rplos

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    33699     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.0155019
#>       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 2016-05-11T00:00:00Z

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   161020     0       NA
#> 
#> $data
#>                             id
#> 1 10.1371/journal.pone.0024229
#> 2 10.1371/journal.pone.0024016
#> 3 10.1371/journal.pone.0094828
#> 4 10.1371/journal.pone.0095065
#> 5 10.1371/journal.pone.0130784

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$data)
#>                             id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pone.0024229                0              1762
#> 2 10.1371/journal.pgen.1004259                0               686
#> 3 10.1371/journal.pone.0024016                0              1774
#> 4 10.1371/journal.pgen.1004316                0              1597
#> 5 10.1371/journal.pone.0094828                0              1024
#> 6 10.1371/journal.pgen.1004352                1              1647
head(out_sorted$data)
#>                                                        id alm_twitterCount
#> 1                            10.1371/journal.pmed.0020124             2480
#> 2 10.1371/annotation/80bd7285-9d2d-403a-8e6f-9c375bf977ca                0
#> 3                            10.1371/journal.pcbi.0030102               53
#> 4                            10.1371/journal.pcbi.1003149              145
#> 5                            10.1371/journal.pmed.0050045              153
#> 6                            10.1371/journal.pone.0069841              860
#>   counter_total_all
#> 1           1707520
#> 2            546738
#> 3            448864
#> 4            409507
#> 5            391646
#> 6            389823

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       43     0       NA
#> 
#> $data
#>                              id alm_twitterCount
#> 1  10.1371/journal.pone.0155885              118
#> 2  10.1371/journal.pmed.1000316              923
#> 3  10.1371/journal.pone.0151588              153
#> 4  10.1371/journal.pone.0069841              860
#> 5  10.1371/journal.pone.0149885              123
#> 6  10.1371/journal.pone.0073791             1667
#> 7  10.1371/journal.pcbi.1003789             1528
#> 8  10.1371/journal.pbio.1001535             1798
#> 9  10.1371/journal.pone.0148405              469
#> 10 10.1371/journal.pone.0156409              121

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      100     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       51     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  1565546     0       NA
#> 
#> $data
#>                                          id     article_type
#> 1        10.1371/journal.pone.0024229/title Research Article
#> 2     10.1371/journal.pone.0024229/abstract Research Article
#> 3   10.1371/journal.pone.0024229/references Research Article
#> 4         10.1371/journal.pone.0024229/body Research Article
#> 5 10.1371/journal.pone.0024229/introduction 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 1319779
#> 2                    plos genetics   51827
#> 3                   plos pathogens   45119
#> 4       plos computational biology   38599
#> 5 plos neglected tropical diseases   37114
#> 
#> $facet_fields$subject
#>                              X1      X2
#> 1     biology and life sciences 1505447
#> 2  medicine and health sciences 1167857
#> 3 research and analysis methods  999924
#> 4                  biochemistry  736199
#> 5                  cell biology  629720
#> 
#> 
#> $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  395
#> 2  15  826
#> 3  25 1106
#> 4  35 1686
#> 5  45 2134
#> 6  55 1979
#> 7  65 1845
#> 8  75 1784
#> 9  85 1441
#> 10 95 1279

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)

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     3050     0       NA
#> 
#> $data
#>                                                    id  journal
#> 1                        10.1371/journal.pone.0021810 PLoS ONE
#> 2                  10.1371/journal.pone.0021810/title PLoS ONE
#> 3               10.1371/journal.pone.0021810/abstract PLoS ONE
#> 4             10.1371/journal.pone.0021810/references PLoS ONE
#> 5                   10.1371/journal.pone.0021810/body PLoS ONE
#> 6           10.1371/journal.pone.0021810/introduction PLoS ONE
#> 7  10.1371/journal.pone.0021810/materials_and_methods PLoS ONE
#> 8                        10.1371/journal.pone.0092590 PLoS ONE
#> 9           10.1371/journal.pone.0092590/introduction 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
#> 3 10.1371/journal.pone.0080365              2003
#> 1 10.1371/journal.pone.0021810              2327
#> 5 10.1371/journal.pone.0149852              4162
#> 4 10.1371/journal.pone.0031775              4805
#> 2 10.1371/journal.pone.0092590              7183

Visualize

Visualize word use across articles

plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#>   No_Articles       Term
#> 1       10480     monkey
#> 2         428 Helianthus
#> 3        1171  sunflower
#> 4      117345    protein
#> 5        1370      whale
#> 
#> $plot

BioCogito/rplos