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new completeness filter, analyses have been split, correlation plot included.

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Andreas Gammelgaard Damsbo 2025-02-07 16:24:09 +01:00
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16
inst/apps/data_analysis_modules/www/intro.html
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@ -354,22 +354,21 @@ display: none;
<div id="welcome" class="section level1">
<h1>Welcome</h1>
<p>This is the <strong><em>freesearcheR</em></strong> web data analysis
<p>This is the <strong><em>freesearcheR</em></strong> data analysis
tool. We intend the <strong><em>freesearcheR</em></strong> to be a
powerful and free tool for easy data evaluation and analysis at the
hands of the clinician.</p>
<p>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.</p>
<p>There are four simple steps to go through (see corresponding tabs in
<p>There are some simple steps to go through (see corresponding tabs in
the top):</p>
<ol style="list-style-type: decimal">
<li><p>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.</p></li>
<li><p>An <em>optional</em> step of data modification (change variable
classes and creating categorical variables (factors) from numeric or
time data)</p></li>
<li><p>Inspec of data modification (change variable classes and creating
categorical variables (factors) from numeric or time data)</p></li>
<li><p>Data analysis of cross-sectionally designed studies (more study
designs are planned to be included)</p>
<ul>
@ -382,10 +381,9 @@ depending on specified outcome variable</p></li>
<li><p>Export the the analyses results for MS Word or <a href="https://www.libreoffice.org/">LibreOffice</a> as well as the data
with preserved metadata.</p></li>
</ol>
<p>Have a look at the <a href>documentations page</a> for further
project description. If you’re interested in the source code, then go
on, <a href="https://github.com/agdamsbo/freesearcheR">have a
look</a>!</p>
<p>Have a look at the <a href="https://agdamsbo.github.io/freesearcheR/">documentations page</a>
for further project description. If you’re interested in the source
code, then go on, <a href="https://github.com/agdamsbo/freesearcheR">have a look</a>!</p>
<p>If you encounter anything strange or the app doesn’t act as expected.
Please <a href="https://github.com/agdamsbo/freesearcheR/issues">report
on Github</a>.</p>

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inst/apps/data_analysis_modules/www/intro.md
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@ -1,24 +1,26 @@
# Welcome
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.
This is the ***freesearcheR*** 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 (see corresponding tabs in the top):
There are some 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) to get started.
2. An *optional* step of data modification (change variable classes and creating categorical variables (factors) from numeric or time data)
1. Data inspection and modification (change variable classes, create new variables (categorical from numeric or time data, or completely new variables from the data)
3. Data analysis of cross-sectionally designed studies (more study designs are planned to be included)
1. Evaluate data using descriptive analyses methods and inspect cross-correlations
- Classic baseline charactieristics (options to stratify and compare variables)
1. Create regression models for even more advanced data analyses
- Linear, dichotomous or ordinal logistic regression will be used depending on specified outcome variable
- Plot regression analysis coefficients
- Evaluation of model assumptions
4. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
1. Export the the analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/) as well as the data with preserved metadata.
Have a look at the [documentations page](https://agdamsbo.github.io/freesearcheR/) for further project description. If you're interested in the source code, then go on, [have a look](https://github.com/agdamsbo/freesearcheR)!

55
inst/apps/data_analysis_modules/www/report.qmd
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@ -1,55 +0,0 @@
---
title: "freesearcheR analysis results"
date: today
format: docx
author: freesearcheR Tool
toc: false
execute:
echo: false
params:
data.file: NA
---
```{r}
#| message: false
#| warning: false
web_data <- readr::read_rds(file = params$data.file)
library(gtsummary)
library(gt)
tbl_merge <- function(data) {
if (is.null(names(data))) {
data |> gtsummary::tbl_merge()
} else {
data |> gtsummary::tbl_merge(tab_spanner = names(data))
}
}
```
## Introduction
Research should be free and open with easy access for all. The freesearcheR tool attempts to help lower the bar to participate in contributing to science by making guided data analysis easily accessible in the web-browser.
## Methods
Analyses were conducted in the *freesearcheR* data analysis web-tool based on R version 4.4.1.
## Results
Below are the baseline characteristics.
```{r, results = 'asis'}
tbl <- gtsummary::as_gt(web_data$table1)
knitr::knit_print(tbl)
```
Below are the results from the
```{r, results = 'asis'}
reg_tbl <- web_data$regression$tables
knitr::knit_print(tbl_merge(reg_tbl))
```
## Discussion
Good luck on your further work!

14
inst/apps/data_analysis_modules/www/report.rmd
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@ -1,8 +1,8 @@
---
title: "freesearcheR analysis results"
date: today
title: "freesearcheR data report"
date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`"
format: docx
author: freesearcheR Tool
author: freesearcheR data analysis tool
toc: false
params:
data.file: NA
@ -10,6 +10,7 @@ params:
```{r setup, echo = FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
# glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}")
```
@ -52,15 +53,18 @@ Analyses were conducted in the *freesearcheR* data analysis web-tool based on R
Below are the baseline characteristics.
```{r, results = 'asis'}
if ("table1" %in% names(web_data)){
tbl <- gtsummary::as_gt(web_data$table1)
knitr::knit_print(tbl)
knitr::knit_print(tbl)}
```
Below are the results from the `r tolower(vec2sentence(names(web_data$regression$tables)))` `r web_data$regression$params$descr`.
`r if ("regression" %in% names(web_data)) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$regression$tables)))} {web_data$regression$params$descr}.")`
```{r, results = 'asis'}
if ("regression" %in% names(web_data)){
reg_tbl <- web_data$regression$tables
knitr::knit_print(tbl_merge(reg_tbl))
}
```
## Discussion