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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).

Load package from CRAN

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                         2073767
#> 2 plos genetics                    77191  
#> 3 plos neglected tropical diseases 72937  
#> 4 plos pathogens                   71789  
#> 5 plos computational biology       66404  
#> 6 plos biology                     44593  
#> 7 plos medicine                    32612  
#> 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 12052
#> 
#> $facet_fields
#> $facet_fields$journal
#> # A tibble: 9 x 2
#>   term                             value  
#>   <chr>                            <chr>  
#> 1 plos one                         2073767
#> 2 plos genetics                    77191  
#> 3 plos neglected tropical diseases 72937  
#> 4 plos pathogens                   71789  
#> 5 plos computational biology       66404  
#> 6 plos biology                     44593  
#> 7 plos medicine                    32612  
#> 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')
#> list()

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.0218147`
#> $`10.1371/journal.pone.0218147`$abstract
#> [1] "Background: Binge drinking, an increasingly common form of <em>alcohol</em> use disorder, is associated"
#> 
#> 
#> $`10.1371/journal.pone.0138021`
#> $`10.1371/journal.pone.0138021`$abstract
#> [1] "Background and Aim: Harmful <em>alcohol</em> consumption has long been recognized as being the major"

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.0218147`
#> $`10.1371/journal.pone.0218147`$abstract
#> [1] " common form of <em>alcohol</em>"
#> 
#> 
#> $`10.1371/journal.pone.0138021`
#> $`10.1371/journal.pone.0138021`$abstract
#> [1] ": Harmful <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>"

Visualize highligted searches

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)

highbrow1

But it works quickly with lots of results too

out <- highplos(q='alcohol', hl.fl = 'abstract', rows=1200)
highbrow(out)

highbrow2