mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2026-06-19 04:27:30 +02:00
new working version with major updates
This commit is contained in:
parent
fb2569c647
commit
e4633421aa
16 changed files with 1678 additions and 85 deletions
|
|
@ -31,15 +31,19 @@ library(IDEAFilter)
|
|||
# }
|
||||
# library(webResearch)
|
||||
|
||||
if (file.exists(here::here("functions.R"))) {
|
||||
source(here::here("functions.R"))
|
||||
}
|
||||
source(here::here("functions.R"))
|
||||
|
||||
server <- function(input, output, session) {
|
||||
## Listing files in www in session start to keep when ending and removing
|
||||
## everything else.
|
||||
files.to.keep <- list.files("www/")
|
||||
|
||||
output$docs_file <- renderUI({
|
||||
# shiny::includeHTML("www/docs.html")
|
||||
HTML(readLines("www/docs.html"))
|
||||
})
|
||||
|
||||
|
||||
rv <- shiny::reactiveValues(
|
||||
list = NULL,
|
||||
ds = NULL,
|
||||
|
|
@ -193,7 +197,7 @@ server <- function(input, output, session) {
|
|||
)
|
||||
|
||||
output$original_str <- renderPrint({
|
||||
str(ds())
|
||||
str(rv$data_original)
|
||||
})
|
||||
|
||||
output$modified_str <- renderPrint({
|
||||
|
|
@ -290,25 +294,25 @@ server <- function(input, output, session) {
|
|||
## Have a look at column filters at some point
|
||||
## There should be a way to use the filtering the filter data for further analyses
|
||||
## Disabled for now, as the JS is apparently not isolated
|
||||
output$data_table <-
|
||||
DT::renderDT(
|
||||
{
|
||||
DT::datatable(ds()[base_vars()])
|
||||
},
|
||||
server = FALSE
|
||||
)
|
||||
|
||||
output$data.classes <- gt::render_gt({
|
||||
shiny::req(input$file)
|
||||
data.frame(matrix(sapply(ds(), \(.x){
|
||||
class(.x)[1]
|
||||
}), nrow = 1)) |>
|
||||
stats::setNames(names(ds())) |>
|
||||
gt::gt()
|
||||
})
|
||||
# output$data_table <-
|
||||
# DT::renderDT(
|
||||
# {
|
||||
# DT::datatable(ds()[base_vars()])
|
||||
# },
|
||||
# server = FALSE
|
||||
# )
|
||||
#
|
||||
# output$data.classes <- gt::render_gt({
|
||||
# shiny::req(input$file)
|
||||
# data.frame(matrix(sapply(ds(), \(.x){
|
||||
# class(.x)[1]
|
||||
# }), nrow = 1)) |>
|
||||
# stats::setNames(names(ds())) |>
|
||||
# gt::gt()
|
||||
# })
|
||||
|
||||
shiny::observeEvent(input$act_start, {
|
||||
bslib::nav_select(id = "main_panel", selected = "Overview and modifications")
|
||||
bslib::nav_select(id = "main_panel", selected = "Modifications")
|
||||
})
|
||||
|
||||
shiny::observeEvent(
|
||||
|
|
|
|||
|
|
@ -30,17 +30,22 @@ ui_elements <- list(
|
|||
shinyWidgets::radioGroupButtons(
|
||||
inputId = "source",
|
||||
# label = "Choice: ",
|
||||
choices = c("File upload" = "file", "REDCap server" = "redcap","Sample data"="env"),
|
||||
checkIcon = list(
|
||||
yes = icon("square-check"),
|
||||
no = icon("square")
|
||||
)
|
||||
choices = c(
|
||||
"File upload" = "file",
|
||||
"REDCap server" = "redcap",
|
||||
"Sample 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")
|
||||
title = "Choose a datafile to upload",
|
||||
file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
|
|
@ -57,13 +62,7 @@ ui_elements <- list(
|
|||
),
|
||||
column(
|
||||
width = 6,
|
||||
shiny::markdown("
|
||||
# Welcome
|
||||
|
||||
This is the ***freesearchR*** web data analysis tool. An opiniotaed tool for easy data analysis at the hands of the clinician.
|
||||
|
||||
By intention, this is a focused app, with only few data modification tools included to keep the workflow streamlined.
