naming and dealing with a dependency issue. ready for first release

.Rbuildignore

@@ -1,9 +1,10 @@
 ^renv$
 ^renv\.lock$
-^webResearch\.Rproj$
+^freesearcheR\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^dev$
 ^\.github$
 ^inst/shiny-examples/casting/functions\.R$
 ^functions\.R$
+^CODE_OF_CONDUCT\.md$

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at agdamsbo@clin.au.dk. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -1,10 +1,10 @@
-Package: webResearch
+Package: freesearcheR
 Title: Browser Based Data Analysis
 Version: 24.12.1
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))
-Description: Browser based basic data analysis and research output.
+Description: Free and open source browser based data exploration and analysis with publication ready output.
 License: AGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -17,7 +17,6 @@ Imports:
     gtsummary,
     haven,
     here,
-    openxlsx2,
     quarto,
     readODS,
     readr,
@@ -50,6 +49,9 @@ Imports:
 Suggests: 
     styler,
     devtools,
-    rhub
+    rhub,
-URL: https://github.com/agdamsbo/webResearch
+    usethis,
-BugReports: https://github.com/agdamsbo/webResearch/issues
+    roxygen2,
+    pak
+URL: https://github.com/agdamsbo/freesearcheR
+BugReports: https://github.com/agdamsbo/freesearcheR/issues

NAMESPACE

@@ -9,12 +9,12 @@ export(cut_variable_ui)
 export(default_format_arguments)
 export(default_parsing)
 export(factorize)
+export(file_export)
 export(format_writer)
 export(getfun)
 export(index_embed)
 export(is_any_class)
 export(is_datetime)
-export(m_datafileUI)
 export(m_redcap_readServer)
 export(m_redcap_readUI)
 export(modal_cut_variable)
@@ -23,11 +23,17 @@ export(read_input)
 export(regression_model)
 export(regression_model_uv)
 export(regression_table)
-export(shiny_webResearch)
+export(shiny_freesearcheR)
 export(specify_qmd_format)
 export(tbl_merge)
 export(winbox_cut_variable)
 export(write_quarto)
+importFrom(REDCapCAST,as_factor)
+importFrom(REDCapCAST,numchar2fct)
+importFrom(REDCapCAST,parse_data)
+importFrom(REDCapCAST,read_redcap_tables)
+importFrom(REDCapCAST,redcap_wider)
+importFrom(REDCapCAST,suffix2label)
 importFrom(classInt,classIntervals)
 importFrom(graphics,abline)
 importFrom(graphics,axis)

R/cut-variable-dates.R

@@ -206,9 +206,11 @@ cut.Date <- function(x,breaks,start.on.monday=TRUE,...){
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' vapply(REDCapCAST::redcapcast_data, \(.x){
 #'   is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt"))
 #' }, logical(1))
+#' }
 is_any_class <- function(data, class.vec) {
   any(class(data) %in% class.vec)
 }

R/file-import-module.R

@@ -1,125 +1,125 @@
-#' Shiny UI module to load a data file
+#' #' Shiny UI module to load a data file
+#' #'
+#' #' @param id id
+#' #'
+#' #' @return shiny UI
+#' #' @export
+#' #'
+#' m_datafileUI <- function(id) {
+#'   ns <- shiny::NS(id)
+#'   shiny::tagList(
+#'     shiny::fileInput(
+#'       inputId = ns("file"),
+#'       label = "Upload a file",
+#'       multiple = FALSE,
+#'       accept = c(
+#'         ".csv",
+#'         ".xlsx",
+#'         ".xls",
+#'         ".dta",
+#'         ".ods",
+#'         ".rds"
+#'       )
+#'     ),
+#'     shiny::h4("Parameter specifications"),
+#'     shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
+#'     shiny::uiOutput(ns("include_vars")),
+#'     DT::DTOutput(ns("data_input")),
+#'     shiny::actionButton(ns("submit"), "Submit")
+#'   )
+#' }
 #'
-#' @param id id
+#' m_datafileServer <- function(id, output.format = "df") {
+#'   shiny::moduleServer(id, function(input, output, session, ...) {
+#'     ns <- shiny::NS(id)
+#'     ds <- shiny::reactive({
+#'       REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
+#'     })
 #'
-#' @return shiny UI
+#'     output$include_vars <- shiny::renderUI({
-#' @export
+#'       shiny::req(input$file)
+#'       shiny::selectizeInput(
+#'         inputId = ns("include_vars"),
+#'         selected = NULL,
+#'         label = "Covariables to include",
+#'         choices = colnames(ds()),
+#'         multiple = TRUE
+#'       )
+#'     })
 #'
-m_datafileUI <- function(id) {
+#'     base_vars <- shiny::reactive({
-  ns <- shiny::NS(id)
+#'       if (is.null(input$include_vars)) {
-  shiny::tagList(
+#'         out <- colnames(ds())
-    shiny::fileInput(
+#'       } else {
-      inputId = ns("file"),
+#'         out <- input$include_vars
-      label = "Upload a file",
+#'       }
-      multiple = FALSE,
+#'       out
-      accept = c(
+#'     })
-        ".csv",
+#'
-        ".xlsx",
+#'     output$data_input <-
-        ".xls",
+#'       DT::renderDT({
-        ".dta",
+#'         shiny::req(input$file)
-        ".ods",
+#'         ds()[base_vars()]
-        ".rds"
+#'       })
-      )
+#'
-    ),
+#'     shiny::eventReactive(input$submit, {
-    shiny::h4("Parameter specifications"),
+#'       # shiny::req(input$file)
-    shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
+#'
-    shiny::uiOutput(ns("include_vars")),
+#'       data <- shiny::isolate({
-    DT::DTOutput(ns("data_input")),
+#'         ds()[base_vars()]
-    shiny::actionButton(ns("submit"), "Submit")
+#'       })
-  )
+#'
-}
+#'       file_export(data,
-
+#'         output.format = output.format,
-m_datafileServer <- function(id, output.format = "df") {
+#'         tools::file_path_sans_ext(input$file$name)
-  shiny::moduleServer(id, function(input, output, session, ...) {
+#'       )
-    ns <- shiny::NS(id)
+#'     })
-    ds <- shiny::reactive({
+#'   })
-      REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
+#' }
-    })
+#'
-
+#'
-    output$include_vars <- shiny::renderUI({
+#'
-      shiny::req(input$file)
+#'
-      shiny::selectizeInput(
+#'
-        inputId = ns("include_vars"),
+#' file_app <- function() {
-        selected = NULL,
+#'   ui <- shiny::fluidPage(
-        label = "Covariables to include",
+#'     m_datafileUI("data"),
-        choices = colnames(ds()),
+#'     # DT::DTOutput(outputId = "redcap_prev")
-        multiple = TRUE
+#'     toastui::datagridOutput2(outputId = "redcap_prev")
-      )
+#'   )
-    })
+#'   server <- function(input, output, session) {
-
+#'     m_datafileServer("data", output.format = "list")
-    base_vars <- shiny::reactive({
+#'   }
-      if (is.null(input$include_vars)) {
+#'   shiny::shinyApp(ui, server)
-        out <- colnames(ds())
+#' }
-      } else {
+#'
-        out <- input$include_vars
+#' file_app()
-      }
+#'
-      out
+#' tdm_data_upload <- teal::teal_data_module(
-    })
+#'   ui <- function(id) {
-
+#'     shiny::fluidPage(
-    output$data_input <-
+#'       m_datafileUI(id)
-      DT::renderDT({
+#'     )
-        shiny::req(input$file)
+#'   },
-        ds()[base_vars()]
+#'   server = function(id) {
-      })
+#'     m_datafileServer(id, output.format = "teal")
-
+#'   }
-    shiny::eventReactive(input$submit, {
+#' )
-      # shiny::req(input$file)
+#'
-
+#' tdm_data_read <- teal::teal_data_module(
-      data <- shiny::isolate({
+#'   ui <- function(id) {
-        ds()[base_vars()]
+#'     shiny::fluidPage(
-      })
+#'       m_redcap_readUI(id = "redcap")
-
+#'     )
-      file_export(data,
+#'   },
-        output.format = output.format,
+#'   server = function(id) {
-        tools::file_path_sans_ext(input$file$name)
+#'     moduleServer(
-      )
+#'       id,
-    })
+#'       function(input, output, session) {
-  })
+#'         ns <- session$ns
-}
+#'
-
+#'         m_redcap_readServer(id = "redcap", output.format = "teal")
-
+#'       }
-
+#'     )
-
+#'   }
-
+#' )
-file_app <- function() {
-  ui <- shiny::fluidPage(
-    m_datafileUI("data"),
-    # DT::DTOutput(outputId = "redcap_prev")
-    toastui::datagridOutput2(outputId = "redcap_prev")
-  )
-  server <- function(input, output, session) {
-    m_datafileServer("data", output.format = "list")
-  }
-  shiny::shinyApp(ui, server)
-}
-
-file_app()
-
-tdm_data_upload <- teal::teal_data_module(
-  ui <- function(id) {
-    shiny::fluidPage(
-      m_datafileUI(id)
-    )
-  },
-  server = function(id) {
-    m_datafileServer(id, output.format = "teal")
-  }
-)
-
-tdm_data_read <- teal::teal_data_module(
-  ui <- function(id) {
-    shiny::fluidPage(
-      m_redcap_readUI(id = "redcap")
-    )
-  },
-  server = function(id) {
-    moduleServer(
-      id,
-      function(input, output, session) {
-        ns <- session$ns
-
-        m_redcap_readServer(id = "redcap", output.format = "teal")
-      }
-    )
-  }
-)

