v001-xrf.Rmd

---
title: "Reformatting and checking raw data (csv files) from the X-ray fluorescence device (ZSX Primus II, Rigaku)"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Reformatting and checking raw data (csv files) from the X-ray fluorescence device (ZSX Primus II, Rigaku)}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
bibliography: "./../inst/REFERENCES.bib"
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
# packages
library(ggplot2)
library(dplyr)
library(tidyr)
library(magrittr)
```

# Introduction

This vignette shows how to

1. Import raw data files (csv files) as exported from the X-ray fluorescence device in the lab (ZSX Primus II, Rigaku).

2. Reformat the data to get a tidy `data.frame`.

3. Check the data via plots.

4. Export the data and metadata as csv files in the tidy format.

## Data import and reformatting

Data import and reformatting are done with function `elco:elco_xrf_import_csv`:

```{r data-import}
# get names of files to import
files <- list.files("./../inst/extdata/xrf/", full.names = TRUE)

# data import
d <- elco::elco_xrf_import_csv(files = files)
```

## Data checks

To check the data, a plot is created for each measured variable and sample and points for which the calibration range was exceeded are colored.

```{r plot-check, fig.width=20, fig.height=7 * nrow(d)/50, out.width="200%"}
# plot for checking
plot(d)
```

## Data export

To export the data, use `elco::elco_xrf_export_csv`.

```{r data-export}
d <- elco::elco_xrf_export_csv(d, file = "./xrf_export.csv")
```

## License

<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br />This Rmarkdown template is licensed under the <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.

Title: Reformatting and checking raw data (csv files) from the X-ray fluorescence device (ZSX Primus II, Rigaku) <br>
Author: Henning Teickner <br>
Date: 2020-08-05 <br>

**Data:** The data are licensed under the [CC-BY-SA-4.0 license](https://creativecommons.org/licenses/by-sa/4.0/deed.en). All data for elco were provided by @Gaka.2019.

## Session Info
```{r session-info}
sessionInfo()
```

## References