rcrossref.Rmd.og

---
title: rcrossref introduction 
author: Scott Chamberlain
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
    %\VignetteIndexEntry{rcrossref introduction}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

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

## Installation

Install stable version from CRAN

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

Or development version from GitHub

```{r eval=FALSE}
remotes::install_github("ropensci/rcrossref")
```

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

## Citation search

CrossRef's DOI Content Negotiation service, where you can citations back in various formats, including `apa`

```{r}
cr_cn(dois = "10.1371/journal.pone.0112608", format = "text", style = "apa")
```

There are a lot more styles. We include a dataset as a character vector within the package, accessible via the `get_styles()` function, e.g.,

```{r}
get_styles()[1:5]
```

`bibtex`

```{r}
cat(cr_cn(dois = "10.1126/science.169.3946.635", format = "bibtex"))
```

`bibentry`

```{r}
cr_cn(dois = "10.6084/m9.figshare.97218", format = "bibentry")
```

## Citation count

Citation count, using OpenURL

```{r}
cr_citation_count(doi="10.1371/journal.pone.0042793")
```

## Search Crossref metadata API

The following functions all use the CrossRef API.

### Look up funder information

```{r}
cr_funders(query="NSF")
```

### Check the DOI minting agency

```{r}
cr_agency(dois = '10.13039/100000001')
```

### Search works (i.e., articles, books, etc.)

```{r}
cr_works(filter=c(has_orcid=TRUE, from_pub_date='2004-04-04'), limit=1)
```

### Search journals

```{r}
cr_journals(issn=c('1803-2427','2326-4225'))
```

### Search license information

```{r}
cr_licenses(query = 'elsevier')
```

### Search based on DOI prefixes

```{r}
cr_prefixes(prefixes=c('10.1016','10.1371','10.1023','10.4176','10.1093'))
```

### Search CrossRef members

```{r}
cr_members(query='ecology', limit = 5)
```

### Get N random DOIs

`cr_r()` uses the function `cr_works()` internally.

```{r}
cr_r()
```

You can pass in the number of DOIs you want back (default is 10)

```{r}
cr_r(2)
```

## Get full text

Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at https://support.crossref.org/hc/en-us/articles/215750183-Crossref-Text-and-Data-Mining-Services

Get some DOIs for articles that provide full text, and that have `CC-BY 3.0` licenses (i.e., more likely to actually be open)

```{r}
out <-
  cr_works(filter = list(has_full_text = TRUE,
    license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$doi)
```

From the output of `cr_works` we can get full text links if we know where to look:

```{r}
do.call("rbind", out$data$link)
```

From there, you can grab your full text, but because most links require
authentication, enter another package: `crminer`.

You'll need package `crminer` for the rest of the work.

Onc we have DOIs, get URLs to full text content

```{r eval=FALSE}
if (!requireNamespace("crminer")) {
  install.packages("crminer")
}
```

```{r}
library(crminer)
(links <- crm_links("10.1155/2014/128505"))
```

Then use those URLs to get full text

```{r eval=FALSE}
crm_pdf(links)
#> <document>/Users/sckott/Library/Caches/R/crminer/128505.pdf
#>   Pages: 1
#>   No. characters: 1565
#>   Created: 2014-09-15
```

See also fulltext (https://github.com/ropensci/fulltext) for getting scholarly text 
for text mining.