Faceted and highlighted searches

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

install.packages("rplos")

library('rplos')

Faceted search

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()

Highlighted search

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

Faceted and highlighted searches

Scott Chamberlain

2021-02-23

Load package from CRAN

Faceted search

Highlighted search

Visualize highligted searches