R/helpers.R

@@ -98,6 +98,7 @@ argsstring2list <- function(string) {
 #' @param vars variables to force factorize
 #'
 #' @return data.frame
+#' @importFrom REDCapCAST as_factor
 #' @export
 factorize <- function(data, vars) {
   if (!is.null(vars)) {
@@ -105,7 +106,7 @@ factorize <- function(data, vars) {
       dplyr::mutate(
         dplyr::across(
           dplyr::all_of(vars),
-          REDCapCAST::as_factor
+          as_factor
         )
       )
   } else {
@@ -128,6 +129,17 @@ dummy_Imports <- function() {
 }
 
 
+#' Title
+#'
+#' @param data data
+#' @param output.format output
+#' @param filename filename
+#' @param ... passed on
+#'
+#' @returns data
+#' @export
+#' @importFrom REDCapCAST as_factor parse_data numchar2fct
+#'
 file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
   output.format <- match.arg(output.format)
 
@@ -139,9 +151,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
       {
         assign(name, value |>
           dplyr::bind_cols() |>
-          REDCapCAST::parse_data() |>
+          parse_data() |>
-          REDCapCAST::as_factor() |>
+          as_factor() |>
-          REDCapCAST::numchar2fct())
+          numchar2fct())
       },
       value = data,
       name = filename
@@ -150,9 +162,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
     datanames(out) <- filename
   } else if (output.format == "df") {
     out <- data|>
-      REDCapCAST::parse_data() |>
+      parse_data() |>
-      REDCapCAST::as_factor() |>
+      as_factor() |>
-      REDCapCAST::numchar2fct()
+      numchar2fct()
   } else if (output.format == "list") {
     out <- list(
       data = data,
@@ -172,13 +184,14 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 #'
 #' @returns data.frame or tibble
 #' @export
+#' @importFrom REDCapCAST as_factor parse_data numchar2fct
 #'
 #' @examples
 #' mtcars |> str()
 #' mtcars |> default_parsing() |> str()
 default_parsing <- function(data){
   data |>
-    REDCapCAST::parse_data() |>
+    parse_data() |>
-    REDCapCAST::as_factor() |>
+    as_factor() |>
-    REDCapCAST::numchar2fct()
+    numchar2fct()
 }

R/redcap_read_shiny_module.R

@@ -100,6 +100,7 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
 #'
 #' @return shiny server module
 #' @export
+#' @importFrom REDCapCAST read_redcap_tables redcap_wider suffix2label
 #'
 m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
   output.format <- match.arg(output.format)
@@ -226,7 +227,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
       shiny::req(input$fields)
       record_id <- dd()[[1]][1]
 
-      redcap_data <- REDCapCAST::read_redcap_tables(
+      redcap_data <- read_redcap_tables(
         uri = input$uri,
         token = input$api,
         fields = unique(c(record_id, input$fields)),
@@ -235,10 +236,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
         raw_or_label = "both",
         filter_logic = input$filter
       ) |>
-        REDCapCAST::redcap_wider() |>
+        redcap_wider() |>
         dplyr::select(-dplyr::ends_with("_complete")) |>
         dplyr::select(-dplyr::any_of(record_id)) |>
-        REDCapCAST::suffix2label()
+        suffix2label()
 
       out_object <- file_export(redcap_data,
                                 output.format = output.format,

R/regression_model.R

@@ -10,6 +10,7 @@
 #' @param ... ignored for now
 #'
 #' @importFrom stats as.formula
+#' @importFrom REDCapCAST as_factor
 #'
 #' @return object of standard class for fun
 #' @export
@@ -66,7 +67,7 @@ regression_model <- function(data,
   data <- data |>
     purrr::map(\(.x){
       if (is.character(.x)) {
-        suppressWarnings(REDCapCAST::as_factor(.x))
+        suppressWarnings(as_factor(.x))
       } else {
         .x
       }

R/regression_table.R

@@ -81,7 +81,7 @@
 #' #' @export
 #' regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
 #'   # Stripping custom class
-#'   class(x) <- class(x)[class(x) != "webresearch_model"]
+#'   class(x) <- class(x)[class(x) != "freesearcher_model"]
 #'
 #'   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
 #'     if (!"exponentiate" %in% names(args.list)) {
@@ -110,7 +110,7 @@ regression_table <- function(x, ...) {
 
 regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
   # Stripping custom class
-  class(x) <- class(x)[class(x) != "webresearch_model"]
+  class(x) <- class(x)[class(x) != "freesearcher_model"]
 
