---
title: "1 - Read your database"
format: 
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    toc: true
vignette: >
  %\VignetteIndexEntry{1 - Read your database}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
knitr:
  opts_chunk:
    collapse: true
    comment: '#>'
---

```{r}
#| include: false
library(EDCimport)
```

## Read your database

If you are reading this vignette, chances are that you have requested an export from an EDC software that provided you with a directory filled with files of datasets.

Wouldn't it be so tedious if you had to load all those files one by one? Lucky you, EDCimport knows a better way!

Depending on the type of files in your export directory, you should use:

-   `read_all_sas()`, to read `.sas7bdat` files

-   `read_all_xpt()`, to read `.xpt` files

-   `read_all_csv()`, to read `.csv` files

-   `read_trialmaster()` to read a [TrialMaster](https://www.anjusoftware.com/trial-master/) zip archive.

Formats are imported through a metadata file, `format_file`, that can be either:

-   a `procformat.sas` file, containing the whole PROC FORMAT

-   a catalog file (`.sas7bcat`)

-   or a data file (`.csv` or `.sas7bdat`) containing 3 columns: the SAS format name (repeated), each level, and its associated label. Use `options(edc_var_format_name="xxx", edc_var_level="xxx", edc_var_label="xxx")` to specify the names of the columns.

You can then load your datasets into the global environment with `load_database()`.

``` r
library(EDCimport)
db = read_all_sas("path/to/my/files/folder", format_file="procformat.sas")
print(db)
load_database(db) #this also removes `db` to save some RAM
mean(dataset1$column5)
```

## Explore your database

Knowing a CRF by hand is not always an easy task, so EDCimport provide a few useful tools:

-   `edc_lookup()`, to remember what are the available datasets.

-   `edc_find_column()` and `edc_find_value()`, to search the database for a column/label or for an actual value.

```{r}
db = edc_example()
load_database(db)
edc_lookup()
edc_find_column("date")
edc_find_value("immune")
```

## Shiny browser

The simplest way to explore your database is by running `edc_viewer()`, which launches a local Shiny application:

``` r
db = edc_example()
load_database(db)
edc_viewer()
```

```{r, echo=FALSE, results='asis'}
if (file.exists("edc_viewer.webp")) {
  cat('![](edc_viewer.webp)')
}
```