In addition to searchplos() and related searching functions, there are a
few slightly different ways to search: faceting and highlighted searches.
Faceting allows you to ask, e.g., how many articles are published in each of
the PLOS journals. Highlighting allows you to ask, e.g., highlight terms that
I search for in the text results given back, which can make downstream
processing easier, and help visualize search results (see highbrow() below).
install.packages("rplos")
library('rplos')
Facet by journal
facetplos(q='*:*', facet.field='journal')
#> $facet_queries
#> NULL
#>
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 9 x 2
#> term value
#> <chr> <chr>
#> 1 plos one 1697963
#> 2 plos genetics 63684
#> 3 plos pathogens 57289
#> 4 plos neglected tropical diseases 52972
#> 5 plos computational biology 49489
#> 6 plos biology 34969
#> 7 plos medicine 25287
#> 8 plos clinical trials 521
#> 9 plos medicin 9
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
Using facet.query to get counts
facetplos(q='*:*', facet.field='journal', facet.query='cell,bird')
#> $facet_queries
#> # A tibble: 1 x 2
#> term value
#> <chr> <int>
#> 1 cell,bird 6
#>
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 9 x 2
#> term value
#> <chr> <chr>
#> 1 plos one 1697963
#> 2 plos genetics 63684
#> 3 plos pathogens 57289
#> 4 plos neglected tropical diseases 52972
#> 5 plos computational biology 49489
#> 6 plos biology 34969
#> 7 plos medicine 25287
#> 8 plos clinical trials 521
#> 9 plos medicin 9
#>
#>
#> $facet_pivot
#> NULL
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
Date faceting
facetplos(q='*:*', url=url, facet.date='publication_date',
facet.date.start='NOW/DAY-5DAYS', facet.date.end='NOW',
facet.date.gap='+1DAY')
#> NULL
Search for the term alcohol in the abstracts of articles, return only 10 results
highplos(q='alcohol', hl.fl = 'abstract', rows=2)
#> $`10.1371/journal.pone.0201042`
#> $`10.1371/journal.pone.0201042`$abstract
#> [1] "\nAcute <em>alcohol</em> administration can lead to a loss of control over drinking. Several models argue"
#>
#>
#> $`10.1371/journal.pone.0185457`
#> $`10.1371/journal.pone.0185457`$abstract
#> [1] "Objectives: <em>Alcohol</em>-related morbidity and mortality are significant public health issues"
Search for the term alcohol in the abstracts of articles, and return fragment size of 20 characters, return only 5 results
highplos(q='alcohol', hl.fl='abstract', hl.fragsize=20, rows=2)
#> $`10.1371/journal.pone.0201042`
#> $`10.1371/journal.pone.0201042`$abstract
#> [1] "\nAcute <em>alcohol</em>"
#>
#>
#> $`10.1371/journal.pone.0185457`
#> $`10.1371/journal.pone.0185457`$abstract
#> [1] "Objectives: <em>Alcohol</em>"
Search for the term experiment across all sections of an article, return
id (DOI) and title fl only, search in full articles only
(via fq='doc_type:full'), and return only 10 results
highplos(q='everything:"experiment"', fl='id,title', fq='doc_type:full',
rows=2)
#> $`10.1371/journal.pone.0154334`
#> $`10.1371/journal.pone.0154334`$everything
#> [1] " and designed the <em>experiments</em>: RJ CM AOC. Performed the <em>experiments</em>: RJ AOC. Analyzed the data: RJ. Contributed"
#>
#>
#> $`10.1371/journal.pone.0039681`
#> $`10.1371/journal.pone.0039681`$everything
#> [1] " Selection of Transcriptomics <em>Experiments</em> Improves Guilt-by-Association Analyses Transcriptomics <em>Experiment</em>"
Browse highlighted fragments in your default browser
This first examle, we only looko at 10 results
out <- highplos(q='alcohol', hl.fl = 'abstract', rows=10)
highbrow(out)
But it works quickly with lots of results too
out <- highplos(q='alcohol', hl.fl = 'abstract', rows=1200)
highbrow(out)
