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Andreas Gammelgaard Damsbo 2025-01-15 16:21:38 +01:00
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1773
inst/apps/data_analysis_modules/app.R
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2
inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
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@ -5,6 +5,6 @@ account: agdamsbo
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 13611288
bundleId: 9546880
bundleId: 9641114
url: https://agdamsbo.shinyapps.io/freesearcheR/
version: 1

83
inst/apps/data_analysis_modules/server.R
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@ -18,8 +18,10 @@ library(broom.helpers)
library(easystats)
library(patchwork)
library(DHARMa)
library(datamods)
library(apexcharter)
library(toastui)
library(datamods)
library(data.table)
library(IDEAFilter)
library(shinyWidgets)
library(DT)
@ -39,9 +41,9 @@ server <- function(input, output, session) {
## everything else.
files.to.keep <- list.files("www/")
output$docs_file <- renderUI({
output$docs_file <- shiny::renderUI({
# shiny::includeHTML("www/docs.html")
HTML(readLines("www/docs.html"))
shiny::HTML(readLines("www/docs.html"))
})
##############################################################################
@ -136,17 +138,35 @@ server <- function(input, output, session) {
rv$data_original <- from_env$data()
})
##############################################################################
#########
######### Data modification section
#########
##############################################################################
######### Modifications
shiny::observeEvent(rv$data_original, rv$data <- rv$data_original |> default_parsing())
shiny::observeEvent(input$data_reset, rv$data <- rv$data_original |> default_parsing())
######### Overview
output$tbl_overview <- toastui::renderDatagrid(
data_filter() |>
overview_vars() |>
create_overview_datagrid()|>
add_sparkline(
column = "vals",
color.main = "#2A004E",
color.sec = "#C62300"
)
)
# data_summary_server(id = "data_summary",
# data = data_filter())
######### Modifications
## Using modified version of the datamods::cut_variable_server function
## Further modifications are needed to have cut/bin options based on class of variable
## Could be defined server-side
@ -187,7 +207,8 @@ server <- function(input, output, session) {
attr(rv$data, "code")
})
updated_data <- datamods::update_variables_server(
# updated_data <- datamods::update_variables_server(
updated_data <- update_variables_server(
id = "vars_update",
data = reactive(rv$data),
return_data_on_init = FALSE
@ -201,7 +222,7 @@ server <- function(input, output, session) {
str(rv$data)
})
observeEvent(updated_data(), {
shiny::observeEvent(updated_data(), {
rv$data <- updated_data()
})
@ -308,10 +329,6 @@ server <- function(input, output, session) {
# gt::gt()
# })
shiny::observeEvent(input$act_start, {
bslib::nav_select(id = "main_panel", selected = "Modifications")
})
shiny::observeEvent(
{
input$load
@ -326,7 +343,8 @@ server <- function(input, output, session) {
data <- data_filter() |>
dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
REDCapCAST::fct_drop.data.frame() |>
factorize(vars = input$factor_vars)
factorize(vars = input$factor_vars) |>
remove_na_attr()
if (input$strat_var == "none") {
by.var <- NULL
@ -479,7 +497,22 @@ server <- function(input, output, session) {
# )
# })
##############################################################################
#########
######### Page navigation
#########
##############################################################################
shiny::observeEvent(input$act_start, {
bslib::nav_select(id = "main_panel", selected = "Modifications")
})
##############################################################################
#########
######### Reactivity
#########
##############################################################################
output$uploaded <- shiny::reactive({
if (is.null(rv$ds)) {
@ -512,6 +545,12 @@ server <- function(input, output, session) {
# shiny::outputOptions(output, "has_input", suspendWhenHidden = FALSE)
##############################################################################
#########
######### Downloads
#########
##############################################################################
# Could be rendered with other tables or should show progress
# Investigate quarto render problems
# On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
@ -533,6 +572,26 @@ server <- function(input, output, session) {
}
)
output$data_modified <- downloadHandler(
filename = shiny::reactive({
paste0("modified_data.", input$data_type)
}),
content = function(file, type = input$data_type) {
if (type == "rds"){
readr::write_rds(rv$list$data,file = file)
} else {
haven::write_dta(as.data.frame(rv$list$data),path = file)
}
}
)
##############################################################################
#########
