make_data.Rmd

---
title: "Preparing the data"
csl: the-american-naturalist.csl
output:
  html_document:
    theme: cerulean
    toc: yes
  pdf_document:
    toc: yes
<!-- bibliography: references.bib -->
---

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REFERENCES:
For references: Put all the bibTeX references in the file "references.bib"
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<style type="text/css">
.main-container {
  max-width: 1370px;
  margin-left: auto;
  margin-right: auto;
}
</style>

```{r general options, include = FALSE}
knitr::knit_hooks$set(
  margin = function(before, options, envir) {
    if (before) par(mgp = c(1.5, .5, 0), bty = "n", plt = c(.105, .97, .13, .97))
    else NULL
  },
  prompt = function(before, options, envir) {
    options(prompt = if (options$engine %in% c("sh", "bash")) "$ " else "> ")
  })

knitr::opts_chunk$set(margin = TRUE, prompt = TRUE, comment = "",
                      collapse = TRUE, cache = FALSE, autodep = TRUE,
                      dev.args = list(pointsize = 11), fig.height = 3.5,
                      fig.width = 4.24725, fig.retina = 2, fig.align = "center")

options(width = 137)
```

## Packages

Installing the required packages:

```{r}
required <- c("magrittr", "readr")
to_install <- setdiff(required, row.names(installed.packages()))
if (length(to_install)) install.packages(to_install)
```

Loading `magrittr`:

```{r}
library(magrittr)
```

## Loading the data ViParc data

```{r}
viparc <- readr::read_csv("https://raw.githubusercontent.com/viparc/clires_data/master/data/viparc.csv",
                          col_types = paste(c("ciillidddllllll", rep("d", 45)), collapse = ""))
```

## Transforming the AMU into qualitative information

If you want to transform the data regarding AMU into qualitative information,
here is the way to do:

```{r}
if (!dir.exists("data")) dir.create("data")
viparc %>%
  dplyr::mutate_at(dplyr::vars(dplyr::ends_with("_g")), list(~ . > 0)) %>%
  dplyr::rename_at(dplyr::vars(dplyr::ends_with("_g")), function(x) sub("_g$", "_use", x)) %>% 
  dplyr::select(-completed, -sampling) %>% 
  write.csv("data/viparc_qualitative.csv", FALSE, row.names = FALSE)
```