bumped to 25.2.1 - new visuals tab - all functions in place - code cleanup has started

inst/apps/freesearcheR/www/intro.md

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+# Welcome
+
+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. If you need more advanced tools for regression models or plotting, you'll probably be better off using *R* or similar directly on your own machine.
+
+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 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.
+
+1.  Data inspection and  modification (change variable classes, create new variables (categorical from numeric or time data, or completely new variables from the data)
+
+1.  Evaluate data using descriptive analyses methods and inspect cross-correlations
+
+1.  Create simple, clean plots for data overview.
+
+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
+
+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)!
+
+If you encounter anything strange or the app doesn't act as expected. Please [report on Github](https://github.com/agdamsbo/freesearcheR/issues).

inst/apps/freesearcheR/www/notes_visuals.md

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+# Basic visualisations
+
+This section on plotting data is kept very minimal, and includes only the most common plot types for clinical projects.
+
+If you want to go further, have a look at these sites with suggestions and sample code for data plotting:
+
+-   [*R* Charts](https://r-charts.com/): Extensive gallery with great plots
+
+-   [*R* Graph gallery](https://r-graph-gallery.com/): Another gallery with great graphs
+
+-   [grphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 

inst/apps/freesearcheR/www/report.rmd

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+---
+title: "freesearcheR data report"
+date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`"
+format: docx
+author: freesearcheR data analysis tool
+toc: false
+params:
+  data.file: NA
+---
+
+```{r setup, echo = FALSE}
+knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
+# glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}")
+```
+
+
+```{r}
+web_data <- readr::read_rds(file = params$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))
+  }
+}
+
+vec2sentence <- function(data, sep.word = "and") {
+  sep.word <- paste0(" ", gsub(" ", "", sep.word), " ")
+  if (length(data) < 2) {
+    out <- data
+  } else if (length(data) == 2) {
+    out <- paste(data, collapse = sep.word)
+  } else {
+    out <- paste(paste(data[-length(data)], collapse = ","), data[length(data)], sep = sep.word)
+  }
+  return(out)
+}
+```
+
+## 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'}
+if ("table1" %in% names(web_data)){
+tbl <- gtsummary::as_gt(web_data$table1)
+knitr::knit_print(tbl)}
+```
+
+`r if ("regression" %in% names(web_data)) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$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
+
+Good luck on your further work!

inst/apps/freesearcheR/www/umami-app.html

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