   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
     if (!"exponentiate" %in% names(args.list)) {

R/shiny_freesearcheR.R

@@ -0,0 +1,25 @@
+#' Launch the freesearcheR tool locally
+#'
+#' @description
+#' All data.frames in the global environment will be accessible through the app.
+#'
+#'
+#' @param ... arguments passed on to `shiny::runApp()`
+#'
+#' @return shiny app
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' data(mtcars)
+#' shiny_freesearcheR(launch.browser = TRUE)
+#' }
+shiny_freesearcheR <- function(...) {
+  appDir <- system.file("apps", "data_analysis_modules", package = "freesearcheR")
+  if (appDir == "") {
+    stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
+  }
+
+  a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
+  return(invisible(a))
+}

R/shiny_webResearch.R

@@ -1,27 +0,0 @@
-#' Test version of the shiny_cast function to launch the app with a data set in
-#' the environment.
-#'
-#' @param data optional data set to provide for analysis
-#' @param ... arguments passed on to `shiny::runApp()`
-#'
-#' @return shiny app
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' mtcars |> shiny_webResearch(launch.browser = TRUE)
-#' }
-shiny_webResearch <- function(data = NULL, ...) {
-  appDir <- system.file("apps", "data_analysis_modules", package = "webResearch")
-  if (appDir == "") {
-    stop("Could not find the app directory. Try re-installing `webResearch`.", call. = FALSE)
-  }
-
-  G <- .GlobalEnv
-
-  if (!is.null(data) && is.data.frame(data)) {
-    assign("webResearch_data", data, envir = G)
-  }
-  a <- shiny::runApp(appDir = appDir, ...)
-  return(invisible(a))
-}

README.md

@@ -1,20 +1,58 @@
-# webResearch
+# freesearcheR
 
 <!-- badges: start -->
 
 <!-- badges: end -->
 
-This package is the backbone of the open and freely accessible browser-based data analysis tool with project name "webResearch".
+This package is the backbone of the free and open browser based data exploration and analysis tool with publication ready output.
+
+This package and the ***freesearcheR***-tool is part of a large project to democratize health data analysis and removing barriers for clinicians to engage in health research.
+
+As of 2024-12-19 the ***freesearcheR***-tool is online and accessible here: [link to shinyapps.io free hosting](https://agdamsbo.shinyapps.io/freesearcheR/). All feedback is welcome and can be shared as a GitHub issue.
+
+Initiatives for to start funding to continue development of the tool and surrounding initiatives will start soon.
 
 ## Roadmap
 
--   A minimally working example
+-   [ ] Stratified analyses
 
-    -   Table 1 of baseline characteristics
+-   Additional study designs:
-    -   Table 2 of main analysis results
-    -   Figure 1 of main results (like forest plot)
-    -   Shiny GUI implementation
 
--   Fundraising for further development
+    -   [x] Cross-sectional data analyses
 
--   Implementation with different focus groups and educational formats.
+    -   [ ] Longitudinal data analyses
+
+    -   [ ] Survival analysis
+
+-   More detailed variable browser
+
+    -   [ ] Add histograms for data distribution
+
+    -   [ ] Option to edit labels
+
+-   [ ] Plot regression analyses results
+
+-   [ ] Export modified data
+
+-   [ ] Include reproducible code for all steps
+
+-   [x] ~~Modify factor levels~~ Factor level modifications is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12
+
+-   [x] More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12
+
+
+## Install locally
+
+The ***freesearcheR***-tool can also be launched locally. Any data.frame available in the global environment will be accessible from the interface.
+
+```
+require("devtools")
+devtools::install_github("agdamsbo/freesearcheR")
+library(freesearcheR)
+
+```
+
+
+## Code of Conduct
+
+Please note that the freesearcheR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

inst/apps/data_analysis/server.R

@@ -1,7 +1,3 @@
-# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
-# source(here::here("app/functions.R"))
-
-# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
 
 library(readr)
 library(MASS)
@@ -19,7 +15,7 @@ library(quarto)
 library(here)
 library(broom)
 library(broom.helpers)
-library(REDCapCAST)
+# library(REDCapCAST)
 library(easystats)
 library(patchwork)
 library(DHARMa)
@@ -32,6 +28,17 @@ if (file.exists(here::here("functions.R"))) {
   source(here::here("functions.R"))
 }
 
+#' freesearcheR server
+#'
+#' @param input input
+#' @param output output
+#' @param session session
+#'
+#' @returns server
+#' @export
+#' @importFrom REDCapCAST numchar2fct
+#'
+#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -68,7 +75,7 @@ server <- function(input, output, session) {
       out <- out |>
         (\(.x){
           suppressWarnings(
-            REDCapCAST::numchar2fct(.x)
+            numchar2fct(.x)
           )
         })()
     }

inst/apps/data_analysis_modules/app.R

@@ -1,7 +1,7 @@
 
 
 ########
-#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/functions.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R 
 ########
 
 
@@ -249,6 +249,8 @@ cut.Date <- function(x,breaks,start.on.monday=TRUE,...){
 
 
 
+
+
 is_any_class <- function(data, class.vec) {
   any(class(data) %in% class.vec)
 }
@@ -685,124 +687,124 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
 
 
 
-m_datafileUI <- function(id) {
-  ns <- shiny::NS(id)
-  shiny::tagList(
-    shiny::fileInput(
-      inputId = ns("file"),
-      label = "Upload a file",
-      multiple = FALSE,
-      accept = c(
-        ".csv",
-        ".xlsx",
-        ".xls",
-        ".dta",
-        ".ods",
-        ".rds"
-      )
-    ),
-    shiny::h4("Parameter specifications"),
-    shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
-    shiny::uiOutput(ns("include_vars")),
-    DT::DTOutput(ns("data_input")),
-    shiny::actionButton(ns("submit"), "Submit")
-  )
-}
-
-m_datafileServer <- function(id, output.format = "df") {
-  shiny::moduleServer(id, function(input, output, session, ...) {
-    ns <- shiny::NS(id)
-    ds <- shiny::reactive({
-      REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
-    })
-
-    output$include_vars <- shiny::renderUI({
-      shiny::req(input$file)
-      shiny::selectizeInput(
-        inputId = ns("include_vars"),
-        selected = NULL,
-        label = "Covariables to include",
-        choices = colnames(ds()),
-        multiple = TRUE
-      )
-    })
-
-    base_vars <- shiny::reactive({
-      if (is.null(input$include_vars)) {
-        out <- colnames(ds())
-      } else {
-        out <- input$include_vars
-      }
-      out
-    })
-
-    output$data_input <-
-      DT::renderDT({
-        shiny::req(input$file)
-        ds()[base_vars()]
-      })
-
-    shiny::eventReactive(input$submit, {
-      # shiny::req(input$file)
-
-      data <- shiny::isolate({
-        ds()[base_vars()]
-      })
-
-      file_export(data,
-        output.format = output.format,
-        tools::file_path_sans_ext(input$file$name)
-      )
-    })
-  })
-}
 
