You can get this package at CRAN here, or install it within R by doing
Or install the development version from GitHub
rplos is a package for accessing full text articles from the Public Library of Science journals using their API.
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.
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.
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 47678 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.0155019 2016-05-11T00:00:00Z
#> 4 10.1371/journal.pone.0080763 2013-12-10T00:00:00Z
#> 5 10.1371/journal.pone.0208370 2019-01-30T00:00:00ZGet 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 217655 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0155491
#> 2 10.1371/journal.pone.0168631
#> 3 10.1371/journal.pone.0168627
#> 4 10.1371/journal.pone.0184491
#> 5 10.1371/journal.pone.0155489Query to get some PLOS article-level metrics, notice difference between two outputs
out <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'), fq='doc_type:full')
out_sorted <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),
fq='doc_type:full', sort='counter_total_all desc')
head(out$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_all
#> <chr> <int> <int>
#> 1 10.1371/journal.pone.0155491 0 2025
#> 2 10.1371/journal.pone.0168631 0 703
#> 3 10.1371/journal.pone.0168627 0 2392
#> 4 10.1371/journal.pone.0184491 10 745
#> 5 10.1371/journal.pone.0155489 0 3085
#> 6 10.1371/journal.pone.0127059 1 1449
head(out_sorted$data)
#> # A tibble: 6 x 3
#> id alm_twitterCount counter_total_a…
#> <chr> <int> <int>
#> 1 10.1371/journal.pmed.0020124 3472 2728832
#> 2 10.1371/journal.pcbi.1003149 200 1322780
#> 3 10.1371/annotation/80bd7285-9d2d-403a-… 0 1235195
#> 4 10.1371/journal.pone.0141854 3438 887162
#> 5 10.1371/journal.pcbi.0030102 65 872604
#> 6 10.1371/journal.pone.0088278 975 699336A 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.pone.0150989 241
#> 2 10.1371/journal.pone.0069841 895
#> 3 10.1371/journal.pmed.1000316 1055
#> 4 10.1371/journal.pone.0183551 405
#> 5 10.1371/journal.pone.0073791 1883
#> 6 10.1371/journal.pone.0175368 1114
#> 7 10.1371/journal.pone.0149777 217
#> 8 10.1371/journal.pone.0138717 180
#> 9 10.1371/journal.pbio.1001535 2142
#> 10 10.1371/journal.pone.0143611 107Show 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>
#> 1 137 0
#>
#> $data
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Child…
#> 2 Alcohol intoxication at Swedish football matches: A study using biologic…
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incid…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 79 0
#>
#> $data
#> # A tibble: 3 x 1
#> title
#> <chr>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Child…
#> 2 Alcohol intoxication at Swedish football matches: A study using biologic…
#> 3 Symptoms of Insomnia and Sleep Duration and Their Association with Incid…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 2131077 0
#>
#> $data
#> # A tibble: 5 x 2
#> id article_type
#> <chr> <chr>
#> 1 10.1371/journal.pone.0058099/materials_and_methods Research Article
#> 2 10.1371/journal.pone.0030394/introduction Research Article
#> 3 10.1371/journal.pone.0030394/results_and_discussion Research Article
#> 4 10.1371/journal.pone.0002157/materials_and_methods Research Article
#> 5 10.1371/journal.pone.0030394/supporting_information Research ArticleFacet 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 27112
#> 2 plos genetics 609
#> 3 plos medicine 532
#> 4 plos neglected tropical diseases 492
#> 5 plos pathogens 367
#>
#> $facet_fields$subject
#> # A tibble: 5 x 2
#> term value
#> <fct> <fct>
#> 1 biology and life sciences 28864
#> 2 medicine and health sciences 25887
#> 3 research and analysis methods 16394
#> 4 biochemistry 13814
#> 5 physical sciences 10851
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULLRange 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 5 969
#> 2 15 521
#> 3 25 730
#> 4 35 1126
#> 5 45 1591
#> 6 55 1860
#> 7 65 1953
#> 8 75 1887
#> 9 85 1783
#> 10 95 1620Search for and highlight the term alcohol in the abstract field only
(out <- highplos(q='alcohol', hl.fl = 'abstract', rows=3))
#> $`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"
#>
#>
#> $`10.1371/journal.pone.0185457`
#> $`10.1371/journal.pone.0185457`$abstract
#> [1] "Objectives: <em>Alcohol</em>-related morbidity and mortality are significant public health issues"
#>
#>
#> $`10.1371/journal.pone.0071284`
#> $`10.1371/journal.pone.0071284`$abstract
#> [1] "\n<em>Alcohol</em> dependence is a heterogeneous disorder where several signalling systems play important"And you can browse the results in your default browser
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"(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."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
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 4010 0
#>
#> $data
#> # A tibble: 10 x 2
#> id journal
#> <chr> <chr>
#> 1 10.1371/journal.pone.0167252 PLOS ONE
#> 2 10.1371/journal.pone.0167252/title PLOS ONE
#> 3 10.1371/journal.pone.0167252/abstract PLOS ONE
#> 4 10.1371/journal.pone.0167252/references PLOS ONE
#> 5 10.1371/journal.pone.0167252/body PLOS ONE
#> 6 10.1371/journal.pone.0149852/title PLOS ONE
#> 7 10.1371/journal.pone.0149852/abstract PLOS ONE
#> 8 10.1371/journal.pone.0149852/references PLOS ONE
#> 9 10.1371/journal.pone.0149852/body PLOS ONE
#> 10 10.1371/journal.pone.0149852/introduction PLOS ONEHowever, 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 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.0201675 0
#> 3 10.1371/journal.pone.0201602 252
#> 1 10.1371/journal.pone.0167252 1379
#> 5 10.1371/journal.pone.0021810 3190
#> 4 10.1371/journal.pone.0149852 11918Visualize word use across articles
plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#> No_Articles Term
#> 1 13216 monkey
#> 2 572 Helianthus
#> 3 1636 sunflower
#> 4 149565 protein
#> 5 1880 whale
#>
#> $plot
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.
