The rplos package interacts with the API services of PLoS (Public Library of Science) Journals. You used to need an API key to work with this package - that is no longer needed!
This tutorial will go through three use cases to demonstrate the kinds
of things possible in rplos.
install.packages("rplos")
library('rplos')
searchplos is a general search, and in this case searches for the term
Helianthus and returns the DOI's of matching papers
searchplos(q= "Helianthus", fl= "id", limit = 5)
#> $meta
#> numFound start maxScore
#> 1 347 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0111982
#> 2 10.1371/journal.pone.0057533
#> 3 10.1371/journal.pone.0045899
#> 4 10.1371/journal.pone.0037191
#> 5 10.1371/journal.pone.0051360
Get only full article DOIs
searchplos(q="*:*", fl='id', fq='doc_type:full', start=0, limit=5)
#> $meta
#> numFound start maxScore
#> 1 158745 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0031384
#> 2 10.1371/journal.pone.0031385
#> 3 10.1371/journal.pone.0107441
#> 4 10.1371/journal.pone.0000339
#> 5 10.1371/journal.pone.0046739
Get DOIs for only PLoS One articles
searchplos(q="*:*", fl='id', fq='cross_published_journal_key:PLoSONE', start=0, limit=5)
#> $meta
#> numFound start maxScore
#> 1 1142335 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0123754/title
#> 2 10.1371/journal.pone.0123754/abstract
#> 3 10.1371/journal.pone.0123754/references
#> 4 10.1371/journal.pone.0123754/body
#> 5 10.1371/journal.pone.0123754/introduction
Get DOIs for full article in PLoS One
searchplos(q="*:*", fl='id',
fq=list('cross_published_journal_key:PLoSONE', 'doc_type:full'),
start=0, limit=5)
#> $meta
#> numFound start maxScore
#> 1 133907 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pone.0031384
#> 2 10.1371/journal.pone.0031385
#> 3 10.1371/journal.pone.0107441
#> 4 10.1371/journal.pone.0000339
#> 5 10.1371/journal.pone.0046739
Search for many terms
q <- c('ecology','evolution','science')
lapply(q, function(x) searchplos(x, limit=2))
#> [[1]]
#> [[1]]$meta
#> numFound start maxScore
#> 1 27832 0 NA
#>
#> [[1]]$data
#> id
#> 1 10.1371/journal.pone.0059813
#> 2 10.1371/journal.pone.0001248
#>
#>
#> [[2]]
#> [[2]]$meta
#> numFound start maxScore
#> 1 46467 0 NA
#>
#> [[2]]$data
#> id
#> 1 10.1371/annotation/9773af53-a076-4946-a3f1-83914226c10d
#> 2 10.1371/annotation/c55d5089-ba2f-449d-8696-2bc8395978db
#>
#>
#> [[3]]
#> [[3]]$meta
#> numFound start maxScore
#> 1 134888 0 NA
#>
#> [[3]]$data
#> id
#> 1 10.1371/journal.pbio.0020122
#> 2 10.1371/journal.pbio.1001166
A suite of functions were created as light wrappers around searchplos as a shorthand to search specific sections of a paper.
plosauthor searchers in authorsplosabstract searches in abstractsplostitle searches in titlesplosfigtabcaps searches in figure and table captionsplossubject searches in subject areasplosauthor searches across authors, and in this case returns the authors of the matching papers. the fl parameter determines what is returned
plosauthor(q = "Eisen", fl = "author", limit = 5)
#> $meta
#> numFound start maxScore
#> 1 764 0 NA
#>
#> $data
#> author
#> 1 Jonathan A Eisen
#> 2 Jonathan A Eisen
#> 3 Jonathan A Eisen
#> 4 Jonathan A Eisen
#> 5 Jonathan A Eisen
plosabstract searches across abstracts, and in this case returns the id and title of the matching papers
plosabstract(q = 'drosophila', fl='id,title', limit = 5)
#> $meta
#> numFound start maxScore
#> 1 2669 0 NA
#>
#> $data
#> id
#> 1 10.1371/journal.pbio.0040198
#> 2 10.1371/journal.pbio.0030246
#> 3 10.1371/journal.pone.0012421
#> 4 10.1371/journal.pbio.0030389
#> 5 10.1371/journal.pbio.1000342
#> title
#> 1 All for All
#> 2 School Students as Drosophila Experimenters
#> 3 Host Range and Specificity of the Drosophila C Virus
#> 4 New Environments Set the Stage for Changing Tastes in Mates
#> 5 Variable Transcription Factor Binding: A Mechanism of Evolutionary Change
plostitle searches across titles, and in this case returns the title and journal of the matching papers
plostitle(q='drosophila', fl='title,journal', limit=5)
#> $meta
#> numFound start maxScore
#> 1 1718 0 NA
#>
#> $data
#> journal title
#> 1 PLoS Biology Identification of Drosophila MicroRNA Targets
#> 2 PLoS ONE A DNA Virus of Drosophila
#> 3 PLoS Biology School Students as Drosophila Experimenters
#> 4 PLoS Biology Expression in Aneuploid Drosophila S2 Cells
#> 5 PLoS ONE Quantification of Food Intake in Drosophila
plosword allows you to search for 1 to K words and visualize the results
as a histogram, comparing number of matching papers for each word
out <- plosword(list("monkey", "Helianthus", "sunflower", "protein", "whale"),
vis = "TRUE")
out$table
#> No_Articles Term
#> 1 9098 monkey
#> 2 347 Helianthus
#> 3 937 sunflower
#> 4 101040 protein
#> 5 1139 whale
out$plot
You can also pass in curl options, in this case get verbose information on the curl call.
plosword('Helianthus', callopts=list(verbose=TRUE))
#> Number of articles with search term
#> 347
plot_throughtime allows you to search for up to 2 words and visualize the results as a line plot through time, comparing number of articles matching through time. Visualize with the ggplot2 package, only up to two terms for now.
plot_throughtime(terms = "phylogeny", limit = 200) + geom_line(size=2, color='black')
See the Faceted and highlighted searches and Full text vignettes for more rplos help.