 
 
 
 
-file_app <- function() {
-  ui <- shiny::fluidPage(
-    m_datafileUI("data"),
-    # DT::DTOutput(outputId = "redcap_prev")
-    toastui::datagridOutput2(outputId = "redcap_prev")
-  )
-  server <- function(input, output, session) {
-    m_datafileServer("data", output.format = "list")
-  }
-  shiny::shinyApp(ui, server)
-}
 
-file_app()
 
-tdm_data_upload <- teal::teal_data_module(
-  ui <- function(id) {
-    shiny::fluidPage(
-      m_datafileUI(id)
-    )
-  },
-  server = function(id) {
-    m_datafileServer(id, output.format = "teal")
-  }
-)
 
-tdm_data_read <- teal::teal_data_module(
-  ui <- function(id) {
-    shiny::fluidPage(
-      m_redcap_readUI(id = "redcap")
-    )
-  },
-  server = function(id) {
-    moduleServer(
-      id,
-      function(input, output, session) {
-        ns <- session$ns
 
-        m_redcap_readServer(id = "redcap", output.format = "teal")
+
-      }
+
-    )
+
-  }
+
-)
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 ########
@@ -910,13 +912,14 @@ argsstring2list <- function(string) {
 
 
 
+
 factorize <- function(data, vars) {
   if (!is.null(vars)) {
     data |>
       dplyr::mutate(
         dplyr::across(
           dplyr::all_of(vars),
-          REDCapCAST::as_factor
+          as_factor
         )
       )
   } else {
@@ -939,6 +942,18 @@ dummy_Imports <- function() {
 }
 
 
+
+
+
+
+
+
+
+
+
+
+
+
 file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
   output.format <- match.arg(output.format)
 
@@ -950,9 +965,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
       {
         assign(name, value |>
           dplyr::bind_cols() |>
-          REDCapCAST::parse_data() |>
+          parse_data() |>
-          REDCapCAST::as_factor() |>
+          as_factor() |>
-          REDCapCAST::numchar2fct())
+          numchar2fct())
       },
       value = data,
       name = filename
@@ -961,9 +976,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
     datanames(out) <- filename
   } else if (output.format == "df") {
     out <- data|>
-      REDCapCAST::parse_data() |>
+      parse_data() |>
-      REDCapCAST::as_factor() |>
+      as_factor() |>
-      REDCapCAST::numchar2fct()
+      numchar2fct()
   } else if (output.format == "list") {
     out <- list(
       data = data,
@@ -987,11 +1002,12 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
 
 
 
+
 default_parsing <- function(data){
   data |>
-    REDCapCAST::parse_data() |>
+    parse_data() |>
-    REDCapCAST::as_factor() |>
+    as_factor() |>
-    REDCapCAST::numchar2fct()
+    numchar2fct()
 }
 
 
@@ -1102,6 +1118,7 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
 
 
 
+
 m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
   output.format <- match.arg(output.format)
 
@@ -1227,7 +1244,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
       shiny::req(input$fields)
       record_id <- dd()[[1]][1]
 
-      redcap_data <- REDCapCAST::read_redcap_tables(
+      redcap_data <- read_redcap_tables(
         uri = input$uri,
         token = input$api,
         fields = unique(c(record_id, input$fields)),
@@ -1236,10 +1253,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
         raw_or_label = "both",
         filter_logic = input$filter
       ) |>
-        REDCapCAST::redcap_wider() |>
+        redcap_wider() |>
         dplyr::select(-dplyr::ends_with("_complete")) |>
         dplyr::select(-dplyr::any_of(record_id)) |>
-        REDCapCAST::suffix2label()
+        suffix2label()
 
       out_object <- file_export(redcap_data,
                                 output.format = output.format,
@@ -1400,6 +1417,7 @@ redcap_app <- function() {
 
 
 
+
 
 
 regression_model <- function(data,
@@ -1437,7 +1455,7 @@ regression_model <- function(data,
   data <- data |>
     purrr::map(\(.x){
       if (is.character(.x)) {
-        suppressWarnings(REDCapCAST::as_factor(.x))
+        suppressWarnings(as_factor(.x))
       } else {
         .x
       }
@@ -1691,7 +1709,7 @@ regression_table <- function(x, ...) {
 
 regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
   # Stripping custom class
-  class(x) <- class(x)[class(x) != "webresearch_model"]
+  class(x) <- class(x)[class(x) != "freesearcher_model"]
 
   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
     if (!"exponentiate" %in% names(args.list)) {
@@ -1811,7 +1829,7 @@ modify_qmd <- function(file, format) {
 
 
 ########
-#### Current file: R//shiny_webResearch.R 
+#### Current file: R//shiny_freesearcheR.R 
 ########
 
 
@@ -1827,18 +1845,16 @@ modify_qmd <- function(file, format) {
 
 
 
-shiny_webResearch <- function(data = NULL, ...) {
+
-  appDir <- system.file("apps", "data_analysis_modules", package = "webResearch")
+
+
+shiny_freesearcheR <- function(...) {
+  appDir <- system.file("apps", "data_analysis_modules", package = "freesearcheR")
   if (appDir == "") {
-    stop("Could not find the app directory. Try re-installing `webResearch`.", call. = FALSE)
+    stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
   }
 
-  G <- .GlobalEnv
+  a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
-
-  if (!is.null(data) && is.data.frame(data)) {
-    assign("webResearch_data", data, envir = G)
-  }
-  a <- shiny::runApp(appDir = appDir, ...)
   return(invisible(a))
 }
 
@@ -1885,7 +1901,7 @@ custom_theme <- function(...,
 
 
 ########
-#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/ui.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R 
 ########
 
 # ns <- NS(id)
@@ -2214,7 +2230,7 @@ ui <- bslib::page_fluid(
         "Data is only stored for analyses and deleted immediately afterwards."),
       shiny::p(
         style = "margin: 1; color: #888;",
-        "Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/webResearch/", target="_blank", rel="noopener noreferrer")
+        "Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target="_blank", rel="noopener noreferrer")
       ),
     )
   )
@@ -2222,14 +2238,9 @@ ui <- bslib::page_fluid(
 
 
 ########
-#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/server.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R 
 ########
 
-# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
-# source(here::here("app/functions.R"))
-
-# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
-
 library(readr)
 library(MASS)
 library(stats)
@@ -2246,7 +2257,7 @@ library(quarto)
 library(here)
 library(broom)
 library(broom.helpers)
-library(REDCapCAST)
+# library(REDCapCAST)
 library(easystats)
 library(patchwork)
 library(DHARMa)
@@ -2255,10 +2266,7 @@ library(toastui)
 library(IDEAFilter)
 library(shinyWidgets)
 library(DT)
-# if (!requireNamespace("webResearch")) {
+# library(freesearcheR)
-#   devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
-# }
-# library(webResearch)
 
 # source("functions.R")
 
@@ -2269,7 +2277,17 @@ library(DT)
 # dark <- custom_theme(bg = "#000",fg="#fff")
 
