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")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 at rOpenSci website here
PLoS API documentation here
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.
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 × 2
#> numFound start
#> <int> <int>
#> 1 37902 0
#>
#> $data
#> # A tibble: 5 × 2
#> id
#> <chr>
#> 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
#> # ... with 1 more variables: publication_date <chr>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 × 2
#> numFound start
#> <int> <int>
#> 1 179090 0
#>
#> $data
#> # A tibble: 5 × 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0014588
#> 2 10.1371/journal.pone.0172512
#> 3 10.1371/journal.pone.0014589
#> 4 10.1371/journal.pone.0001359
#> 5 10.1371/journal.pone.0145699Query to get some PLOS article-level metrics, notice difference between two outputs
out <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'), fq='doc_type:full')
out_sorted <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),
fq='doc_type:full', sort='counter_total_all desc')
head(out$data)
#> # A tibble: 6 × 3
#> id alm_twitterCount counter_total_all
#> <chr> <int> <int>
#> 1 10.1371/journal.pone.0014588 0 2177
#> 2 10.1371/journal.pone.0172512 0 388
#> 3 10.1371/journal.pone.0014589 0 3028
#> 4 10.1371/journal.pone.0001359 0 4246
#> 5 10.1371/journal.pone.0145699 6 949
#> 6 10.1371/journal.pone.0014661 0 3464
head(out_sorted$data)
#> # A tibble: 6 × 3
#> id alm_twitterCount
#> <chr> <int>
#> 1 10.1371/journal.pmed.0020124 2952
#> 2 10.1371/annotation/80bd7285-9d2d-403a-8e6f-9c375bf977ca 0
#> 3 10.1371/journal.pone.0141854 3112
#> 4 10.1371/journal.pcbi.1003149 153
#> 5 10.1371/journal.pcbi.0030102 58
#> 6 10.1371/journal.pone.0069841 875
#> # ... with 1 more variables: counter_total_all <int>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 × 2
#> numFound start
#> <int> <int>
#> 1 54 0
#>
#> $data
#> # A tibble: 10 × 2
#> id alm_twitterCount
#> <chr> <int>
#> 1 10.1371/journal.pone.0175368 991
#> 2 10.1371/journal.pcbi.1005399 480
#> 3 10.1371/journal.pcbi.1005373 165
#> 4 10.1371/journal.pone.0069841 875
#> 5 10.1371/journal.pmed.1000316 972
#> 6 10.1371/journal.pone.0073791 1723
#> 7 10.1371/journal.pone.0171774 275
#> 8 10.1371/journal.pone.0151588 323
#> 9 10.1371/journal.pone.0148405 499
#> 10 10.1371/journal.pone.0150989 238Show 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 × 2
#> numFound start
#> <int> <int>
#> 1 122 0
#>
#> $data
#> # A tibble: 3 × 1
#> title
#> <chr>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children
#> 2 Correction: Alcohol Advertising in Sport and Non-Sport TV in Australia, dur
#> 3 The Effect of Significant International Sports Events on Qualified DetoxifiNarrow 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 × 2
#> numFound start
#> <int> <int>
#> 1 63 0
#>
#> $data
#> # A tibble: 3 × 1
#> title
#> <chr>
#> 1 Alcohol Advertising in Sport and Non-Sport TV in Australia, during Children
#> 2 Correction: Alcohol Advertising in Sport and Non-Sport TV in Australia, dur
#> 3 The Effect of Significant International Sports Events on Qualified DetoxifiRemove 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 × 2
#> numFound start
#> <int> <int>
#> 1 1742228 0
#>
#> $data
#> # A tibble: 5 × 2
#> id article_type
#> <chr> <chr>
#> 1 10.1371/journal.pone.0014588 Research Article
#> 2 10.1371/journal.pone.0014588/title Research Article
#> 3 10.1371/journal.pone.0014588/abstract Research Article
#> 4 10.1371/journal.pone.0014588/references Research Article
#> 5 10.1371/journal.pone.0014588/body 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 × 2
#> term value
#> <chr> <chr>
#> 1 plos one 1477360
#> 2 plos genetics 56995
#> 3 plos pathogens 50262
#> 4 plos neglected tropical diseases 43287
#> 5 plos computational biology 42831
#>
#> $facet_fields$subject
#> # A tibble: 5 × 2
#> term value
#> <chr> <chr>
#> 1 biology and life sciences 1666224
#> 2 medicine and health sciences 1303618
#> 3 research and analysis methods 1089302
#> 4 biochemistry 806513
#> 5 cell biology 684480
#>
#>
#> $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 × 2
#> term value
#> <chr> <chr>
#> 1 5 67
#> 2 15 340
#> 3 25 626
#> 4 35 1147
#> 5 45 1603
#> 6 55 1957
#> 7 65 1861
#> 8 75 1694
#> 9 85 1667
#> 10 95 1347Search 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)
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 × 2
#> numFound start
#> <int> <int>
#> 1 3604 0
#>
#> $data
#> # A tibble: 10 × 2
#> id journal
#> <chr> <chr>
#> 1 10.1371/journal.pone.0167252/title PLOS ONE
#> 2 10.1371/journal.pone.0167252/abstract PLOS ONE
#> 3 10.1371/journal.pone.0167252/references PLOS ONE
#> 4 10.1371/journal.pone.0167252/body PLOS ONE
#> 5 10.1371/journal.pone.0167252 PLOS ONE
#> 6 10.1371/journal.pone.0021810/body PLoS ONE
#> 7 10.1371/journal.pone.0021810/introduction PLoS ONE
#> 8 10.1371/journal.pone.0021810/materials_and_methods PLoS ONE
#> 9 10.1371/journal.pone.0021810/title PLoS ONE
#> 10 10.1371/journal.pone.0021810/abstract 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
#> 1 10.1371/journal.pone.0167252 1191
#> 5 10.1371/journal.pone.0080365 2269
#> 2 10.1371/journal.pone.0021810 2674
#> 4 10.1371/journal.pone.0149852 6597
#> 3 10.1371/journal.pone.0092590 8264Visualize word use across articles
plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#> No_Articles Term
#> 1 11330 monkey
#> 2 470 Helianthus
#> 3 1309 sunflower
#> 4 128377 protein
#> 5 1513 whale
#>
#> $plot
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rplosin R doingcitation(package = 'rplos') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
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.
