---
title: "Validating passport data"
author: "Matija Obreza"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Validating passport data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Validating passport data
========================

[Genesys PGR](https://www.genesys-pgr.org) is the global database on plant genetic resources
maintained *ex situ* in national, regional and international genebanks around the world.

**genesysr** provides functions to check accession passport data with the [Genesys Validator](https://validator.genesys-pgr.org). This service provides
tools to check spelling of taxonomic names against the GRIN-Taxonomy database
and coordinates of the collecting site against the country of origin.

# Scientific names spell-check

The tool checks data against the GRIN-Global Taxonomy database maintained by USDA-ARS, distributed with the GRIN-Global installer. See [GRIN Taxonomy for Plants](https://npgsweb.ars-grin.gov/gringlobal/taxon/abouttaxonomy). 

Only the following MCPD columns will be checked for taxonomic data: `GENUS`, `SPECIES`, `SPAUTHOR`, `SUBTAXA`, `SUBTAUTHOR`.

|id|GENUS|SPECIES|SPAUTHOR|SUBTAXA|SUBTAUTHOR|
|--|--|--|--|--|--|
|1|Onobrychis||viciifolia|||
|2|Agrostis|tenuis|Sibth.|||
|3|Arachis|hypogaea|L.|||
|4|Arrhenatherum|elatius|(L.) J. et C.Presl.|var. elatius|(L.) J. et C.|Presl.|
|5|Avena|sativa||||
|6|Dactylis|glomerata|L.|subsp juncinella||
|7|Linum|usitatissimum|L.|var intermedium|Vav. et Ell.|
|8|Prunus|domestica|L.|subsp||domestica||
|9|Prunus||hybrid|||

```
taxaCheck <- genesysr::check_taxonomy(mcpd);
```

The validator returns all incoming columns, but annotates the taxonomic 
data with new `*_check` columns.


# Checking coordinates

Geo tests require `DECLATITUDE`, `DECLONGITUDE` and `ORIGCTY` for country border check and suggested coordinate fixes.


|...|ORIGCTY|DECLATITUDE|DECLONGITUDE|
|--|--|--|--|
|...|DEU|20|30|
|...|SVN|40|*NA*|
|...|NGA|*NA*|*NA*|
|...|GTM|-90|30|

```
geoCheck <- genesysr::check_country(mcpd)
```

The Validator returns all incoming columns, but annotates the taxonomic 
data with new `*_check` columns.