######### Clearing the session on end
#########
##############################################################################
session$onSessionEnded(function() {
cat("Session Ended\n")
files <- list.files("www/")

355
inst/apps/data_analysis_modules/ui.R
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@ -1,6 +1,16 @@
# ns <- NS(id)
ui_elements <- list(
##############################################################################
#########
######### Home panel
#########
##############################################################################
"home" = bslib::nav_panel(
title = "freesearcheR",
shiny::markdown(readLines("www/intro.md")),
icon = shiny::icon("home")
),
##############################################################################
#########
######### Import panel
@ -8,70 +18,61 @@ ui_elements <- list(
##############################################################################
"import" = bslib::nav_panel(
title = "Import",
shiny::fluidRow(
column(
width = 6,
shiny::h4("Choose your data source"),
# shiny::conditionalPanel(
# condition = "output.has_input=='yes'",
# # Input: Select a file ----
# shiny::helpText("Analyses are performed on provided data")
shiny::tagList(
shiny::h4("Choose your data source"),
# shiny::conditionalPanel(
# condition = "output.has_input=='yes'",
# # Input: Select a file ----
# shiny::helpText("Analyses are performed on provided data")
# ),
# shiny::conditionalPanel(
# condition = "output.has_input=='no'",
# Input: Select a file ----
shinyWidgets::radioGroupButtons(
inputId = "source",
selected = "env",
# label = "Choice: ",
choices = c(
"File upload" = "file",
"REDCap server" = "redcap",
"Local data" = "env"
),
# checkIcon = list(
# yes = icon("square-check"),
# no = icon("square")
# ),
# shiny::conditionalPanel(
# condition = "output.has_input=='no'",
# Input: Select a file ----
shinyWidgets::radioGroupButtons(
inputId = "source",
# label = "Choice: ",
choices = c(
"File upload" = "file",
"REDCap server" = "redcap",
"Local data" = "env"
),
# checkIcon = list(
# yes = icon("square-check"),
# no = icon("square")
# ),
width = "100%"
),
shiny::conditionalPanel(
condition = "input.source=='file'",
datamods::import_file_ui("file_import",
title = "Choose a datafile to upload",
file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
m_redcap_readUI("redcap_import")
),
shiny::conditionalPanel(
condition = "input.source=='env'",
import_globalenv_ui(id = "env", title = NULL)
)
# )
width = "100%"
),
column(
width = 6,
shiny::markdown(readLines("www/intro.md"))
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
DT::DTOutput(outputId = "redcap_prev")
),
shiny::br(),
shiny::actionButton(
inputId = "act_start",
label = "Start",
width = "100%",
icon = shiny::icon("play")
),
shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'),
shiny::br(),
shiny::br()
shiny::conditionalPanel(
condition = "input.source=='file'",
datamods::import_file_ui("file_import",
title = "Choose a datafile to upload",
file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
m_redcap_readUI("redcap_import")
),
shiny::conditionalPanel(
condition = "input.source=='env'",
import_globalenv_ui(id = "env", title = NULL)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
DT::DTOutput(outputId = "redcap_prev")
),
shiny::br(),
shiny::actionButton(
inputId = "act_start",
label = "Start",
width = "100%",
icon = shiny::icon("play")
),
shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'),
shiny::br(),
shiny::br()
)
),
##############################################################################
#########
@ -79,47 +80,24 @@ ui_elements <- list(
#########
##############################################################################
"overview" =
# bslib::nav_panel_hidden(
# bslib::nav_panel_hidden(
bslib::nav_panel(
# value = "overview",
title = "Modifications",
title = "Data",
bslib::navset_bar(
fillable = TRUE,
# bslib::nav_panel(
# title = "Edit",
# datamods::edit_data_ui(id = "edit_data")
# ),
# bslib::nav_panel(
# title = "Overview",
# DT::DTOutput(outputId = "table")
# ),
bslib::nav_panel(
title = "Rename and select",
tags$h3("Select, rename and convert variables"),
title = "Summary & filter",
tags$h3("Data summary and filtering"),
fluidRow(
column(
width = 6,
# radioButtons(),
shiny::actionButton("data_reset", "Restore original data"),
shiny::tags$br(),
shiny::helpText("Reset to original imported dataset"),
shiny::tags$br(),
datamods::update_variables_ui("vars_update")
),
column(
width = 6,
tags$b("Original data:"),
# verbatimTextOutput("original"),
verbatimTextOutput("original_str"),
tags$b("Modified data:"),
# verbatimTextOutput("modified"),
verbatimTextOutput("modified_str")
shiny::column(
width = 9,
shiny::tags$p(
"Below is a short summary table of the provided data.
On the right hand side you have the option to create filters.
At the bottom you'll find a raw overview of the original vs the modified data.")