 
-
+#' freesearcheR server
+#'
+#' @param input input
+#' @param output output
+#' @param session session
+#'
+#' @returns server
+#' @export
+#' @importFrom REDCapCAST fct_drop.data.frame
+#'
+#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -2308,7 +2326,6 @@ server <- function(input, output, session) {
   rv <- shiny::reactiveValues(
     list = list(),
     ds = NULL,
-    input = exists("webResearch_data"),
     local_temp = NULL,
     ready = NULL,
     test = "no",
@@ -2373,33 +2390,6 @@ server <- function(input, output, session) {
     rv$data_original <- from_env$data()
   })
 
-  # ds <-
-  # shiny::reactive({
-  #   # input$file1 will be NULL initially. After the user selects
-  #   # and uploads a file, head of that data file by default,
-  #   # or all rows if selected, will be shown.
-  #   # if (v$input) {
-  #   #   out <- webResearch_data
-  #   # } else if (input$source == "file") {
-  #   #   req(data_file$data())
-  #   #   out <- data_file$data()
-  #   # } else if (input$source == "redcap") {
-  #   #   req(purrr::pluck(data_redcap(), "data")())
-  #   #   out <- purrr::pluck(data_redcap(), "data")()
-  #   # }
-  #
-  #   req(rv$data_original)
-  #
-  #   rv$ds <- "loaded"
-  #
-  #   rv$data <- rv$data_original
-  #
-  #
-  #   # rv$data <- rv$data_original
-  #
-  #   # rv$data_original
-  # })
-
   ##############################################################################
   #########
   #########  Data modification section
@@ -2589,7 +2579,7 @@ server <- function(input, output, session) {
         {
           data <- data_filter() |>
             dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
-            REDCapCAST::fct_drop.data.frame() |>
+            fct_drop.data.frame() |>
             factorize(vars = input$factor_vars)
 
           if (input$strat_var == "none") {
@@ -2809,7 +2799,7 @@ server <- function(input, output, session) {
 
 
 ########
-#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/launch.R 
+#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R 
 ########
 
 shinyApp(ui, server)

inst/apps/data_analysis_modules/server.R

@@ -1,8 +1,3 @@
-# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
-# source(here::here("app/functions.R"))
-
-# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
-
 library(readr)
 library(MASS)
 library(stats)
@@ -19,7 +14,7 @@ library(quarto)
 library(here)
 library(broom)
 library(broom.helpers)
-library(REDCapCAST)
+# library(REDCapCAST)
 library(easystats)
 library(patchwork)
 library(DHARMa)
@@ -28,10 +23,7 @@ library(toastui)
 library(IDEAFilter)
 library(shinyWidgets)
 library(DT)
-# if (!requireNamespace("webResearch")) {
+# library(freesearcheR)
-#   devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
-# }
-# library(webResearch)
 
 # source("functions.R")
 
@@ -42,7 +34,17 @@ library(DT)
 # dark <- custom_theme(bg = "#000",fg="#fff")
 
 
-
+#' freesearcheR server
+#'
+#' @param input input
+#' @param output output
+#' @param session session
+#'
+#' @returns server
+#' @export
+#' @importFrom REDCapCAST fct_drop.data.frame
+#'
+#' @examples
 server <- function(input, output, session) {
   ## Listing files in www in session start to keep when ending and removing
   ## everything else.
@@ -81,7 +83,6 @@ server <- function(input, output, session) {
   rv <- shiny::reactiveValues(
     list = list(),
     ds = NULL,
-    input = exists("webResearch_data"),
     local_temp = NULL,
     ready = NULL,
     test = "no",
@@ -146,33 +147,6 @@ server <- function(input, output, session) {
     rv$data_original <- from_env$data()
   })
 
-  # ds <-
-  # shiny::reactive({
-  #   # input$file1 will be NULL initially. After the user selects
-  #   # and uploads a file, head of that data file by default,
-  #   # or all rows if selected, will be shown.
-  #   # if (v$input) {
-  #   #   out <- webResearch_data
-  #   # } else if (input$source == "file") {
-  #   #   req(data_file$data())
-  #   #   out <- data_file$data()
-  #   # } else if (input$source == "redcap") {
-  #   #   req(purrr::pluck(data_redcap(), "data")())
-  #   #   out <- purrr::pluck(data_redcap(), "data")()
-  #   # }
-  #
-  #   req(rv$data_original)
-  #
-  #   rv$ds <- "loaded"
-  #
-  #   rv$data <- rv$data_original
-  #
-  #
-  #   # rv$data <- rv$data_original
-  #
-  #   # rv$data_original
-  # })
-
   ##############################################################################
   #########
   #########  Data modification section
@@ -362,7 +336,7 @@ server <- function(input, output, session) {
         {
           data <- data_filter() |>
             dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
-            REDCapCAST::fct_drop.data.frame() |>
+            fct_drop.data.frame() |>
             factorize(vars = input$factor_vars)
 
           if (input$strat_var == "none") {

inst/apps/data_analysis_modules/ui.R

@@ -324,7 +324,7 @@ ui <- bslib::page_fluid(
         "Data is only stored for analyses and deleted immediately afterwards."),
       shiny::p(
         style = "margin: 1; color: #888;",
-        "Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/webResearch/", target="_blank", rel="noopener noreferrer")
+        "Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target="_blank", rel="noopener noreferrer")
       ),
     )
   )

inst/apps/data_analysis_modules/www/docs.html

@@ -40,7 +40,7 @@ margin: 0 0.8em 0.2em -1em;  vertical-align: middle;
 <p>So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.</p>
 <p>Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.</p>
 <h2 id="contribute">Contribute</h2>
-<p>Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please <a href="https://github.com/agdamsbo/webResearch/issues">share and report on the project page on GitHub</a>.</p>
+<p>Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please <a href="https://github.com/agdamsbo/freesearcheR/issues">share and report on the project page on GitHub</a>.</p>
 <h2 id="roadmap">Roadmap</h2>
 <ul>
 <li><p><label><input type="checkbox">Stratified analyses</label></p></li>
@@ -58,8 +58,8 @@ margin: 0 0.8em 0.2em -1em;  vertical-align: middle;
 <li><p><label><input type="checkbox">Plot regression analyses results</label></p></li>
 <li><p><label><input type="checkbox">Export modified data</label></p></li>
 <li><p><label><input type="checkbox">Include reproducible code for all steps</label></p></li>
-<li><p><label><input type="checkbox">Modify factor levels (including naming, order, collapsing, removing)</label></p></li>
+<li><p><label><input type="checkbox" checked><del>Modify factor levels</del> Factor level modification is possible through converting factors to numeric &gt; cutting numeric with desired fixed values. 2024-12-12</label></p></li>
-<li><p><label><input type="checkbox">More options for date/datetime/time grouping/factoring</label></p></li>
+<li><p><label><input type="checkbox" checked>More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12</label></p></li>
 </ul>
 
 

inst/apps/data_analysis_modules/www/docs.md

@@ -1,34 +0,0 @@
-# Documentation on the freesearcheR platform
-
-Welcome! So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.
-
-Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.
-
-
-## Roadmap
-
--   [ ] Stratified analyses
-
--   Additional study designs:
-
-    -   [x] Cross-sectional data analyses
-
-    -   [ ] Longitudinal data analyses
-
-    -   [ ] Survival analysis
-
--   More detailed variable browser
-
-    -   [ ] Add histograms for datadistribution
-
-    -   [ ] Option to edit labels
-
--   [ ] Plot regression analyses results
-
--   [ ] Export modified data
-
--   [ ] Include reproducible code for all steps
-
--   [ ] Modify factor levels
-
--   [ ] More options for date/datetime/time grouping/factoring

inst/apps/data_analysis_modules/www/docs.qmd

@@ -14,7 +14,7 @@ Below will be a more detailed description of the included features and possibili
 
 ## Contribute
 
-Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please [share and report on the project page on GitHub](https://github.com/agdamsbo/webResearch/issues).
+Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please [share and report on the project page on GitHub](https://github.com/agdamsbo/freesearcheR/issues).
 
