Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ropensci-archive/rplos
:warning: ARCHIVED :warning: R client for the PLoS Journals API
https://github.com/ropensci-archive/rplos
metadata pdf plos r r-package rstats text-mining web-api xml
Last synced: 3 months ago
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:warning: ARCHIVED :warning: R client for the PLoS Journals API
- Host: GitHub
- URL: https://github.com/ropensci-archive/rplos
- Owner: ropensci-archive
- License: other
- Archived: true
- Created: 2011-06-02T01:06:42.000Z (over 13 years ago)
- Default Branch: master
- Last Pushed: 2022-09-09T12:06:05.000Z (about 2 years ago)
- Last Synced: 2024-07-18T20:39:02.773Z (4 months ago)
- Topics: metadata, pdf, plos, r, r-package, rstats, text-mining, web-api, xml
- Language: R
- Homepage:
- Size: 4.82 MB
- Stars: 312
- Watchers: 69
- Forks: 106
- Open Issues: 0
-
Metadata Files:
- Readme: README-not.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
rplos
=====
[](https://www.repostatus.org/#active)
[](https://cranchecks.info/pkgs/rplos)
[](https://github.com/ropensci/rplos/actions?query=workflow%3AR-check)
[](https://codecov.io/github/ropensci/rplos?branch=master)
[](https://github.com/r-hub/cranlogs.app)
[](https://cran.r-project.org/package=rplos)
## Install
You can get this package at CRAN [here](https://cran.r-project.org/package=rplos), or install it within R by doing
```r
install.packages("rplos")
```
Or install the development version from GitHub
```r
remotes::install_github("ropensci/rplos")
```
```r
library("rplos")
```
## What is this?
`rplos` is a package for accessing full text articles from the Public Library of Science journals using their API.
## Information
You used to need a key to use `rplos` - you no longer do as of 2015-01-13 (or `v0.4.5.999`).
rplos vignetttes:
PLOS API documentation:
PLOS Solr schema is at but is 1.5 years old so may not be up to date.
Crossref API documentation can be found at . See also [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.
## Throttling
Beware, PLOS recently has started throttling requests. That is,
they will give error messages like "(503) Service Unavailable -
The server cannot process the request due to a high load", which
means you've done too many requests in a certain time period. Here's
[what they say](http://api.plos.org/solr/faq/#solr_api_recommended_usage) on the matter:
> Please limit your API requests to 7200 requests a day, 300 per hour, 10 per minute and allow 5 seconds for your search to return results. If you exceed this threshold, we will lock out your IP address. If you're a high-volume user of the PLOS Search API and need more API requests a day, please contact us at [email protected] to discuss your options. We currently limit API users to no more than five concurrent connections from a single IP address.
## Quick start
### Search
Search for the term ecology, and return id (DOI) and publication date, limiting to 5 items
```r
searchplos('ecology', 'id,publication_date', limit = 5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 55873 0
#>
#> $data
#> # A tibble: 5 x 2
#> id publication_date
#>
#> 1 10.1371/journal.pone.0001248 2007-11-28T00:00:00Z
#> 2 10.1371/journal.pone.0059813 2013-04-24T00:00:00Z
#> 3 10.1371/journal.pone.0080763 2013-12-10T00:00:00Z
#> 4 10.1371/journal.pone.0246749 2021-02-08T00:00:00Z
#> 5 10.1371/journal.pone.0220747 2019-08-01T00:00:00Z
```
Get DOIs for full article in PLoS One
```r
searchplos(q="*:*", fl='id', fq=list('journal_key:PLoSONE',
'doc_type:full'), limit=5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 246927 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#>
#> 1 10.1371/journal.pone.0002399
#> 2 10.1371/journal.pone.0002401
#> 3 10.1371/journal.pone.0002403
#> 4 10.1371/journal.pone.0002405
#> 5 10.1371/journal.pone.0002407
```
Query to get some PLOS article-level metrics, notice difference between two outputs
```r
out <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'), fq='doc_type:full')
out_sorted <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),
fq='doc_type:full', sort='counter_total_all desc')
head(out$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_all
#>
#> 1 10.1371/journal.pcbi.0020071 0 17862
#> 2 10.1371/journal.pbio.1000152 0 7180
#> 3 10.1371/journal.pbio.1000153 5 27702
#> 4 10.1371/journal.pbio.1000159 0 14256
#> 5 10.1371/journal.pbio.1000165 8 30629
#> 6 10.1371/journal.pbio.1000166 0 6884
head(out_sorted$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_all
#>
#> 1 10.1371/journal.pmed.0020124 3890 3226572
#> 2 10.1371/journal.pone.0133079 312 2481307
#> 3 10.1371/journal.pcbi.1003149 216 1766230
#> 4 10.1371/journal.pmed.1000376 9 1213573
