---
title: "Introduction to the wikitaxa package"
author: "Scott Chamberlain"
date: "`r Sys.Date()`"
output: 
    html_document:
        toc: true
        toc_float: true
        theme: readable
vignette: >
  %\VignetteIndexEntry{Introduction to the wikitaxa package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

`wikitaxa` - Taxonomy data from Wikipedia

The goal of `wikitaxa` is to allow search and taxonomic data retrieval from
across many Wikimedia sites, including: Wikipedia, Wikicommons, and
Wikispecies.

There are lower level and higher level parts to the package API:

### Low level API

The low level API is meant for power users and gives you more control,
but requires more knowledge.

* `wt_wiki_page()`
* `wt_wiki_page_parse()`
* `wt_wiki_url_build()`
* `wt_wiki_url_parse()`
* `wt_wikispecies_parse()`
* `wt_wikicommons_parse()`
* `wt_wikipedia_parse()`

### High level API

The high level API is meant to be easier and faster to use.

* `wt_data()`
* `wt_data_id()`
* `wt_wikispecies()`
* `wt_wikicommons()`
* `wt_wikipedia()`

Search functions:

* `wt_wikicommons_search()`
* `wt_wikispecies_search()`
* `wt_wikipedia_search()`

## Installation

CRAN version

```{r eval=FALSE}  
install.packages("wikitaxa")
```

Dev version

```{r eval=FALSE}
devtools::install_github("ropensci/wikitaxa")
```

```{r}
library("wikitaxa")
```

## wiki data

```{r eval=FALSE}
wt_data("Poa annua")
```

Get a Wikidata ID

```{r}
wt_data_id("Mimulus foliatus")
```

## wikipedia

lower level

```{r}
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
res <- wt_wiki_page_parse(pg)
res$iwlinks
```

higher level

```{r}
res <- wt_wikipedia("Malus domestica")
res$common_names
res$classification
```

choose a wikipedia language

```{r eval=FALSE}
# French
wt_wikipedia(name = "Malus domestica", wiki = "fr")
# Slovak
wt_wikipedia(name = "Malus domestica", wiki = "sk")
# Vietnamese
wt_wikipedia(name = "Malus domestica", wiki = "vi")
```

search

```{r}
wt_wikipedia_search(query = "Pinus")
```

search supports languages

```{r eval=FALSE}
wt_wikipedia_search(query = "Pinus", wiki = "fr")
```


## wikicommons

lower level

```{r}
pg <- wt_wiki_page("https://commons.wikimedia.org/wiki/Abelmoschus")
res <- wt_wikicommons_parse(pg)
res$common_names[1:3]
```

higher level

```{r}
res <- wt_wikicommons("Abelmoschus")
res$classification
res$common_names
```

search

```{r}
wt_wikicommons_search(query = "Pinus")
```


## wikispecies

lower level

```{r}
pg <- wt_wiki_page("https://species.wikimedia.org/wiki/Malus_domestica")
res <- wt_wikispecies_parse(pg, types = "common_names")
res$common_names[1:3]
```

higher level

```{r}
res <- wt_wikispecies("Malus domestica")
res$classification
res$common_names
```

search

```{r}
wt_wikispecies_search(query = "Pinus")
```
