---
title: "Create tables for EPPO Pest Risk Assessment"
output:
  rmarkdown::html_vignette:
    css: alert_style.css
vignette: >
  %\VignetteIndexEntry{Create tables for EPPO Pest Risk Assessment}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = FALSE,
  fig.show = "hold",
  fig.width = 7,
  fig.height = 5
)
```

<!-- logo: start -->

<img src="https://raw.githubusercontent.com/mczyzj/pestr/master/inst/figures/pestr-hex_center.png" width="250px" align="right" alt="pestr package hexsticker" style="border: 0px"/>

<!-- logo: end -->

```{r setup}
### Load packages
library("pestr")
library("dplyr")
```

# Overview

**EPPO** *Express Pest Risk Analysis* -- [PM5/5(1) Additional guidance](https://www.eppo.int/RESOURCES/eppo_standards/pm5_pra) -- requires information that can be easily obtained using `pestr` package functions. Particularly the information needed for *Stage 2. Pest Risk Assessment*:

* **1. Taxonomy** -- `eppo_tabletools_taxo`, `eppo_names_tables`
* **2. Pest overview** -- `eppo_tabletools_hosts`
* **5. Regulatory status of the pest** -- `eppo_tabletools_cat`
* **6. Distribution -- `eppo_tabletools_distri`**
* **7. Host plants / habitats and their distribution in the PRA area**  -- `eppo_tabletools_hosts`

For the purpose of this vignette, lets assume that you are working on well known pest -- *Anoplophora chinensis*. This beetle is know for it's voracious larvae which bore into the wood of living trees. More detailed info can be found at [EPPO Datasheet: Anoplophora chinensis](https://gd.eppo.int/taxon/ANOLCN/datasheet).

<div class="alert alert-warning">

**Please** bear in mind that the workflow presented in this vignette can be also adjusted to other *Pest Risk Analyses / Assessments* of other authorities with some basic knowledge on `R` tools like `dplyr`, `tidyr` or `stringr`. 

</div>

Prior to downloading data, please ensure that you set up variables.

```{r eval = FALSE, echo = TRUE}
### assign token to variable
eppo_token <- create_eppo_token("<<your eppo token>>")
### assign name to variable
ac_name <- "Anoplophora chinensis"
### assign eppocode to variable
ac_eppocode <- "ANOLCN" 
### assign database connection to variable
eppoDB <- eppo_database_connect()
```

## Taxonomy and names of pest

```{r eval = FALSE, echo = TRUE}
ac_names_table <- eppo_names_tables(ac_name, eppo_DB)

ac_other_names <- eppo_tabletools_names(ac_names_table) %>%
  .[2] %>%
  dplyr::select(Other_names) %>%
  unlist()

ac_taxonomy <- eppo_tabletools_taxo(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )
```

## Host of pest -- as text or as table

```{r eval = FALSE, echo = TRUE}
ac_hosts <- eppo_tabletools_hosts(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )
```

## Categorization table

```{r eval = FALSE, echo = TRUE}
ac_categorization <- eppo_tabletools_cat(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )
```

## Distribution of pest

```{r eval = FALSE, echo = TRUE}
ac_distribution <- eppo_tabletools_distri(
  token = eppo_token,
  raw_eppocodes = ac_eppocode,
  use_raw_codes = TRUE
  )
```