#> 5 10.1371/journal.pone.0141854 3804 996693
#> 6 10.1371/journal.pcbi.0030102 65 986338
```
A list of articles about social networks that are popular on a social network
```r
searchplos(q="*:*",fl=c('id','alm_twitterCount'),
fq=list('doc_type:full','subject:"Social networks"','alm_twitterCount:[100 TO 10000]'),
sort='counter_total_month desc')
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 64 0
#>
#> $data
#> # A tibble: 10 x 2
#> id alm_twitterCount
#>
#> 1 10.1371/journal.pmed.1000316 1199
#> 2 10.1371/journal.pone.0069841 896
#> 3 10.1371/journal.pone.0073791 1884
#> 4 10.1371/journal.pcbi.1005399 604
#> 5 10.1371/journal.pcbi.1007513 122
#> 6 10.1371/journal.pone.0236517 123
#> 7 10.1371/journal.pbio.1002195 778
#> 8 10.1371/journal.pone.0118093 133
#> 9 10.1371/journal.pone.0155923 200
#> 10 10.1371/journal.pone.0162678 172
```
Show all articles that have these two words less then about 15 words apart
```r
searchplos(q='everything:"sports alcohol"~15', fl='title', fq='doc_type:full', limit=3)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 163 0
#>
#> $data
#> # A tibble: 3 x 1
#> title
#>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s…
#> 2 Alcohol intoxication at Swedish football matches: A study using biological sa…
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incident S…
```
Narrow results to 7 words apart, changing the ~15 to ~7
```r
searchplos(q='everything:"sports alcohol"~7', fl='title', fq='doc_type:full', limit=3)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 91 0
#>
#> $data
#> # A tibble: 3 x 1
#> title
#>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s…
#> 2 Alcohol intoxication at Swedish football matches: A study using biological sa…
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incident S…
```
Remove DOIs for annotations (i.e., corrections) and Viewpoints articles
```r
searchplos(q='*:*', fl=c('id','article_type'),
fq=list('-article_type:correction','-article_type:viewpoints'), limit=5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 2434439 0
#>
#> $data
#> # A tibble: 5 x 2
#> id article_type
#>
#> 1 10.1371/journal.pbio.1000146/title Unsolved Mystery
#> 2 10.1371/journal.pbio.1000146/abstract Unsolved Mystery
#> 3 10.1371/journal.pbio.1000146/references Unsolved Mystery
#> 4 10.1371/journal.pbio.1000146/body Unsolved Mystery
#> 5 10.1371/journal.pbio.1000146/supporting_information Unsolved Mystery
```
### Faceted search
Facet on multiple fields
```r
facetplos(q='alcohol', facet.field=c('journal','subject'), facet.limit=5)
#> $facet_queries
#> NULL
#>
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 5 x 2
#> term value
#>
#> 1 plos one 31656
#> 2 plos genetics 702
#> 3 plos medicine 699
#> 4 plos neglected tropical diseases 637
#> 5 plos pathogens 459
#>
#> $facet_fields$subject
#> # A tibble: 5 x 2
#> term value
#>
#> 1 biology and life sciences 33275
#> 2 medicine and health sciences 30309
#> 3 research and analysis methods 17340
#> 4 biochemistry 14587
#> 5 physical sciences 12502
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
```
Range faceting
```r
facetplos(q='*:*', url=url, facet.range='counter_total_all',
facet.range.start=5, facet.range.end=100, facet.range.gap=10)
#> $facet_queries
#> NULL
#>
#> $facet_fields
#> NULL
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> $facet_ranges$counter_total_all
#> # A tibble: 10 x 2
#> term value
#>
#> 1 5 39
#> 2 15 12
#> 3 25 33
#> 4 35 47
#> 5 45 47
#> 6 55 44
#> 7 65 59
#> 8 75 80
#> 9 85 114
#> 10 95 136
```
### Highlight searches
Search for and highlight the term _alcohol_ in the abstract field only
```r
(out <- highplos(q='alcohol', hl.fl = 'abstract', rows=3))
#> $`10.1371/journal.pone.0218147`
#> $`10.1371/journal.pone.0218147`$abstract
#> [1] "Background: Binge drinking, an increasingly common form of alcohol use disorder, is associated"
#>
#>
#> $`10.1371/journal.pone.0138021`
#> $`10.1371/journal.pone.0138021`$abstract
#> [1] "Background and Aim: Harmful alcohol consumption has long been recognized as being the major"
#>
#>
#> $`10.1371/journal.pone.0201042`
#> $`10.1371/journal.pone.0201042`$abstract
#> [1] "\nAcute alcohol administration can lead to a loss of control over drinking. Several models argue"
```
And you can browse the results in your default browser
```r
highbrow(out)
```
### Full text urls
Simple function to get full text urls for a DOI
```r
full_text_urls(doi='10.1371/journal.pone.0086169')
#> [1] "http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0086169&type=manuscript"
```
### Full text xml given a DOI
```r
(out <- plos_fulltext(doi='10.1371/journal.pone.0086169'))
#> 1 full-text articles retrieved
#> Min. Length: 110717 - Max. Length: 110717
#> DOIs: 10.1371/journal.pone.0086169 ...
