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R client for the PLoS Journals API
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README.md

rplos

Build Status Build status Coverage Status 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

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    25382     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   121044     0       NA
#> 
#> $data
#>                             id
#> 1 10.1371/journal.pone.0074638
#> 2 10.1371/journal.pone.0074637
#> 3 10.1371/journal.pone.0060237
#> 4 10.1371/journal.pone.0074528
#> 5 10.1371/journal.pone.0074552

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$data)
#>                             id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pone.0074638                3               784
#> 2 10.1371/journal.pone.0074637                0               631
#> 3 10.1371/journal.pone.0060237                0               811
#> 4 10.1371/journal.ppat.1000789                0              4804
#> 5 10.1371/journal.ppat.1000586                0              6324
#> 6 10.1371/journal.pone.0074528                0              1054
head(out_sorted$data)
#>                             id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pmed.0020124             1768           1061691
#> 2 10.1371/journal.pmed.0050045              116            330846
#> 3 10.1371/journal.pone.0007595              197            321260
#> 4 10.1371/journal.pone.0033288               39            307543
#> 5 10.1371/journal.pone.0069841              820            298973
#> 6 10.1371/journal.pone.0044864               87            239859

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       24     0       NA
#> 
#> $data
#>                              id alm_twitterCount
#> 1  10.1371/journal.pmed.1001772              297
#> 2  10.1371/journal.pone.0069841              820
#> 3  10.1371/journal.pone.0073791              782
#> 4  10.1371/journal.pbio.1001535             1669
#> 5  10.1371/journal.pcbi.1003789             1080
#> 6  10.1371/journal.pone.0090315              402
#> 7  10.1371/journal.pone.0064417              144
#> 8  10.1371/journal.pone.0110329              183
#> 9  10.1371/journal.pone.0069215              209
#> 10 10.1371/journal.pone.0064841              120

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       64     0       NA
#> 
#> $data
#>                                                                                                                                                                                                     title
#> 1                                                                  Alcohol Ingestion Impairs Maximal Post-Exercise Rates of Myofibrillar Protein Synthesis following a Single Bout of Concurrent Training
#> 2                             “Like Throwing a Bowling Ball at a Battle Ship” Audience Responses to Australian News Stories about Alcohol Pricing and Promotion Policies: A Qualitative Focus Group Study
#> 3 Investigating the Associations of Self-Rated Health: Heart Rate Variability Is More Strongly Associated than Inflammatory and Other Frequently Used Biomarkers in a Cross Sectional Occupational Sample

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       29     0       NA
#> 
#> $data
#>                                                                                                                                                                                                     title
#> 1                                                                  Alcohol Ingestion Impairs Maximal Post-Exercise Rates of Myofibrillar Protein Synthesis following a Single Bout of Concurrent Training
#> 2                             “Like Throwing a Bowling Ball at a Battle Ship” Audience Responses to Australian News Stories about Alcohol Pricing and Promotion Policies: A Qualitative Focus Group Study
#> 3 Investigating the Associations of Self-Rated Health: Heart Rate Variability Is More Strongly Associated than Inflammatory and Other Frequently Used Biomarkers in a Cross Sectional Occupational Sample

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  1190889     0       NA
#> 
#> $data
#>                                        id     article_type
#> 1            10.1371/journal.pone.0074638 Research Article
#> 2      10.1371/journal.pone.0074638/title Research Article
#> 3   10.1371/journal.pone.0074638/abstract Research Article
#> 4 10.1371/journal.pone.0074638/references Research Article
#> 5       10.1371/journal.pone.0074638/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 972714
#> 2                    plos genetics  42377
#> 3                   plos pathogens  36842
#> 4       plos computational biology  30967
#> 5 plos neglected tropical diseases  26744
#> 
#> $facet_fields$subject
#>                              X1      X2
#> 1     biology and life sciences 1150509
#> 2  medicine and health sciences  876702
#> 3 research and analysis methods  744342
#> 4                  biochemistry  565308
#> 5                  cell biology  513774
#> 
#> 
#> $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  17
#> 2  15  30
#> 3  25  24
#> 4  35  92
#> 5  45 131
#> 6  55 217
#> 7  65 243
#> 8  75 401
#> 9  85 327
#> 10 95 505

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: 111132 - Max. Length: 111132 
#> 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 (Nâ\u0080\u008a=â\u0080\u008a113,750 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 â\u0088¼445 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     2250     0       NA
#> 
#> $data
#>                                                     id  journal
#> 1                         10.1371/journal.pone.0022881 PLoS ONE
#> 2                   10.1371/journal.pone.0022881/title PLoS ONE
#> 3                10.1371/journal.pone.0022881/abstract PLoS ONE
#> 4              10.1371/journal.pone.0022881/references PLoS ONE
#> 5                    10.1371/journal.pone.0022881/body PLoS ONE
#> 6            10.1371/journal.pone.0022881/introduction PLoS ONE
#> 7  10.1371/journal.pone.0022881/results_and_discussion PLoS ONE
#> 8   10.1371/journal.pone.0022881/materials_and_methods PLoS ONE
#> 9  10.1371/journal.pone.0022881/supporting_information 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
#> 5 10.1371/journal.pone.0028556              1285
#> 2 10.1371/journal.pone.0021810              1523
#> 3 10.1371/journal.pone.0070647              1580
#> 4 10.1371/journal.pone.0092590              4411
#> 1 10.1371/journal.pone.0022881              8022

Visualize

Visualize word use across articles

plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#>   No_Articles       Term
#> 1        8459     monkey
#> 2         302 Helianthus
#> 3         840  sunflower
#> 4       93342    protein
#> 5        1054      whale
#> 
#> $plot

wordusage

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rplos in R doing citation(package = 'rplos')

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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