 ## Roadmap
 
@@ -40,6 +40,6 @@ Contributions are very welcome. If you find anything odd, or you think of featur
 
 -   [ ] Include reproducible code for all steps
 
--   [ ] Modify factor levels (including naming, order, collapsing, removing)
+-   [x] ~~Modify factor levels~~ Factor level modification is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12
 
--   [ ] More options for date/datetime/time grouping/factoring
+-   [x] More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12

inst/apps/teal_test/app.R

@@ -56,8 +56,8 @@ tm_variable_browser_module <- tm_variable_browser(
 
 filters <- teal::teal_slices()
 
-app_source <- "https://github.com/agdamsbo/webresearch"
+app_source <- "https://github.com/agdamsbo/freesearcheR"
-gh_issues_page <- "https://github.com/agdamsbo/webresearch/issues"
+gh_issues_page <- "https://github.com/agdamsbo/freesearcheR/issues"
 
 header <- tags$span(
   style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",

man/file_export.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{file_export}
+\alias{file_export}
+\title{Title}
+\usage{
+file_export(data, output.format = c("df", "teal", "list"), filename, ...)
+}
+\arguments{
+\item{data}{data}
+
+\item{output.format}{output}
+
+\item{filename}{filename}
+
+\item{...}{passed on}
+}
+\value{
+data
+}
+\description{
+Title
+}

man/is_any_class.Rd

@@ -18,7 +18,9 @@ factor
 Test class
 }
 \examples{
+\dontrun{
 vapply(REDCapCAST::redcapcast_data, \(.x){
   is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt"))
 }, logical(1))
 }
+}

man/m_datafileUI.Rd

@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/file-import-module.R
-\name{m_datafileUI}
-\alias{m_datafileUI}
-\title{Shiny UI module to load a data file}
-\usage{
-m_datafileUI(id)
-}
-\arguments{
-\item{id}{id}
-}
-\value{
-shiny UI
-}
-\description{
-Shiny UI module to load a data file
-}

man/regression_table.Rd

@@ -93,7 +93,7 @@ regression_table.list <- function(x, ...) {
 #' @export
 regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
   # Stripping custom class
-  class(x) <- class(x)[class(x) != "webresearch_model"]
+  class(x) <- class(x)[class(x) != "freesearcher_model"]
 
   if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
     if (!"exponentiate" \%in\% names(args.list)) {

man/shiny_freesearcheR.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shiny_freesearcheR.R
+\name{shiny_freesearcheR}
+\alias{shiny_freesearcheR}
+\title{Launch the freesearcheR tool locally}
+\usage{
+shiny_freesearcheR(...)
+}
+\arguments{
+\item{...}{arguments passed on to \code{shiny::runApp()}}
+}
+\value{
+shiny app
+}
+\description{
+All data.frames in the global environment will be accessible through the app.
+}
+\examples{
+\dontrun{
+data(mtcars)
+shiny_freesearcheR(launch.browser = TRUE)
+}
+}

man/shiny_webResearch.Rd

@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/shiny_webResearch.R
-\name{shiny_webResearch}
-\alias{shiny_webResearch}
-\title{Test version of the shiny_cast function to launch the app with a data set in
-the environment.}
-\usage{
-shiny_webResearch(data = NULL, ...)
-}
-\arguments{
-\item{data}{optional data set to provide for analysis}
-
-\item{...}{arguments passed on to \code{shiny::runApp()}}
-}
-\value{
-shiny app
-}
-\description{
-Test version of the shiny_cast function to launch the app with a data set in
-the environment.
-}
-\examples{
-\dontrun{
-mtcars |> shiny_webResearch(launch.browser = TRUE)
-}
-}

