In ropensci/rplos: Interface to the Search API for 'PLoS' Journals
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.
- Search across PLoS papers in various sections of papers
- Search for terms and visualize results as a histogram OR as a plot through
time
- Text mining of scientific literature
Load package from CRAN
install.packages("rplos")
library('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
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
#> 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')
More
See the Faceted and highlighted searches and Full text vignettes for
more rplos help.
ropensci/rplos documentation built on Sept. 12, 2022, 2:10 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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.
- Search across PLoS papers in various sections of papers
- Search for terms and visualize results as a histogram OR as a plot through time
- Text mining of scientific literature
Load package from CRAN
install.packages("rplos")
library('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.
plosauthorsearchers in authorsplosabstractsearches in abstractsplostitlesearches in titlesplosfigtabcapssearches in figure and table captionsplossubjectsearches 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
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 #> 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')
More
See the Faceted and highlighted searches and Full text vignettes for
more rplos help.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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