---
title: "FreesearchR"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{FreesearchR}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,eval = FALSE)
library(FreesearchR)
```

# Getting started with ***FreesearchR***

Below is a simple walk-trough and basic instructions for the functions on the FreesearchR app.

## Launching

The easiest way to get started is to launch [the hosted version of the app on shinyapps.io (click this link)](https://agdamsbo.shinyapps.io/freesearcheR/).

Additionally you have the option to run the app locally with access to any data in your current working environment.

To do this, open *R* (or RStudio or similar), and run the following code to install the latest version of ***FreesearchR*** and launch the app:

```{r}
require("pak")
pak::pak("agdamsbo/FreesearchR")
library(FreesearchR)
FreesearchR::launch_FreesearchR()
```

As a small note, a standalone Windows app version is on the drawing board as well, but no time frame is available.

## Importing data

Once in the app and in the "**Import**", you have three options available for importing data: file upload, REDCap server export and local or sample data.

After choosing a data source, you can set a threshold to filter data be completenes and further manually specify variables to include for analyses.

### File upload

Currently several data file formats are supported for easy import (csv, txt, xls(x), ods, rds, dta). If importing workbooks (xls(x) or ods), you are prompted to specify sheet(s) to import. If choosing multiple sheets, these are automatically merged by common variable(s), so please make sure that key variables are correctly named identically.

A notification is posted with error or success. After succesfull import data can be previewed directly by clicking "click to see data" in the notification.

### REDCap server export

Export data directly from a REDCap server. You need to first generate an API-token ([see these instruction](https://confluence.research.cchmc.org/pages/viewpage.action?pageId=50987698)) in REDCap. Make sure you have the necessary rights to do so.

Please don't store the API-key on your device unless encrypted or in a keyring, as this may compromise data safety. Log in to your REDCap server and retrieve the token when needed.

Type the correct webaddress of your REDCap server.

The module will validate the information and you can click "Connect".

This will unfold options to preview your data dictionary (the main database metadata), choose fields/variables to download as well as filtering options.

### Local or sample data

## Evaluate

### Baseline

### Correlation matrix

## Visuals

There are a number of plotting options to visualise different aspects of the data.

Below are the available plot types listed.

```{r echo = FALSE, eval = TRUE}
c("continuous", "dichotomous", "ordinal", "categorical") |> 
  lapply(\(.x){
    dplyr::bind_cols(
      dplyr::tibble("Data type"=.x),
      supported_plots() |> 
      lapply(\(.y){
        if (.x %in% .y$primary.type){
          .y[c("descr","note")]|> dplyr::bind_cols()
        }
})|> 
  dplyr::bind_rows() |> 
  setNames(c("Plot type","Description")))
  }) |> 
  dplyr::bind_rows() |> 
  toastui::datagrid(filters=TRUE,theme="striped")
```

## Regression

## Download

### Report

### Data

### Code
