rplos

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks Build Status Build status codecov.io rstudio mirror downloads cran version

Install

You can get this package at CRAN here, or install it within R by doing

install.packages("rplos")

Or install the development version from GitHub

remotes::install_github("ropensci/rplos")
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 tutorial: http://ropensci.org/tutorials/rplos_tutorial.html

PLOS API documentation: http://api.plos.org/

PLOS Solr schema is at https://gist.github.com/openAccess/9e76aa7fa6135be419968b1372c86957 but is 1.5 years old so may not be up to date.

Crossref API documentation here, and here. Note that we are working on a new package rcrossref (on CRAN) 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 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 api@plos.org to discuss your options. We currently limit API users to no more than five concurrent connections from a single IP address.

Quick start

Search for the term ecology, and return id (DOI) and publication date, limiting to 5 items

searchplos('ecology', 'id,publication_date', limit = 5)
#> $meta
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1    51686     0
#> 
#> $data
#> # A tibble: 5 x 2
#>   id                           publication_date    
#>   <chr>                        <chr>               
#> 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.0220747 2019-08-01T00:00:00Z
#> 5 10.1371/journal.pone.0155019 2016-05-11T00:00:00Z

Get DOIs for full article in PLoS One

searchplos(q="*:*", fl='id', fq=list('journal_key:PLoSONE',
   'doc_type:full'), limit=5)
#> $meta
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1   231685     0
#> 
#> $data
#> # A tibble: 5 x 1
#>   id                          
#>   <chr>                       
#> 1 10.1371/journal.pone.0020843
#> 2 10.1371/journal.pone.0022257
#> 3 10.1371/journal.pone.0023139
#> 4 10.1371/journal.pone.0023138
#> 5 10.1371/journal.pone.0023119

Query to get some PLOS article-level metrics, notice difference between two outputs

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$data)
#> # A tibble: 6 x 3
#>   id                           alm_twitterCount counter_total_all
#>   <chr>                                   <int>             <int>
#> 1 10.1371/journal.pone.0020843                1              8131
#> 2 10.1371/journal.pone.0022257                0              2463
#> 3 10.1371/journal.pone.0023139                1              9560
#> 4 10.1371/journal.pone.0023138                2              4244
#> 5 10.1371/journal.pone.0023119                0              4314
#> 6 10.1371/journal.pone.0023113                0              4788
head(out_sorted$data)
#> # A tibble: 6 x 3
#>   id                                           alm_twitterCount counter_total_a…
#>   <chr>                                                   <int>            <int>
#> 1 10.1371/journal.pmed.0020124                             3474          2958845
#> 2 10.1371/journal.pcbi.1003149                              200          1509253
#> 3 10.1371/annotation/80bd7285-9d2d-403a-8e6f-…                0          1445367
#> 4 10.1371/journal.pone.0133079                              301          1161184
#> 5 10.1371/journal.pmed.1000376                                9          1086212
#> 6 10.1371/journal.pcbi.0030102                               65           945793

A list of articles about social networks that are popular on a social network

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
#>      <int> <int>
#> 1       60     0
#> 
#> $data
#> # A tibble: 10 x 2
#>    id                           alm_twitterCount
#>    <chr>                                   <int>
#>  1 10.1371/journal.pmed.1000316             1060
#>  2 10.1371/journal.pone.0069841              896
#>  3 10.1371/journal.pone.0073791             1883
#>  4 10.1371/journal.pone.0150989              245
#>  5 10.1371/journal.pcbi.1005399              603
#>  6 10.1371/journal.pone.0118093              131
#>  7 10.1371/journal.pone.0162678              155
#>  8 10.1371/journal.pone.0149885              179
#>  9 10.1371/journal.pone.0151588              337
#> 10 10.1371/journal.pone.0196087              154

Show all articles that have these two words less then about 15 words apart

searchplos(q='everything:"sports alcohol"~15', fl='title', fq='doc_type:full', limit=3)
#> $meta
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1      149     0
#> 
#> $data
#> # A tibble: 3 x 1
#>   title                                                                         
#>   <chr>                                                                         
#> 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

searchplos(q='everything:"sports alcohol"~7', fl='title', fq='doc_type:full', limit=3)
#> $meta
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1       84     0
#> 
#> $data
#> # A tibble: 3 x 1
#>   title                                                                         
#>   <chr>                                                                         
#> 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

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
#>      <int> <int>
#> 1  2281799     0
#> 
#> $data
#> # A tibble: 5 x 2
#>   id                           article_type    
#>   <chr>                        <chr>           
#> 1 10.1371/journal.pone.0020843 Research Article
#> 2 10.1371/journal.pone.0022257 Research Article
#> 3 10.1371/journal.pone.0023139 Research Article
#> 4 10.1371/journal.pone.0023138 Research Article
#> 5 10.1371/journal.pone.0023119 Research Article

Facet on multiple fields

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
#>   <fct>                            <fct>
#> 1 plos one                         29296
#> 2 plos genetics                    654  
#> 3 plos medicine                    613  
#> 4 plos neglected tropical diseases 559  
#> 5 plos pathogens                   404  
#> 
#> $facet_fields$subject
#> # A tibble: 5 x 2
#>   term                          value
#>   <fct>                         <fct>
#> 1 biology and life sciences     31180
#> 2 medicine and health sciences  28115
#> 3 research and analysis methods 17534
#> 4 biochemistry                  14624
#> 5 physical sciences             11686
#> 
#> 
#> $facet_pivot
#> NULL
#> 
#> $facet_dates
#> NULL
#> 
#> $facet_ranges
#> NULL

Range faceting

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
#>    <fct> <fct>
#>  1 5     53   
#>  2 15    12   
#>  3 25    5    
#>  4 35    11   
#>  5 45    20   
#>  6 55    30   
#>  7 65    43   
#>  8 75    56   
#>  9 85    59   
#> 10 95    84

Highlight searches

Search for and highlight the term alcohol in the abstract field only

(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 <em>alcohol</em> use disorder, is associated"
#> 
#> 
#> $`10.1371/journal.pone.0138021`
#> $`10.1371/journal.pone.0138021`$abstract
#> [1] "Background and Aim: Harmful <em>alcohol</em> consumption has long been recognized as being the major"
#> 
#> 
#> $`10.1371/journal.pone.0201042`
#> $`10.1371/journal.pone.0201042`$abstract
#> [1] "\nAcute <em>alcohol</em> administration can lead to a loss of control over drinking. Several models argue"

And you can browse the results in your default browser

highbrow(out)
highbrow

Full text urls

Simple function to get full text urls for a DOI

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

(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['<doi>']

Then parse the XML any way you like, here getting the abstract

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.

For example:

plossubject(q='marine ecology',  fl = c('id','journal'), limit = 10)
#> $meta
#> # A tibble: 1 x 2
#>   numFound start
#>      <int> <int>
#> 1     4158     0
#> 
#> $data
#> # A tibble: 10 x 2
#>    id                                                  journal 
#>    <chr>                                               <chr>   
#>  1 10.1371/journal.pone.0092590/title                  PLoS ONE
#>  2 10.1371/journal.pone.0092590/abstract               PLoS ONE
#>  3 10.1371/journal.pone.0092590/references             PLoS ONE
#>  4 10.1371/journal.pone.0092590/body                   PLoS ONE
#>  5 10.1371/journal.pone.0092590/introduction           PLoS ONE
#>  6 10.1371/journal.pone.0092590/results_and_discussion PLoS ONE
#>  7 10.1371/journal.pone.0092590/materials_and_methods  PLoS ONE
#>  8 10.1371/journal.pone.0092590/conclusions            PLoS ONE
#>  9 10.1371/journal.pone.0092590                        PLoS ONE
#> 10 10.1371/journal.pone.0021810                        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

plosviews(search='marine ecology', byfield='subject', limit=5)
#>                             id counter_total_all
#> 3   10.1371/image.pbio.v14.i03                 0
#> 5 10.1371/journal.pone.0201602              1498
#> 2 10.1371/journal.pone.0021810              3442
#> 1 10.1371/journal.pone.0092590             12019
#> 4 10.1371/journal.pone.0149852             16082

Visualize

Visualize word use across articles

plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#>   No_Articles       Term
#> 1       13867     monkey
#> 2         608 Helianthus
#> 3        1759  sunflower
#> 4      156937    protein
#> 5        2001      whale
#> 
#> $plot
wordusage

progress bars

res <- searchplos(q='*:*', limit = 2000, progress = httr::progress())
#>  |=====================================| 100%
#>  |=====================================| 100%
#>  |=====================================| 100%
#>  |=====================================| 100%

Meta

This package is part of a richer suite called 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.

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