|
||||
")
|
||||
shiny::markdown(readLines("www/intro.md"))
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
|
|
@ -79,10 +78,10 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"overview" =
|
||||
# bslib::nav_panel_hidden(
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "overview",
|
||||
title = "Overview and modifications",
|
||||
title = "Modifications",
|
||||
bslib::navset_bar(
|
||||
fillable = TRUE,
|
||||
# bslib::nav_panel(
|
||||
|
|
@ -170,7 +169,7 @@ ui_elements <- list(
|
|||
#########
|
||||
##############################################################################
|
||||
"analyze" =
|
||||
# bslib::nav_panel_hidden(
|
||||
# bslib::nav_panel_hidden(
|
||||
bslib::nav_panel(
|
||||
# value = "analyze",
|
||||
title = "Analyses",
|
||||
|
|
@ -230,8 +229,8 @@ 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 = "primary",
|
||||
auto_reset = TRUE
|
||||
|
|
@ -260,7 +259,8 @@ ui_elements <- list(
|
|||
##############################################################################
|
||||
"docs" = bslib::nav_panel(
|
||||
title = "Documentation",
|
||||
shiny::markdown(readLines(here::here("inst/apps/data_analysis_modules/www/intro.md"))),
|
||||
# shiny::tags$iframe("www/docs.html", height=600, width=535),
|
||||
shiny::htmlOutput("docs_file"),
|
||||
shiny::br()
|
||||
)
|
||||
)
|
||||
|
|
|
|||
69
inst/apps/data_analysis_modules/www/docs.html
Normal file
69
inst/apps/data_analysis_modules/www/docs.html
Normal file
|
|
@ -0,0 +1,69 @@
|
|||
<!DOCTYPE html>
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
|
||||
|
||||
<meta charset="utf-8">
|
||||
<meta name="generator" content="quarto-1.5.57">
|
||||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
|
||||
|
||||
|
||||
<title>freesearcheR platform documentation</title>
|
||||
<style>
|
||||
code{white-space: pre-wrap;}
|
||||
span.smallcaps{font-variant: small-caps;}
|
||||
div.columns{display: flex; gap: min(4vw, 1.5em);}
|
||||
div.column{flex: auto; overflow-x: auto;}
|
||||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||||
ul.task-list{list-style: none;}
|
||||
ul.task-list li input[type="checkbox"] {
|
||||
width: 0.8em;
|
||||
margin: 0 0.8em 0.2em -1em; vertical-align: middle;
|
||||
}
|
||||
.display.math{display: block; text-align: center; margin: 0.5rem auto;}
|
||||
</style>
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<header id="title-block-header">
|
||||
<h1 class="title"><strong><em>freesearcheR</em></strong> platform documentation</h1>
|
||||
|
||||
</header>
|
||||
|
||||
|
||||
<h1 id="welcome">Welcome!</h1>
|
||||
<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>
|
||||
<h2 id="roadmap">Roadmap</h2>
|
||||
<ul>
|
||||
<li><p><label><input type="checkbox">Stratified analyses</label></p></li>
|
||||
<li><p>Additional study designs:</p>
|
||||
<ul class="task-list">
|
||||
<li><p><label><input type="checkbox" checked>Cross-sectional data analyses</label></p></li>
|
||||
<li><p><label><input type="checkbox">Longitudinal data analyses</label></p></li>
|
||||
<li><p><label><input type="checkbox">Survival analysis</label></p></li>
|
||||
</ul></li>
|
||||
<li><p>More detailed variable browser</p>
|
||||
<ul class="task-list">
|
||||
<li><p><label><input type="checkbox">Add histograms for data distribution</label></p></li>
|
||||
<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">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">More options for date/datetime/time grouping/factoring</label></p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body></html>
|
||||
34
inst/apps/data_analysis_modules/www/docs.md
Normal file
34
inst/apps/data_analysis_modules/www/docs.md
Normal file
|
|
@ -0,0 +1,34 @@
|
|||
# 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
|
||||
45
inst/apps/data_analysis_modules/www/docs.qmd
Normal file
45
inst/apps/data_analysis_modules/www/docs.qmd
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
---
|
||||
title: "***freesearcheR*** platform documentation"
|
||||
format:
|
||||
html:
|
||||
self-contained: true
|
||||
minimal: true
|
||||
---
|
||||
|
||||
# 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.
|
||||
|
||||
## 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).
|
||||
|
||||
## Roadmap
|
||||
|
||||
- [ ] Stratified analyses
|
||||
|
||||
- Additional study designs:
|
||||
|
||||
- [x] Cross-sectional data analyses
|
||||
|
||||
- [ ] Longitudinal data analyses
|
||||
|
||||
- [ ] Survival analysis
|
||||
|
||||
- More detailed variable browser
|
||||
|
||||
- [ ] Add histograms for data distribution
|
||||
|
||||
- [ ] Option to edit variable labels for nicer tables
|
||||
|
||||
- [ ] Plot regression analyses results
|
||||
|
||||
- [ ] Export modified data
|
||||
|
||||
- [ ] Include reproducible code for all steps
|
||||
|
||||
- [ ] Modify factor levels (including naming, order, collapsing, removing)
|
||||
|
||||
- [ ] More options for date/datetime/time grouping/factoring
|
||||
|
|
@ -1,3 +1,21 @@
|
|||
# Intro to webResearch/freesearcheR/VOICE
|
||||
# Welcome
|
||||
|
||||
This is just placeholder text.
|
||||
This is the ***freesearchR*** web data analysis tool. The ***freesearchR*** is an opinioated tool for easy data evaluation and analysis at the hands of the clinician. We intend it to be a powerful to, that is easy and secure to use.
|
||||
|
||||
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:
|
||||
|
||||
1. Import data (this can be a spreadsheet on your machine or direct export from a REDCap server)
|
||||
|
||||
2. A *optional* step of data modification (change variable classes and creating categorical variables (factors) from numeric or time data)
|
||||
|
||||
3. Data analysis of cross-sectionally designed studies
|
||||
|
||||
- Classic baseline charactieristics (options to stratify and compare variables)
|
||||
|
||||
- Linear, dichotomous or ordinal logistic regression will be used depending on specified outcome variable
|
||||
|
||||
- Evaluation of model assumptions
|
||||
|
||||
4. Export the the analyses results as .docx or .odt.
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue