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R client for the PLoS Journals API
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README.md

rplos

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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

install.packages("devtools")
devtools::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 at rOpenSci website here

PLoS API documentation here

Crossref API documentation here, 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.

Quick start

Search

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

searchplos('ecology', 'id,publication_date', limit = 5)
#> $meta
#>   numFound start maxScore
#> 1    32563     0       NA
#> 
#> $data
#>                                                        id
#> 1                            10.1371/journal.pone.0059813
#> 2                            10.1371/journal.pone.0001248
#> 3 10.1371/annotation/69333ae7-757a-4651-831c-f28c5eb02120
#> 4                            10.1371/journal.pone.0080763
#> 5                            10.1371/journal.pone.0102437
#>       publication_date
#> 1 2013-04-24T00:00:00Z
#> 2 2007-11-28T00:00:00Z
#> 3 2013-10-29T00:00:00Z
#> 4 2013-12-10T00:00:00Z
#> 5 2014-07-22T00:00:00Z

Get DOIs for full article in PLoS One

searchplos(q="*:*", fl='id', fq=list('cross_published_journal_key:PLoSONE',
   'doc_type:full'), limit=5)
#> $meta
#>   numFound start maxScore
#> 1   156005     0       NA
#> 
#> $data
#>                             id
#> 1 10.1371/journal.pone.0084520
#> 2 10.1371/journal.pone.0027194
#> 3 10.1371/journal.pone.0073075
#> 4 10.1371/journal.pone.0050158
#> 5 10.1371/journal.pone.0050268

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$data)
#>                             id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pone.0084520                0              1088
#> 2 10.1371/journal.pone.0027194                1              1966
#> 3 10.1371/journal.pone.0073075                0              2118
#> 4 10.1371/journal.pone.0050158                0              1709
#> 5 10.1371/journal.pone.0050268                4              1642
#> 6 10.1371/journal.pone.0084489                0              1223
head(out_sorted$data)
#>                             id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pmed.0020124             2314           1602293
#> 2 10.1371/journal.pmed.0050045              151            382347
#> 3 10.1371/journal.pone.0069841              857            378155
#> 4 10.1371/journal.pcbi.0030102               52            377892
#> 5 10.1371/journal.pone.0007595              242            365498
#> 6 10.1371/journal.pcbi.0030077               53            317609

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
#>   numFound start maxScore
#> 1       38     0       NA
#> 
#> $data
#>                              id alm_twitterCount
#> 1  10.1371/journal.pmed.1000316              899
#> 2  10.1371/journal.pbio.1002413              246
#> 3  10.1371/journal.pone.0069841              857
#> 4  10.1371/journal.pone.0073791             1642
#> 5  10.1371/journal.pone.0151387              197
#> 6  10.1371/journal.pone.0148405              447
#> 7  10.1371/journal.pbio.1001535             1763
#> 8  10.1371/journal.pbio.1002373              342
#> 9  10.1371/journal.pone.0150989              183
#> 10 10.1371/journal.pone.0149777              113

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
#>   numFound start maxScore
#> 1       95     0       NA
#> 
#> $data
#>                                                                                                                                                       title
#> 1                                                               Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s Viewing Times
#> 2                                                   Correction: Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s Viewing Times
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incident Strokes: Findings from the Population-Based MONICA/KORA Augsburg Cohort Study

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
#>   numFound start maxScore
#> 1       47     0       NA
#> 
#> $data
#>                                                                                                                                                       title
#> 1                                                               Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s Viewing Times
#> 2                                                   Correction: Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children’s Viewing Times
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incident Strokes: Findings from the Population-Based MONICA/KORA Augsburg Cohort Study

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
#>   numFound start maxScore
#> 1  1516083     0       NA
#> 
#> $data
#>                                        id     article_type
#> 1            10.1371/journal.pone.0084520 Research Article
#> 2      10.1371/journal.pone.0084520/title Research Article
#> 3   10.1371/journal.pone.0084520/abstract Research Article
#> 4 10.1371/journal.pone.0084520/references Research Article
#> 5       10.1371/journal.pone.0084520/body Research Article

Faceted search

Facet on multiple fields

facetplos(q='alcohol', facet.field=c('journal','subject'), facet.limit=5)
#> $facet_queries
#> NULL
#> 
#> $facet_fields
#> $facet_fields$journal
#>                                 X1      X2
#> 1                         plos one 1275921
#> 2                    plos genetics   50342
#> 3                   plos pathogens   43597
#> 4       plos computational biology   37219
#> 5 plos neglected tropical diseases   35331
#> 
#> $facet_fields$subject
#>                              X1      X2
#> 1     biology and life sciences 1459514
#> 2  medicine and health sciences 1131931
#> 3 research and analysis methods  963634
#> 4                  biochemistry  719264
#> 5                  cell biology  615901
#> 
#> 
#> $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_dates
#> NULL
#> 
#> $facet_ranges
#> $facet_ranges$counter_total_all
#>    X1   X2
#> 1   5  318
#> 2  15  842
#> 3  25 1590
#> 4  35 2022
#> 5  45 2202
#> 6  55 2068
#> 7  65 1791
#> 8  75 1433
#> 9  85 1465
#> 10 95 1225

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.pmed.0040151`
#> $`10.1371/journal.pmed.0040151`$abstract
#> [1] "Background: <em>Alcohol</em> consumption causes an estimated 4% of the global disease burden, prompting"
#> 
#> 
#> $`10.1371/journal.pone.0027752`
#> $`10.1371/journal.pone.0027752`$abstract
#> [1] "Background: The negative influences of <em>alcohol</em> on TB management with regard to delays in seeking"
#> 
#> 
#> $`10.1371/journal.pmed.0050108`
#> $`10.1371/journal.pmed.0050108`$abstract
#> [1] " study that links retail <em>alcohol</em> sales and violent assaults.\n      "

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://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0086169&representation=XML"

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.

  • plosauthor()
  • plosabstract()
  • plosfigtabcaps()
  • plostitle()
  • plossubject()

For example:

plossubject(q='marine ecology',  fl = c('id','journal'), limit = 10)
#> $meta
#>   numFound start maxScore
#> 1     2902     0       NA
#> 
#> $data
#>                                                     id  journal
#> 1                10.1371/journal.pone.0080365/abstract PLoS ONE
#> 2              10.1371/journal.pone.0080365/references PLoS ONE
#> 3                    10.1371/journal.pone.0080365/body 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.0092590/title 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
#> 2 10.1371/journal.pone.0080365              1954
#> 3 10.1371/journal.pone.0021810              2229
#> 4 10.1371/journal.pone.0149852              3368
#> 1 10.1371/journal.pone.0092590              6526
#> 5 10.1371/journal.pone.0047598              8610

Visualize

Visualize word use across articles

plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#>   No_Articles       Term
#> 1       10237     monkey
#> 2         419 Helianthus
#> 3        1133  sunflower
#> 4      114217    protein
#> 5        1325      whale
#> 
#> $plot

wordusage

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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