#>
#> NOTE: extract xml strings like output['']
```
Then parse the XML any way you like, here getting the abstract
```r
library("XML")
xpathSApply(xmlParse(out$`10.1371/journal.pone.0086169`), "//abstract", xmlValue)
#> [1] "Mammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daughters, however few studies have addressed sex-biased milk synthesis. Here we leverage the dairy cow model to investigate such phenomena. Using 2.39 million lactation records from 1.49 million dairy cows, we demonstrate that the sex of the fetus influences the capacity of the mammary gland to synthesize milk during lactation. Cows favor daughters, producing significantly more milk for daughters than for sons across lactation. Using a sub-sample of this dataset (N = 113,750 subjects) we further demonstrate that the effects of fetal sex interact dynamically across parities, whereby the sex of the fetus being gestated can enhance or diminish the production of milk during an established lactation. Moreover the sex of the fetus gestated on the first parity has persistent consequences for milk synthesis on the subsequent parity. Specifically, gestation of a daughter on the first parity increases milk production by ∼445 kg over the first two lactations. Our results identify a dramatic and sustained programming of mammary function by offspring in utero. Nutritional and endocrine conditions in utero are known to have pronounced and long-term effects on progeny, but the ways in which the progeny has sustained physiological effects on the dam have received little attention to date."
```
### Search within a field
There are a series of convience functions for searching within sections of articles.
* `plosauthor()`
* `plosabstract()`
* `plosfigtabcaps()`
* `plostitle()`
* `plossubject()`
For example:
```r
plossubject(q='marine ecology', fl = c('id','journal'), limit = 10)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#>
#> 1 2287 0
#>
#> $data
#> # A tibble: 10 x 2
#> id journal
#>
#> 1 10.1371/journal.pone.0092590 PLoS ONE
#> 2 10.1371/journal.pone.0092590/title PLoS ONE
#> 3 10.1371/journal.pone.0092590/abstract PLoS ONE
#> 4 10.1371/journal.pone.0092590/references PLoS ONE
#> 5 10.1371/journal.pone.0092590/body PLoS ONE
#> 6 10.1371/journal.pone.0092590/introduction PLoS ONE
#> 7 10.1371/journal.pone.0092590/results_and_discussion PLoS ONE
#> 8 10.1371/journal.pone.0092590/materials_and_methods PLoS ONE
#> 9 10.1371/journal.pone.0092590/conclusions PLoS ONE
#> 10 10.1371/journal.pone.0149852 PLOS ONE
```
However, you can always just do this in `searchplos()` like `searchplos(q = "subject:science")`. See also the `fq` parameter. The above convenience functions are simply wrappers around `searchplos`, so take all the same parameters.
### Search by article views
Search with term _marine ecology_, by field _subject_, and limit to 5 results
```r
plosviews(search='marine ecology', byfield='subject', limit=5)
#> id counter_total_all
#> 5 10.1371/journal.pone.0012946 5309
#> 3 10.1371/journal.pone.0167128 5423
#> 1 10.1371/journal.pone.0092590 12839
#> 2 10.1371/journal.pone.0149852 18954
#> 4 10.1371/journal.pone.0011372 28244
```
### Visualize
Visualize word use across articles
```r
plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#> No_Articles Term
#> 1 14528 monkey
#> 2 646 Helianthus
#> 3 1876 sunflower
#> 4 164537 protein
#> 5 2142 whale
#>
#> $plot
```
### progress bars
```r
res <- searchplos(q='*:*', limit = 2000, progress = httr::progress())
#> |=====================================| 100%
#> |=====================================| 100%
#> |=====================================| 100%
#> |=====================================| 100%
```
## Meta
* Please [report any issues or bugs](https://github.com/ropensci/rplos/issues).
* License: MIT
* Get citation information for `rplos` in R doing `citation(package = 'rplos')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
---
This package is part of a richer suite called [fulltext](https://github.com/ropensci/fulltext), along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles. We recommend using `fulltext` as the primary R interface to `rplos` unless your needs are limited to this single source.
---