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, 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
#> numFound start maxScore
#> 1 24936 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 2014-07-22T00:00:00ZGet 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 118989 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0093878
#> 2 10.1371/journal.pone.0094012
#> 3 10.1371/journal.pone.0094113
#> 4 10.1371/journal.pone.0094154
#> 5 10.1371/journal.pone.0094152Query to get some PLOS article-level metrics, notice difference between two outputs
out <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'), fq='doc_type:full')
out_sorted <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),
fq='doc_type:full', sort='counter_total_all desc')
head(out$data)
#> id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pbio.1000156 0 3569
#> 2 10.1371/journal.pbio.1000106 0 5475
#> 3 10.1371/journal.pmed.1001197 0 3575
#> 4 10.1371/journal.pbio.0040294 0 1396
#> 5 10.1371/journal.pone.0093878 0 176
#> 6 10.1371/journal.pbio.0040247 0 2202
head(out_sorted$data)
#> id alm_twitterCount counter_total_all
#> 1 10.1371/journal.pmed.0020124 1760 1036112
#> 2 10.1371/journal.pmed.0050045 116 328315
#> 3 10.1371/journal.pone.0007595 197 318697
#> 4 10.1371/journal.pone.0033288 39 307098
#> 5 10.1371/journal.pone.0069841 819 289945
#> 6 10.1371/journal.pone.0044864 87 239574A 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 21 0 NA
#>
#> $data
#> id alm_twitterCount
#> 1 10.1371/journal.pbio.1001535 1664
#> 2 10.1371/journal.pone.0069841 819
#> 3 10.1371/journal.pone.0073791 782
#> 4 10.1371/journal.pone.0090315 402
#> 5 10.1371/journal.pcbi.1003789 1077
#> 6 10.1371/journal.pone.0061981 2381
#> 7 10.1371/journal.pone.0064841 120
#> 8 10.1371/journal.pone.0059030 216
#> 9 10.1371/journal.pone.0069215 209
#> 10 10.1371/journal.pone.0047523 110Show 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 63 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 Development and Validation of a Risk Score Predicting Substantial Weight Gain over 5 Years in Middle-Aged European Men and WomenNarrow 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 28 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 Development and Validation of a Risk Score Predicting Substantial Weight Gain over 5 Years in Middle-Aged European Men and WomenRemove 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 1171078 0 NA
#>
#> $data
#> id article_type
#> 1 10.1371/journal.pbio.1000156 Community Page
#> 2 10.1371/journal.pbio.1000156/title Community Page
#> 3 10.1371/journal.pbio.1000156/abstract Community Page
#> 4 10.1371/journal.pbio.1000156/references Community Page
#> 5 10.1371/journal.pbio.1000156/body Community PageFacet 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 955046
#> 2 plos genetics 41615
#> 3 plos pathogens 36230
#> 4 plos computational biology 30535
#> 5 plos biology 26456
#>
#> $facet_fields$subject
#> X1 X2
#> 1 biology and life sciences 1127571
#> 2 medicine and health sciences 859581
#> 3 research and analysis methods 736031
#> 4 biochemistry 554096
#> 5 cell biology 505958
#>
#>
#> $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_dates
#> NULL
#>
#> $facet_ranges
#> $facet_ranges$counter_total_all
#> X1 X2
#> 1 5 0
#> 2 15 0
#> 3 25 0
#> 4 35 0
#> 5 45 0
#> 6 55 0
#> 7 65 5
#> 8 75 51
#> 9 85 100
#> 10 95 183Search 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://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0086169&representation=XML"(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."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 2142 0 NA
#>
#> $data
#> id journal
#> 1 10.1371/journal.pone.0070647 PLoS ONE
#> 2 10.1371/journal.pone.0070647/title PLoS ONE
#> 3 10.1371/journal.pone.0070647/abstract PLoS ONE
#> 4 10.1371/journal.pone.0070647/references PLoS ONE
#> 5 10.1371/journal.pone.0070647/body PLoS ONE
#> 6 10.1371/journal.pone.0070647/introduction PLoS ONE
#> 7 10.1371/journal.pone.0070647/results_and_discussion PLoS ONE
#> 8 10.1371/journal.pone.0070647/materials_and_methods PLoS ONE
#> 9 10.1371/journal.pone.0070647/supporting_information PLoS ONE
#> 10 10.1371/journal.pone.0028556 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.0028556 1264
#> 1 10.1371/journal.pone.0070647 1501
#> 3 10.1371/journal.pone.0012946 3348
#> 5 10.1371/journal.pone.0092590 4277
#> 4 10.1371/journal.pone.0022881 7838Visualize word use across articles
plosword(list('monkey','Helianthus','sunflower','protein','whale'), vis = 'TRUE')
#> $table
#> No_Articles Term
#> 1 8335 monkey
#> 2 300 Helianthus
#> 3 818 sunflower
#> 4 91971 protein
#> 5 1023 whale
#>
#> $plot
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rplosin R doingcitation(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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