This tutorial will go through three use cases to demonstrate the kinds of things possible in rplos.
Search across PLoS papers in various sections of papers
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
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 646 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0198869
#> 2 10.1371/journal.pone.0213065
#> 3 10.1371/journal.pone.0148280
#> 4 10.1371/journal.pone.0111982
#> 5 10.1371/journal.pone.0212371
Get only full article DOIs
searchplos(q = "*:*", fl = 'id', fq = 'doc_type:full', start = 0, limit = 5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 292789 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pcbi.0020071
#> 2 10.1371/journal.pbio.1000152
#> 3 10.1371/journal.pbio.1000153
#> 4 10.1371/journal.pbio.1000159
#> 5 10.1371/journal.pbio.1000165
Get DOIs for only PLoS One articles
searchplos(q = "*:*", fl = 'id', fq = 'journal_key:PLoSONE',
start = 0, limit = 5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 2125942 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0002397/title
#> 2 10.1371/journal.pone.0002397/abstract
#> 3 10.1371/journal.pone.0002397/references
#> 4 10.1371/journal.pone.0002397/body
#> 5 10.1371/journal.pone.0002397/introduction
Get DOIs for full article in PLoS One
searchplos(q = "*:*", fl = 'id',
fq = list('journal_key:PLoSONE', 'doc_type:full'),
start = 0, limit = 5)
#> $meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 246927 0
#>
#> $data
#> # A tibble: 5 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0002399
#> 2 10.1371/journal.pone.0002401
#> 3 10.1371/journal.pone.0002403
#> 4 10.1371/journal.pone.0002405
#> 5 10.1371/journal.pone.0002407
Search for many terms
q <- c('ecology','evolution','science')
lapply(q, function(x) searchplos(x, limit = 2))
#> [[1]]
#> [[1]]$meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 55873 0
#>
#> [[1]]$data
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0001248
#> 2 10.1371/journal.pone.0059813
#>
#>
#> [[2]]
#> [[2]]$meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 82168 0
#>
#> [[2]]$data
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pbio.2002255
#> 2 10.1371/journal.pone.0205798
#>
#>
#> [[3]]
#> [[3]]$meta
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 260220 0
#>
#> [[3]]$data
#> # A tibble: 2 x 1
#> id
#> <chr>
#> 1 10.1371/journal.pone.0229237
#> 2 10.1371/journal.pone.0202320
Search on specific sections
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 areas
plosauthor 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
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 1107 0
#>
#> $data
#> # A tibble: 5 x 1
#> author
#> <chr>
#> 1 Myungsun Kang,Timothy J Eisen,Ellen A Eisen,Arup K Chakraborty,Herman N Eisen
#> 2 Myungsun Kang,Timothy J Eisen,Ellen A Eisen,Arup K Chakraborty,Herman N Eisen
#> 3 Myungsun Kang,Timothy J Eisen,Ellen A Eisen,Arup K Chakraborty,Herman N Eisen
#> 4 Myungsun Kang,Timothy J Eisen,Ellen A Eisen,Arup K Chakraborty,Herman N Eisen
#> 5 Myungsun Kang,Timothy J Eisen,Ellen A Eisen,Arup K Chakraborty,Herman N 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
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 3944 0
#>
#> $data
#> # A tibble: 5 x 2
#> id title
#> <chr> <chr>
#> 1 10.1371/journal.pone.… Host Range and Specificity of the Drosophila C Virus
#> 2 10.1371/journal.pgen.… Drosophila Myc restores immune homeostasis of Imd path…
#> 3 10.1371/journal.pone.… Exogenous expression of Drp1 plays neuroprotective rol…
#> 4 10.1371/journal.pone.… A Drosophila model for developmental nicotine exposure
#> 5 10.1371/image.pbio.v0… PLoS Biology Issue Image | Vol. 6(5) May 2008
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
#> # A tibble: 1 x 2
#> numFound start
#> <int> <int>
#> 1 2480 0
#>
#> $data
#> # A tibble: 5 x 2
#> journal title
#> <chr> <chr>
#> 1 PLOS ONE Tandem Duplications and the Limits of Natural Selection in Drosophil…
#> 2 PLoS ONE A DNA Virus of Drosophila
#> 3 PLOS ONE Nematocytes: Discovery and characterization of a novel anculeate hem…
#> 4 PLOS ONE Peptidergic control in a fruit crop pest: The spotted-wing drosophil…
#> 5 PLoS ONE In Vivo RNAi Rescue in Drosophila melanogaster with Genomic Transgen…
Search terms & visualize results as a histogram OR as a plot through time
plosword allows you to search for 1 to K words and visualize the results as a histogram, comparing number of matching papers for each word
out <- plosword(list("monkey", "Helianthus", "sunflower", "protein", "whale"),
vis = "TRUE")
out$table
#> No_Articles Term
#> 1 14528 monkey
#> 2 646 Helianthus
#> 3 1876 sunflower
#> 4 164537 protein
#> 5 2142 whale
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
#> 646
Visualize terms
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.
library("ggplot2")
plot_throughtime(terms = "phylogeny", limit = 200) +
geom_line(size = 2, color = 'black')
