Ezra Porter [ctb] (), Matthew Schuelke [ctb] ()", + "Author": "Will Beasley [aut, cre] (ORCID: ), David Bard [ctb] (ORCID: ), Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb] (ORCID: ), Benjamin Nutter [ctb], Andrew Peters [ctb] (ORCID: ), Hao Zhu [ctb] (ORCID: ), Janosch Linkersdörfer [ctb] (ORCID: ), Jonathan Mang [ctb] (ORCID: ), Felix Torres [ctb], Philip Chase [ctb] (ORCID: ), Victor Castro [ctb] (ORCID: ), Greg Botwin [ctb], Stephan Kadauke [ctb] (ORCID: ), Ezra Porter [ctb] (ORCID: ), Matthew Schuelke [ctb] (ORCID: )", "Maintainer": "Will Beasley ", "Repository": "CRAN" }, @@ -762,7 +784,7 @@ }, "V8": { "Package": "V8", - "Version": "6.0.4", + "Version": "6.0.6", "Source": "Repository", "Type": "Package", "Title": "Embedded JavaScript and WebAssembly Engine for R", @@ -771,7 +793,7 @@ "License": "MIT + file LICENSE", "URL": "https://jeroen.r-universe.dev/V8", "BugReports": "https://github.com/jeroen/v8/issues", - "SystemRequirements": "V8 engine version 6+ is needed for ES6 and WASM support. On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", + "SystemRequirements": "On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). We also provide static libv8 binaries for most platforms, see the README for details.", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Imports": [ @@ -1209,17 +1231,17 @@ }, "broom": { "Package": "broom", - "Version": "1.0.8", + "Version": "1.0.9", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", - "Authors@R": "c(person(given = \"David\", family = \"Robinson\", role = \"aut\", email = \"admiral.david@gmail.com\"), person(given = \"Alex\", family = \"Hayes\", role = \"aut\", email = \"alexpghayes@gmail.com\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Simon\", family = \"Couch\", role = c(\"aut\", \"cre\"), email = \"simon.couch@posit.co\", comment = c(ORCID = \"0000-0001-5676-5107\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"ctb\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = 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Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", - "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = \"ctb\"), person(\"Yves\", \"Rosseel\", , \"yrosseel@gmail.com\", role = \"ctb\"), person(\"Michael\", \"Kuehn\", , \"mkuehn10@gmail.com\", role = \"ctb\"), person(\"Jorge\", \"Cimentada\", , \"cimentadaj@gmail.com\", role = \"ctb\"), person(\"Erle\", \"Holgersen\", , \"erle.holgersen@gmail.com\", role = \"ctb\"), person(\"Karl\", \"Dunkle Werner\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Ethan\", \"Christensen\", , \"christensen.ej@gmail.com\", role = \"ctb\"), person(\"Steven\", \"Pav\", , \"shabbychef@gmail.com\", role = \"ctb\"), person(\"Paul\", \"PJ\", , \"pjpaul.stephens@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Patrick\", \"Kennedy\", , \"pkqstr@protonmail.com\", role = \"ctb\"), person(\"Lily\", \"Medina\", , \"lilymiru@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Fannin\", , \"captain@pirategrunt.com\", role = \"ctb\"), person(\"Jason\", \"Muhlenkamp\", , \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", "License": "MIT + file LICENSE", "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", "BugReports": "https://github.com/tidymodels/broom/issues", "Depends": [ - "R (>= 3.5)" + "R (>= 4.1)" ], "Imports": [ "backports", @@ -1253,7 +1275,7 @@ "drc", "e1071", "emmeans", - "epiR", + "epiR (>= 2.0.85)", "ergm (>= 3.10.4)", "fixest (>= 0.9.0)", "gam (>= 1.15)", @@ -1264,8 +1286,8 @@ "glmnetUtils", "gmm", "Hmisc", - "irlba", "interp", + "irlba", "joineRML", "Kendall", "knitr", @@ -1304,8 +1326,8 @@ "robustbase", "rsample", "sandwich", - "spdep (>= 1.1)", "spatialreg", + "spdep (>= 1.1)", "speedglm", "spelling", "survey", @@ -1318,13 +1340,14 @@ ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", - 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"Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", "Maintainer": "Simon Couch ", "Repository": "CRAN" }, @@ -3051,7 +3074,7 @@ "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "RSPM" + "Repository": "CRAN" }, "flextable": { "Package": "flextable", @@ -4445,7 +4468,7 @@ }, "insight": { "Package": "insight", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Type": "Package", "Title": "Easy Access to Model Information for Various Model Objects", @@ -4491,7 +4514,7 @@ "cplm", "crch", "curl", - "datawizard", + "datawizard (>= 1.2.0)", "dbarts", "effectsize", "emmeans", @@ -4547,6 +4570,7 @@ "modelbased (>= 0.9.0)", "multgee", "MuMIn", + "mvtnorm", "nestedLogit", "nlme", "nnet", @@ -4559,7 +4583,6 @@ "performance", "phylolm", "plm", - "poorman", "PROreg (>= 1.3.0)", "pscl", "psych", @@ -4577,6 +4600,7 @@ "RWiener", "sandwich", "sdmTMB", + "sampleSelection", "serp", "speedglm", "splines", @@ -5652,8 +5676,7 @@ "Maintainer": "Paul Gilbert ", "URL": "http://optimizer.r-forge.r-project.org/", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "officer": { "Package": "officer", @@ -5768,7 +5791,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.17", + "Version": "1.18", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -6841,36 +6864,56 @@ }, "quarto": { "Package": "quarto", - "Version": "1.4.4", + "Version": "1.5.0", "Source": "Repository", "Title": "R Interface to 'Quarto' Markdown Publishing System", - "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Gordon\", \"Woodhull\", role = \"ctb\") )", "Description": "Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.", - "License": "GPL (>= 2)", + "License": "MIT + file LICENSE", "URL": "https://github.com/quarto-dev/quarto-r, https://quarto-dev.github.io/quarto-r/", "BugReports": "https://github.com/quarto-dev/quarto-r/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "cli", + "fs", + "htmltools", "jsonlite", "later", + "lifecycle", "processx", "rlang", "rmarkdown", "rstudioapi", "tools", "utils", - "yaml" + "xfun", + "yaml (>= 2.3.10)" ], "Suggests": [ + "bslib", + "callr", "curl", + "dplyr", + "flextable", + "ggiraph", + "ggplot2", + "gt", + "heatmaply", + "kableExtra", "knitr", + "palmerpenguins", + "patchwork", + "pkgload", + "plotly", "rsconnect (>= 0.8.26)", "testthat (>= 3.1.7)", - "withr", - "xfun" + "thematic", + "tidyverse", + "tinytable", + "whoami", + "withr" ], "VignetteBuilder": "quarto", "Config/testthat/edition": "3", @@ -6878,7 +6921,7 @@ "RoxygenNote": "7.3.2", "SystemRequirements": "Quarto command line tool ().", "NeedsCompilation": "no", - "Author": "JJ Allaire [aut] (), Christophe Dervieux [cre, aut] (), Posit Software, PBC [cph, fnd]", + "Author": "JJ Allaire [aut] (ORCID: ), Christophe Dervieux [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd], Gordon Woodhull [ctb]", "Maintainer": "Christophe Dervieux ", "Repository": "CRAN" }, @@ -7329,7 +7372,7 @@ }, "renv": { "Package": "renv", - "Version": "1.1.4", + "Version": "1.1.5", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -7348,6 +7391,7 @@ "covr", "cpp11", "devtools", + "generics", "gitcreds", "jsonlite", "jsonvalidate", @@ -7376,7 +7420,7 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", "NeedsCompilation": "no", - "Author": "Kevin Ushey [aut, cre] (), Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Kevin Ushey [aut, cre] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Kevin Ushey ", "Repository": "CRAN" }, diff --git a/app_docker/www/scripts.js b/app_docker/www/scripts.js index 3382b4e..f98dffc 100644 --- a/app_docker/www/scripts.js +++ b/app_docker/www/scripts.js @@ -6,24 +6,52 @@ $(document).on('shown.bs.tab', '#main_panel', function(e) { $('#main_panel .dropdown-toggle').removeClass('show').attr('aria-expanded', 'false'); }); + $(document).on('shiny:sessioninitialized', function() { -// Function to collapse navbar on mobile -function collapseNavbar() { - var navbar = $('.navbar-collapse'); - if (navbar.hasClass('show')) { - navbar.removeClass('show'); - $('.navbar-toggler').addClass('collapsed'); - $('.navbar-toggler').attr('aria-expanded', 'false'); - } + // Function to collapse navbar on mobile + function collapseNavbar() { + var navbar = $('.navbar-collapse'); + if (navbar.hasClass('show')) { + navbar.removeClass('show'); + $('.navbar-toggler').addClass('collapsed'); + $('.navbar-toggler').attr('aria-expanded', 'false'); + } } - // Add click event to navigation tabs - $(document).on('click', '.nav-link[data-bs-toggle=\"tab\"]', function() { + // Main approach: Handle clicks on nav elements + $(document).on('click', '.navbar-nav .nav-link, .dropdown-item', function(event) { + var $target = $(event.currentTarget); + + // Don't collapse if this is a dropdown toggle + if ($target.hasClass('dropdown-toggle')) { + return; + } + + // Don't collapse if this is inside a dropdown and the dropdown should stay open + if ($target.hasClass('nav-link') && $target.closest('.dropdown').length && + !$target.attr('data-bs-toggle')) { + return; + } + + // Collapse the navbar after a short delay setTimeout(collapseNavbar, 10); }); - // Also handle direct clicks on nav items - $(document).on('click', '.navbar-nav .nav-link', function() { - setTimeout(collapseNavbar, 10); + // Handle tab toggles specifically + $(document).on('click', '.nav-link[data-bs-toggle="tab"]', function() { + if (!$(this).hasClass('dropdown-toggle')) { + setTimeout(collapseNavbar, 10); + } + }); + + // Optional: Handle clicks outside the navbar to close it + $(document).on('click', function(event) { + var navbar = $('.navbar-collapse'); + + // Check if click is outside navbar and navbar is open + if (navbar.hasClass('show') && + !$(event.target).closest('.navbar').length) { + collapseNavbar(); + } }); });