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
#> X1 X2
#> 1 plos one 1083485
#> 2 plos genetics 45073
#> 3 plos pathogens 39357
#> 4 plos computational biology 32816
#> 5 plos neglected tropical diseases 29607
#> 6 plos biology 27463
#> 7 plos medicine 19179
#> 8 plos clinical trials 521
#> 9 plos collections 15
#> 10 plos medicin 9
#>
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL
Using facet.query to get counts
facetplos(q='*:*', facet.field='journal', facet.query='cell,bird')
#> $facet_queries
#> term value
#> 1 cell,bird 21
#>
#> $facet_fields
#> $facet_fields$journal
#> X1 X2
#> 1 plos one 1083485
#> 2 plos genetics 45073
#> 3 plos pathogens 39357
#> 4 plos computational biology 32816
#> 5 plos neglected tropical diseases 29607
#> 6 plos biology 27463
#> 7 plos medicine 19179
#> 8 plos clinical trials 521
#> 9 plos collections 15
#> 10 plos medicin 9
#>
#>
#> $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')
#> $facet_queries
#> NULL
#>
#> $facet_fields
#> NULL
#>
#> $facet_dates
#> $facet_dates$publication_date
#> date value
#> 1 2015-06-26T00:00:00Z 1918
#> 2 2015-06-27T00:00:00Z 0
#> 3 2015-06-28T00:00:00Z 1814
#> 4 2015-06-29T00:00:00Z 2573
#> 5 2015-06-30T00:00:00Z 759
#> 6 2015-07-01T00:00:00Z 0
#>
#>
#> $facet_ranges
#> 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.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"
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.pmed.0040151`
#> $`10.1371/journal.pmed.0040151`$abstract
#> [1] "Background: <em>Alcohol</em>"
#>
#>
#> $`10.1371/journal.pone.0027752`
#> $`10.1371/journal.pone.0027752`$abstract
#> [1] " of <em>alcohol</em> on TB management"
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.0039681`
#> $`10.1371/journal.pone.0039681`$everything
#> [1] " Selection of Transcriptomics <em>Experiments</em> Improves Guilt-by-Association Analyses Transcriptomics <em>Experiment</em>"
#>
#>
#> $`10.1371/annotation/9b8741e2-0f5f-49f9-9eaa-1b0cb9b8d25f`
#> $`10.1371/annotation/9b8741e2-0f5f-49f9-9eaa-1b0cb9b8d25f`$everything
#> [1] " in the labels under the bars. The labels should read <em>Experiment</em> 3 / <em>Experiment</em> 4 instead of <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)