renv.lock

@@ -57,27 +57,6 @@
       ],
       "Hash": "64ff3427f559ce3f2597a4fe13255cb6"
     },
-    "Deriv": {
-      "Package": "Deriv",
-      "Version": "4.1.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods"
-      ],
-      "Hash": "cd52c065c9e687c60c56b51f10f7bcd3"
-    },
-    "Formula": {
-      "Package": "Formula",
-      "Version": "1.2-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats"
-      ],
-      "Hash": "7a29697b75e027767a53fde6c903eca7"
-    },
     "IDEAFilter": {
       "Package": "IDEAFilter",
       "Version": "0.2.0",
@@ -138,30 +117,6 @@
       ],
       "Hash": "5122bb14d8736372411f955e1b16bc8a"
     },
-    "MatrixModels": {
-      "Package": "MatrixModels",
-      "Version": "0.5-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Matrix",
-        "R",
-        "methods",
-        "stats"
-      ],
-      "Hash": "0776bf7526869e0286b0463cb72fb211"
-    },
-    "PKI": {
-      "Package": "PKI",
-      "Version": "0.1-14",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc"
-      ],
-      "Hash": "f5b9c6b2f62f1fa3dd53fd1ddccbb241"
-    },
     "R.cache": {
       "Package": "R.cache",
       "Version": "0.16.0",
@@ -238,9 +193,13 @@
     },
     "REDCapCAST": {
       "Package": "REDCapCAST",
-      "Version": "24.12.1",
+      "Version": "24.11.3",
-      "Source": "Repository",
+      "Source": "GitHub",
-      "Repository": "CRAN",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "REDCapCAST",
+      "RemoteUsername": "agdamsbo",
+      "RemoteSha": "45315080c596d3c1ea5f2e815ef27d2a50230326",
       "Requirements": [
         "R",
         "REDCapR",
@@ -250,7 +209,6 @@
         "forcats",
         "glue",
         "gt",
-        "gtsummary",
         "haven",
         "here",
         "keyring",
@@ -265,7 +223,7 @@
         "vctrs",
         "zip"
       ],
-      "Hash": "d0925e579ddfbedeb536c5cbf65fc42f"
+      "Hash": "9a9744292f30f1fb7fad55c2dd2e9baf"
     },
     "REDCapR": {
       "Package": "REDCapR",
@@ -325,20 +283,6 @@
       ],
       "Hash": "a9e2118c664c2cd694f03de074e8d4b3"
     },
-    "SparseM": {
-      "Package": "SparseM",
-      "Version": "1.84-2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "e78499cbcbbca98200254bd171379165"
-    },
     "V8": {
       "Package": "V8",
       "Version": "6.0.0",
@@ -352,18 +296,6 @@
       ],
       "Hash": "6603bfcbc7883a5fed41fb13042a3899"
     },
-    "abind": {
-      "Package": "abind",
-      "Version": "1.4-8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods",
-        "utils"
-      ],
-      "Hash": "2288423bb0f20a457800d7fc47f6aa54"
-    },
     "ape": {
       "Package": "ape",
       "Version": "5.8-1",
@@ -605,41 +537,6 @@
       ],
       "Hash": "d7e13f49c19103ece9e58ad2d83a7354"
     },
-    "car": {
-      "Package": "car",
-      "Version": "3.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Formula",
-        "MASS",
-        "R",
-        "abind",
-        "carData",
-        "grDevices",
-        "graphics",
-        "lme4",
-        "mgcv",
-        "nlme",
-        "nnet",
-        "pbkrtest",
-        "quantreg",
-        "scales",
-        "stats",
-        "utils"
-      ],
-      "Hash": "82067bf302d1440b730437693a86406a"
-    },
-    "carData": {
-      "Package": "carData",
-      "Version": "3.0-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "ac6cdb8552c61bd36b0e54d07cf2aab7"
-    },
     "cards": {
       "Package": "cards",
       "Version": "0.4.0",
@@ -658,9 +555,9 @@
     },
     "cardx": {
       "Package": "cardx",
-      "Version": "0.2.2",
+      "Version": "0.2.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cards",
@@ -671,7 +568,7 @@
         "rlang",
         "tidyr"
       ],
-      "Hash": "21f5ce5381d529b08783dca434af3003"
+      "Hash": "e5458dd65b0602136b16aed802d3bd50"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -794,23 +691,6 @@
       ],
       "Hash": "8b6512d8f60685736ee3bafdc292190d"
     },
-    "cowplot": {
-      "Package": "cowplot",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "ggplot2",
-        "grDevices",
-        "grid",
-        "gtable",
-        "methods",
-        "rlang",
-        "scales"
-      ],
-      "Hash": "8ef2084dd7d28847b374e55440e4f8cb"
-    },
     "cpp11": {
       "Package": "cpp11",
       "Version": "0.5.1",
@@ -917,30 +797,6 @@
       ],
       "Hash": "33698c4b3127fc9f506654607fb73676"
     },
-    "doBy": {
-      "Package": "doBy",
-      "Version": "4.6.24",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Deriv",
-        "MASS",
-        "Matrix",
-        "R",
-        "boot",
-        "broom",
-        "cowplot",
-        "dplyr",
-        "ggplot2",
-        "methods",
-        "microbenchmark",
-        "modelr",
-        "rlang",
-        "tibble",
-        "tidyr"
-      ],
-      "Hash": "8ddf795104defe53c5392a588888ec68"
-    },
     "doParallel": {
       "Package": "doParallel",
       "Version": "1.0.17",
@@ -1033,34 +889,6 @@
       ],
       "Hash": "b289af101f62cb7b46c53d1a45ed5198"
     },
-    "emmeans": {
-      "Package": "emmeans",
-      "Version": "1.10.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "estimability",
-        "graphics",
-        "methods",
-        "mvtnorm",
-        "numDeriv",
-        "stats",
-        "utils"
-      ],
-      "Hash": "6b0c6fcbdbefe525d2ee713f95880f90"
-    },
-    "estimability": {
-      "Package": "estimability",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats"
-      ],
-      "Hash": "21ec52af13afbcab1cb317567b639b0a"
-    },
     "evaluate": {
       "Package": "evaluate",
       "Version": "1.0.1",
@@ -1316,25 +1144,6 @@
       ],
       "Hash": "14b3b3b923944afb9542dbef4c68bf4b"
     },
-    "ggmosaic": {
-      "Package": "ggmosaic",
-      "Version": "0.3.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "dplyr",
-        "ggplot2",
-        "ggrepel",
-        "plotly",
-        "productplots",
-        "purrr",
-        "rlang",
-        "scales",
-        "tidyr"
-      ],
-      "Hash": "9c716443a2b821aa997c5675386bd34b"
-    },
     "ggplot2": {
       "Package": "ggplot2",
       "Version": "3.5.1",
@@ -1360,22 +1169,6 @@
       ],
       "Hash": "44c6a2f8202d5b7e878ea274b1092426"
     },
-    "ggrepel": {
-      "Package": "ggrepel",
-      "Version": "0.9.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "ggplot2",
-        "grid",
-        "rlang",
-        "scales",
-        "withr"
-      ],
-      "Hash": "3d4156850acc1161f2f24bc61c9217c1"
-    },
     "glue": {
       "Package": "glue",
       "Version": "1.8.0",
@@ -1387,20 +1180,6 @@
       ],
       "Hash": "5899f1eaa825580172bb56c08266f37c"
     },
-    "gridExtra": {
-      "Package": "gridExtra",
-      "Version": "2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grDevices",
-        "graphics",
-        "grid",
-        "gtable",
-        "utils"
-      ],
-      "Hash": "7d7f283939f563670a697165b2cf5560"
-    },
     "gt": {
       "Package": "gt",
       "Version": "0.11.1",
@@ -1470,7 +1249,7 @@
       "Package": "haven",
       "Version": "2.5.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cli",
@@ -1491,7 +1270,7 @@
       "Package": "here",
       "Version": "1.0.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "rprojroot"
       ],
@@ -1512,7 +1291,7 @@
       "Package": "hms",
       "Version": "1.1.3",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "lifecycle",
         "methods",
@@ -1814,7 +1593,7 @@
     },
     "lubridate": {
       "Package": "lubridate",
-      "Version": "1.9.4",
+      "Version": "1.9.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1823,7 +1602,7 @@
         "methods",
         "timechange"
       ],
-      "Hash": "be38bc740fc51783a78edb5a157e4104"
+      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -1876,18 +1655,6 @@
       ],
       "Hash": "110ee9d83b496279960e162ac97764ce"
     },
-    "microbenchmark": {
-      "Package": "microbenchmark",
-      "Version": "1.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "graphics",
-        "stats"
-      ],
-      "Hash": "f9d226d88d4087d817d4e616626ce8e5"
-    },
     "mime": {
       "Package": "mime",
       "Version": "0.12",
@@ -1939,24 +1706,6 @@
       ],
       "Hash": "f519814037d08eee1343c2e7b5992cc4"
     },
