publishing with docker

app_docker/.dockerignore

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+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+.Rproj.user

app_docker/Dockerfile

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+FROM rocker/geospatial:4.4.1
+RUN apt-get update -y && apt-get install -y  cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libfftw3-dev libsodium-dev && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
+RUN R -e 'install.packages("remotes")'
+RUN R -e 'remotes::install_version("renv", version = "1.1.4")'
+COPY renv.lock renv.lock
+RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()'
+WORKDIR /srv/shiny-server/
+COPY . /srv/shiny-server/
+EXPOSE 3838
+CMD R -e 'shiny::runApp("/srv/shiny-server",host="0.0.0.0",port=3838)'

app_docker/www/intro.md

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+# Welcome <img style="float: right;" src="FreesearchR-logo.png">
+
+This is the ***FreesearchR*** data analysis tool. We intend ***FreesearchR*** to be a free tool for easy data evaluation and analysis. If you need more advanced tools, start with ***FreesearchR*** and then you'll probably be better off using *R* or similar directly.
+
+Here is a brief summary of the functions:
+
+1.  **Import data** from a spreadsheet/file on your machine, direct export from a REDCap server, sample data or data from a your local environment if run locally.
+
+1.  **Data inspection** and  **modification** like modifying variables or creating new (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 and export simple, clean plots** for data overview and insights
+
+1.  **Create regression simple 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
+
+    -   Evaluate model assumptions
+
+1.  **Export results**
+
+    -   Descriptive and regression analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/)
+    
+    -   Modified data with preserved metadata
+    
+    -   Code to recreate all steps locally
+
+The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8).

app_docker/www/references.bib

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+
+@book{andreasgammelgaarddamsbo2025,
+	title = {agdamsbo/FreesearchR: FreesearchR 25.4.3},
+	author = {Damsbo, Andreas Gammelgaard},
+	year = {2025},
+	month = {04},
+	date = {2025-04-24},
+	publisher = {Zenodo},
+	doi = {10.5281/ZENODO.14527429},
+	url = {https://zenodo.org/doi/10.5281/zenodo.14527429}
+}

app_docker/www/report.rmd

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+---
+title: "FreesearchR data report"
+date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`"
+format: docx
+author: FreesearchR data analysis tool
+toc: false
+params:
+  data.file: NA
+  version: NA
+  regression.p: 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)
+# web_data <- readr::read_rds(file = "~/FreesearchR/inst/apps/FreesearchR/www/web_data.rds")
+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 *FreesearchR* tool attempts to help lower the bar to participate in research by making basic data exploration and analyses easily accessible.
+
+## Methods
+
+Analyses were conducted using the *FreesearchR* data analysis web-tool version `r params$version` based on *R* version 4.4.1.
+
+## Results
+
+Below are the baseline characteristics.
+
+```{r, results = 'asis'}
+if ("table1" %in% names(web_data)) {
+  tbl <- gtsummary::as_gt(web_data$table1)
+  knitr::knit_print(tbl)
+}
+```
+
+`r if (length(web_data$regression) > 0) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$regression$regression$tables)))} {web_data$regression$regression$params$descr}.")`
+
+```{r, results = 'asis'}
+if ("regression" %in% names(web_data) && length(web_data$regression) > 0) {
+  reg_tbl <- web_data$regression$regression$tables
+  
+  merged <- tbl_merge(reg_tbl)
+  
+  if (params$regression.p == "no") {
+            merged <- merged |>
+              gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
+          }
+  
+  knitr::knit_print(merged)
+}
+```
+
+## Discussion
+
+Good luck on your further work!

app_docker/www/style.css

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+
+/*!
+ * Copyright (c) 2025 FreesearchR
+ *
+ * FreesearchR, CSS styles
+ * https://github.com/agdamsbo/FreesearchR
+ *
+ * @version 0.0.1
+ */
+
+.container-fluid > .nav > li >
+                        a[data-value='FreesearchR'] {font-size: 28px}
+
+
+/* from datamods */
+.show-block {
+  display: block !important;
+}
+.show-inline {
+  display: inline !important;
+}
+.hidden {
+  display: none !important;
+}
+.invisible {
+  visibility: hidden;
+}
+
+.container-rule {
+  position: relative;
+  text-align: center;
+  height: 25px;
+  margin-bottom: 5px;
+}
+
+.horizontal-rule {
+  position: absolute;
+  top: 11px;
+  right: 0;
+  left: 0;
+  background-color: #d0cfcf;
+  height: 1px;
+  z-index: 100;
+  margin: 0;
+  border: none;
+}
+
+.label-rule {
+  background: #FFF;
+  opacity: 1;
+  z-index: 101;
+  background-color: #FFF;
+  position: relative;
+  padding: 0 10px 0 10px;
+}
+
+.datamods-table-container {
+  overflow: auto;
+  word-break: keep-all;
+  white-space: nowrap;
+}
+
+.datamods-table-container > .table {
+  margin-bottom: 0 !important;
+}
+
+.datamods-file-import {
+  display: grid;
+  grid-template-columns: auto 50px;
+  grid-column-gap: 10px;
+}
+
+.datamods-dt-nowrap {
+  word-break: keep-all;
+  white-space: nowrap;
+}
+
+
+
+/* validation */
+.datamods-validation-results {
+  display: grid;
+  grid-template-columns: repeat(3, 1fr);
+  grid-template-rows: 1fr;
+  height: 50px;
+  line-height: 50px;
+  font-size: large;
+}
+
+.datamods-validation-summary {
+  font-weight: bold;
+  text-align: center;
+}
+
+.datamods-validation-item {
+  font-size: larger;
+}
+
+
+
+/* modified from esquisse for data types */
+.btn-column-categorical {
+  background-color: #00C896;
+  color: #FFFFFF;
+}
+.btn-column-continuous {
+  background-color: #FFB100;
+  color: #FFFFFF;
+}
+.btn-column-dichotomous {
+  background-color: #8A4FFF;
+  color: #FFFFFF;
+}
+.btn-column-datetime {
+  background-color: #11A0EC;
+  color: #FFFFFF;
+}
+.btn-column-id {
+  background-color: #848484;
+  color: #FFFFFF;
+}
+.btn-column-text {
+  background-color: #2E2E2E;
+  color: #FFFFFF;
+}

app_docker/www/umami-app.html

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+<script defer src="https://stats.freesearchr.org/script.js" data-website-id="63976000-9836-45bc-90da-37ec5717fb22"></script>