)
)
),
bslib::nav_panel(
title = "Filter and modify",
shinyWidgets::html_dependency_winbox(),
),
fluidRow(
# column(
# width = 3,
@ -136,23 +114,117 @@ ui_elements <- list(
# verbatimTextOutput(outputId = "filtered_code")
# ),
shiny::column(
width = 8,
toastui::datagridOutput(outputId = "table_mod"),
width = 9,
toastui::datagridOutput(outputId = "tbl_overview"),
# data_summary_ui(id = "data_summary"),
shiny::tags$b("Reproducible code:"),
shiny::verbatimTextOutput(outputId = "filtered_code")
),
shiny::column(
width = 4,
shiny::actionButton("modal_cut", "Create factor from a variable"),
width = 3,
IDEAFilter::IDEAFilter_ui("data_filter") # ,
# shiny::actionButton("save_filter", "Apply the filter")
)
),
fluidRow(
column(
width = 6,
tags$b("Original data:"),
# verbatimTextOutput("original"),
verbatimTextOutput("original_str")
),
column(
width = 6,
tags$b("Modified data:"),
# verbatimTextOutput("modified"),
verbatimTextOutput("modified_str")
)
)
),
# bslib::nav_panel(
# title = "Overview",
# DT::DTOutput(outputId = "table")
# ),
bslib::nav_panel(
title = "Modify",
tags$h3("Subset, rename and convert variables"),
fluidRow(
shiny::column(
width = 9,
shiny::tags$p("Below, you can subset the data (by not selecting the variables to exclude on applying changes), rename variables, set new labels (for nicer tables in the analysis report) and change variable classes.
Italic text can be edited/changed.
On the right, you can create and modify factor/categorical variables as well as resetting the data to the originally imported data.")
)
),
fluidRow(
shiny::column(
width = 9,
update_variables_ui("vars_update")
),
shiny::column(
width = 3,
shiny::actionButton("modal_cut", "Create factor variable"),
shiny::tags$br(),
shiny::helpText("Create factor/categorical variable from an other value."),
shiny::tags$br(),
shiny::tags$br(),
shiny::actionButton("modal_update", "Reorder factor levels"),
shiny::tags$br(),
shiny::helpText("Reorder the levels of factor/categorical variables."),
shiny::tags$br(),
IDEAFilter::IDEAFilter_ui("data_filter") # ,
shiny::tags$br(),
shiny::actionButton("data_reset", "Restore original data"),
shiny::tags$br(),
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
shiny::tags$br() # ,
# shiny::tags$br(),
# shiny::tags$br(),
# IDEAFilter::IDEAFilter_ui("data_filter") # ,
# shiny::actionButton("save_filter", "Apply the filter")
)
# datamods::update_variables_ui("vars_update")
)
),
bslib::nav_panel(
title = "Browser",
tags$h3("Browse the provided data"),
shiny::tags$p(
"Below is a data table with all the modified data provided to browse and understand data."
),
shinyWidgets::html_dependency_winbox(),
# fluidRow(
# column(
# width = 3,
# shiny::uiOutput("filter_vars"),
# shiny::conditionalPanel(
# condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
# datamods::filter_data_ui("filtering", max_height = "500px")
# )
# ),
# column(
# width = 9,
# DT::DTOutput(outputId = "filtered_table"),
# tags$b("Code dplyr:"),
# verbatimTextOutput(outputId = "filtered_code")
# ),
# shiny::column(
# width = 8,
toastui::datagridOutput(outputId = "table_mod") # ,
# shiny::tags$b("Reproducible code:"),
# shiny::verbatimTextOutput(outputId = "filtered_code")
# ),
# shiny::column(
# width = 4,
# shiny::actionButton("modal_cut", "Create factor from a variable"),
# shiny::tags$br(),
# shiny::tags$br(),
# shiny::actionButton("modal_update", "Reorder factor levels")#,
# # shiny::tags$br(),
# # shiny::tags$br(),
# # IDEAFilter::IDEAFilter_ui("data_filter") # ,
# # shiny::actionButton("save_filter", "Apply the filter")
# )
# )
)
@ -170,7 +242,7 @@ ui_elements <- list(
#########
##############################################################################
"analyze" =
# bslib::nav_panel_hidden(
# bslib::nav_panel_hidden(
bslib::nav_panel(
# value = "analyze",
title = "Analyses",
@ -181,6 +253,20 @@ ui_elements <- list(
sidebar = bslib::sidebar(
shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
shiny::uiOutput("outcome_var"),
shiny::radioButtons(
inputId = "all",
label = "Specify covariables",
inline = TRUE, selected = 2,
choiceNames = c(
"Yes",
"No"
),
choiceValues = c(1, 2)
),
shiny::conditionalPanel(
condition = "input.all==1",
shiny::uiOutput("include_vars")
),
shiny::uiOutput("strat_var"),
shiny::conditionalPanel(
condition = "input.strat_var!='none'",
@ -196,20 +282,6 @@ ui_elements <- list(
),
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
),
shiny::radioButtons(
inputId = "all",
label = "Specify covariables",
inline = TRUE, selected = 2,
choiceNames = c(
"Yes",
"No"
),
choiceValues = c(1, 2)
),
shiny::conditionalPanel(
condition = "input.all==1",
shiny::uiOutput("include_vars")
),
shiny::radioButtons(
inputId = "specify_factors",
label = "Specify categorical variables?",
@ -230,8 +302,8 @@ ui_elements <- list(
icon = shiny::icon("pencil", lib = "glyphicon"),
label_busy = "Working...",
icon_busy = fontawesome::fa_i("arrows-rotate",
class = "fa-spin",
"aria-hidden" = "true"
class = "fa-spin",
"aria-hidden" = "true"
),
type = "secondary",
auto_reset = TRUE
@ -258,13 +330,29 @@ ui_elements <- list(
# Button
shiny::downloadButton(
outputId = "report",
label = "Download",
label = "Download report",
icon = shiny::icon("download")
),
shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead.")