-    "modelr": {
-      "Package": "modelr",
-      "Version": "0.1.11",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "broom",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "tibble",
-        "tidyr",
-        "tidyselect",
-        "vctrs"
-      ],
-      "Hash": "4f50122dc256b1b6996a4703fecea821"
-    },
     "munsell": {
       "Package": "munsell",
       "Version": "0.5.1",
@@ -1968,17 +1717,6 @@
       ],
       "Hash": "4fd8900853b746af55b81fda99da7695"
     },
-    "mvtnorm": {
-      "Package": "mvtnorm",
-      "Version": "1.3-2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats"
-      ],
-      "Hash": "9e8405eacb262c0a939e121650247f4b"
-    },
     "nlme": {
       "Package": "nlme",
       "Version": "3.1-166",
@@ -2000,28 +1738,6 @@
       "Repository": "CRAN",
       "Hash": "27550641889a3abf3aec4d91186311ec"
     },
-    "nnet": {
-      "Package": "nnet",
-      "Version": "7.3-19",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats",
-        "utils"
-      ],
-      "Hash": "2c797b46eea7fb58ede195bc0b1f1138"
-    },
-    "numDeriv": {
-      "Package": "numDeriv",
-      "Version": "2016.8-1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "df58958f293b166e4ab885ebcad90e02"
-    },
     "officer": {
       "Package": "officer",
       "Version": "0.6.7",
@@ -2089,18 +1805,6 @@
       ],
       "Hash": "c519244e5080a630292e1fdc36717f0d"
     },
-    "packrat": {
-      "Package": "packrat",
-      "Version": "0.9.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "tools",
-        "utils"
-      ],
-      "Hash": "55ddd2d4a1959535f18393478b0c14a6"
-    },
     "parameters": {
       "Package": "parameters",
       "Version": "0.24.0",
@@ -2137,24 +1841,6 @@
       ],
       "Hash": "e23fb9ecb1258207bcb763d78d513439"
     },
-    "pbkrtest": {
-      "Package": "pbkrtest",
-      "Version": "0.5.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "MASS",
-        "Matrix",
-        "R",
-        "broom",
-        "doBy",
-        "dplyr",
-        "lme4",
-        "methods",
-        "numDeriv"
-      ],
-      "Hash": "938e6bbc4ac57534f8b43224506a8966"
-    },
     "pbmcapply": {
       "Package": "pbmcapply",
       "Version": "1.5.1",
@@ -2194,12 +1880,11 @@
     },
     "pillar": {
       "Package": "pillar",
-      "Version": "1.9.0",
+      "Version": "1.10.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "cli",
-        "fansi",
         "glue",
         "lifecycle",
         "rlang",
@@ -2207,7 +1892,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+      "Hash": "101ca350beea21261a15ba169d7a8513"
     },
     "pkgconfig": {
       "Package": "pkgconfig",
@@ -2299,17 +1984,6 @@
       ],
       "Hash": "0c90a7d71988856bad2a2a45dd871bb9"
     },
-    "productplots": {
-      "Package": "productplots",
-      "Version": "0.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "ggplot2",
-        "plyr"
-      ],
-      "Hash": "75630cc31052ba299a52bb1adbf59fae"
-    },
     "progress": {
       "Package": "progress",
       "Version": "1.2.3",
@@ -2423,24 +2097,6 @@
       ],
       "Hash": "a22b3777f51fd005a7cd4c2bccc385ae"
     },
-    "quantreg": {
-      "Package": "quantreg",
-      "Version": "5.99.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "MASS",
-        "Matrix",
-        "MatrixModels",
-        "R",
-        "SparseM",
-        "graphics",
-        "methods",
-        "stats",
-        "survival"
-      ],
-      "Hash": "c48844cd7961de506a1b4d22b2e082c7"
-    },
     "quarto": {
       "Package": "quarto",
       "Version": "1.4.4",
@@ -2579,7 +2235,7 @@
       "Package": "rematch",
       "Version": "2.0.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
     },
     "renv": {
@@ -2706,29 +2362,6 @@
       ],
       "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144"
     },
-    "rsconnect": {
-      "Package": "rsconnect",
-      "Version": "1.3.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "PKI",
-        "R",
-        "cli",
-        "curl",
-        "digest",
-        "jsonlite",
-        "lifecycle",
-        "openssl",
-        "packrat",
-        "renv",
-        "rlang",
-        "rstudioapi",
-        "tools",
-        "yaml"
-      ],
-      "Hash": "d466c98fdce812325feb4ad406c6ca4b"
-    },
     "rstudioapi": {
       "Package": "rstudioapi",
       "Version": "0.17.1",
@@ -2854,22 +2487,6 @@
       ],
       "Hash": "836c3464fb0f2ea865ed4c35dcdc1eda"
     },
-    "shinyTree": {
-      "Package": "shinyTree",
-      "Version": "0.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmlwidgets",
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@@ -2928,25 +2545,12 @@
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     "sodium": {
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-      "Hash": "ae00d33a499e429a04409bc1167c4995"
+      "Hash": "869b09ca565ecaa9efc62534ebfa3efd"
     },
     "sourcetools": {
       "Package": "sourcetools",
@@ -3018,22 +2622,6 @@
       ],
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     },
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-        "utils"
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-      "Hash": "5aaa9cbaf4aba20f8e06fdea1850a398"
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     "sys": {
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@@ -3129,44 +2717,6 @@
       ],
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     },
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-        "ggplot2",
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-        "shiny",
-        "shinyTree",
-        "shinyWidgets",
-        "shinyjs",
-        "shinyvalidate",
-        "stats",
-        "stringr",
-        "teal",
-        "teal.code",
-        "teal.data",
-        "teal.logger",
-        "teal.reporter",
-        "teal.transform",
-        "teal.widgets",
-        "tern",
-        "tibble",
-        "tidyr",
-        "tools",
-        "utils"
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-      "Hash": "f54d7bc27cd048cec3a842f980c74e9b"
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     "teal.reporter": {
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@@ -3219,31 +2769,6 @@
       ],
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-        "dplyr",
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-        "logger",
-        "methods",
-        "rlang",
-        "shiny",
-        "shinyjs",
-        "shinyvalidate",
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-        "teal.data",
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-        "teal.widgets",
-        "tidyr",
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-      "Hash": "988a30f3f0f20b2633b41103a8eb4e56"
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     "teal.widgets": {
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       "Version": "0.4.2",
@@ -3267,42 +2792,6 @@
       ],
       "Hash": "46a99bbdcd97f8f25070ad23c3b23ad9"
     },
-    "tern": {
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-      "Version": "0.9.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
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-        "Rdpack",
-        "broom",
-        "car",
-        "checkmate",
-        "cowplot",
-        "dplyr",
-        "emmeans",
-        "forcats",
-        "formatters",
-        "ggplot2",
-        "grid",
-        "gridExtra",
-        "gtable",
-        "labeling",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "rlang",
-        "rtables",
-        "scales",
-        "stats",
-        "survival",
-        "tibble",
-        "tidyr",
-        "utils"
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-      "Hash": "35fe86bc358b15525217e775f5318d33"
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     "textshaping": {
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@@ -3447,7 +2936,7 @@
       "Package": "tzdb",
       "Version": "0.4.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cpp11"
@@ -3502,7 +2991,7 @@
       "Package": "vroom",
       "Version": "1.6.5",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "bit64",

renv/settings.json

@@ -0,0 +1,19 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "explicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}