## https://github.com/quarto-dev/quarto-cli/issues/7151
# )
# )
shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
shiny::tags$hr(),
shiny::h4("Download data"),
shiny::helpText("Choose your favourite output data format to download the modified data."),
shiny::selectInput(
inputId = "data_type",
label = "Data format",
selected = NULL,
choices = list(
"R" = "rds",
"stata" = "dta"
)
),
shiny::br(),
# Button
shiny::downloadButton(
outputId = "data_modified",
label = "Download data",
icon = shiny::icon("download")
)
),
bslib::nav_panel(
title = "Baseline characteristics",
@ -303,28 +391,39 @@ dark <- custom_theme(
# Fonts to consider:
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
ui <- bslib::page_fluid(
ui <- bslib::page_fixed(
shiny::tags$style(
type = "text/css",
# add the name of the tab you want to use as title in data-value
shiny::HTML(
".container-fluid > .nav > li >
a[data-value='freesearcheR'] {font-size: 28px}"
)
),
title = "freesearcheR",
theme = light,
shiny::useBusyIndicators(),
bslib::page_navbar(title = "freesearcheR",
bslib::page_navbar(
# title = "freesearcheR",
id = "main_panel",
# header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")),
ui_elements$home,
ui_elements$import,
ui_elements$overview,
ui_elements$analyze,
ui_elements$docs,
# bslib::nav_spacer(),
# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
fillable = TRUE,
fillable = FALSE,
footer = shiny::tags$footer(
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
shiny::p(
style = "margin: 1",
"Data is only stored for analyses and deleted immediately afterwards."),
"Data is only stored for analyses and deleted immediately afterwards."
),
shiny::p(
style = "margin: 1; color: #888;",
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", 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")
),
)
)

2
inst/apps/data_analysis_modules/www/docs.html
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@ -56,7 +56,7 @@ margin: 0 0.8em 0.2em -1em; vertical-align: middle;
<li><p><label><input type="checkbox">Option to edit variable labels for nicer tables</label></p></li>
</ul></li>
<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" checked>Export modified data. 2025-01-09</label></p></li>
<li><p><label><input type="checkbox">Include reproducible code for all steps</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" checked>More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12</label></p></li>

2
inst/apps/data_analysis_modules/www/docs.qmd
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@ -36,7 +36,7 @@ Contributions are very welcome. If you find anything odd, or you think of featur
- [ ] Plot regression analyses results
- [ ] Export modified data
- [x] Export modified data. 2025-01-09
- [ ] Include reproducible code for all steps

432
inst/apps/data_analysis_modules/www/intro.html Normal file
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8
inst/apps/data_analysis_modules/www/intro.md
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@ -1,12 +1,12 @@
# Welcome
This is the ***freesearchR*** web data analysis tool. We intend the ***freesearchR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician.
This is the ***freesearcheR*** web data analysis tool. We intend the ***freesearcheR*** to be a powerful and free tool for easy data evaluation and analysis at the hands of the clinician.
By intention, this tool has been designed to be simple to use with a minimum of mandatory options to keep the workflow streamlined, while also including a few options to go even further.
There are four simple steps to go through:
There are four simple steps to go through (see corresponding tabs in the top):
1. Import data (a spreadsheet/file on your machine, direct export from a REDCap server, or a local file provided with a package).
1. Import data (a spreadsheet/file on your machine, direct export from a REDCap server, or a local file provided with a package) to get started.
2. An *optional* step of data modification (change variable classes and creating categorical variables (factors) from numeric or time data)
@ -18,4 +18,4 @@ There are four simple steps to go through:
- Evaluation of model assumptions
4. Export the the analyses results as for MS Word or [LibreOffice](https://www.libreoffice.org/).
4. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.

4
inst/apps/teal_test/app.R
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@ -97,9 +97,9 @@ footer <- tags$p(
# redcap_browser_app <- teal_init(data = tdm_data_upload)
app <- teal::init(
# data=tdm_data_read,
data=tdm_data_read,
# data = tdm_data_upload,
data = tdm_redcap_read,
# data = tdm_redcap_read,
filter = filters,
modules = modules(
tm_data_table("Data Table"),