searchplos: Base function to search PLoS Journals

Description

Base function to search PLoS Journals

Usage

searchplos(q = NULL, fl = "id", fq = NULL, sort = NULL, start = 0, limit = 10, key = NULL, sleep = 6, callopts = list(), terms = NULL, fields = NULL, toquery = NULL)

Arguments

Search terms (character). You can search on specific fields by doing 'field:your query'. For example, a real query on a specific field would be 'author:Smith'.

Fields to return from search (character) [e.g., 'id,title'], any combination of search fields [type 'data(plosfields)', then 'plosfields'].

List specific fields to filter the query on (if NA, all queried). The options for this parameter are the same as those for the fl parameter. Note that using this parameter doesn't influence the actual query, but is used to filter the resuls to a subset of those you want returned. For example, if you want full articles only, you can do 'doc_type:full'. In another example, if you want only results from the journal PLOS One, you can do 'cross_published_journal_key:PLoSONE'. See journalnamekey() for journal abbreviations.

sort

Sort results according to a particular field, and specify ascending (asc) or descending (desc) after a space; see examples. For example, to sort the counter_total_all field in descending fashion, do sort='counter_total_all desc'

start

Record to start at (used in combination with limit when you need to cycle through more results than the max allowed=1000)

limit

Number of results to return (integer)

key

Your PLoS API key, either enter as the key, or loads from .Rprofile. See details.

sleep

Number of seconds to wait between requests. No need to use this for a single call to searchplos. However, if you are using searchplos in a loop or lapply type call, do sleep parameter is used to prevent your IP address from being blocked. You can only do 10 requests per minute, so one request every 6 seconds is about right.

callopts

Optional additional curl options (debugging tools mostly)

terms

DEPRECATED PARAMETER - replaced with the q param.

fields

DEPRECATED PARAMETER - replaced with the fl param.

toquery

DEPRECATED PARAMETER - replaced with the fq param.

Value

An object of class "plos", with a list of length two, each element being a list itself.

Details

Get a PLOS API key at http://alm.plos.org/. Note that the API key you recieve at that URL works for the PLOS ALM (article-level metrics) API as well. See the alm package http://cran.r-project.org/web/packages/alm/index.html to access PLOS ALM data.

You can store your PLOS Search API key in your .Rprofile file so that you don't have to enter the key each function call. Open up your .Rprofile file on your computer, and put it an entry like:

options(PlosApiKey = "your plos api key")

Faceting: Read more about faceting here: urlhttp://wiki.apache.org/solr/SimpleFacetParameters

Examples

Run this code

## Not run: 
# searchplos(q='ecology', fl=c('id','publication_date'), limit = 2)
# searchplos('ecology', fl=c('id','publication_date'), limit = 2)
# searchplos('ecology', c('id','title'), limit = 2)
# 
# # Get only full article DOIs
# out <- searchplos(q="*:*", fl='id', fq='doc_type:full', start=0, limit=250)
# head(out)
# 
# # Get DOIs for only PLoS One articles
# out <- searchplos(q="*:*", fl='id', fq='cross_published_journal_key:PLoSONE', start=0, limit=15)
# head(out)
# 
# # Get DOIs for full article in PLoS One
# out <- searchplos(q="*:*", fl='id', fq=list('cross_published_journal_key:PLoSONE',
#    'doc_type:full'), limit=50)
# head(out)
# 
# # Serch for many q
# q <- c('ecology','evolution','science')
# lapply(q, function(x) searchplos(x, limit=2))
# 
# # Query to get some PLOS article-level metrics, notice difference between two outputs
# out <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),fq='doc_type:full')
# out_sorted <- searchplos(q="*:*", fl=c('id','counter_total_all','alm_twitterCount'),
#    fq='doc_type:full', sort='counter_total_all desc')
# head(out)
# head(out_sorted)
# 
# # A list of articles about social networks that are popular on a social network
# searchplos(q="*:*",fl=c('id','alm_twitterCount'),
#    fq=list('doc_type:full','subject:"Social networks"','alm_twitterCount:[100 TO 10000]'),
#    sort='counter_total_month desc')
# 
# # Show me all articles that have these two words less then about 15 words apart.
# searchplos(q='everything:"sports alcohol"~15', fl='title', fq='doc_type:full')
# 
# # Now let's try to narrow our results to 7 words apart. Here I'm changing the ~15 to ~7
# searchplos(q='everything:"sports alcohol"~7', fl='title', fq='doc_type:full')
# 
# # Now, lets also only look at articles that have seen some activity on twitter.
# # Add "fq=alm_twitterCount:[1 TO *]" as a parameter within the fq argument.
# searchplos(q='everything:"sports alcohol"~7', fl=c('alm_twitterCount','title'),
#    fq=list('doc_type:full','alm_twitterCount:[1 TO *]'))
# searchplos(q='everything:"sports alcohol"~7', fl=c('alm_twitterCount','title'),
#    fq=list('doc_type:full','alm_twitterCount:[1 TO *]'),
#    sort='counter_total_month desc')
# 
# # Return partial doc parts
# ## Return Abstracts only
# out <- searchplos(q='*:*', fl=c('doc_partial_body','doc_partial_parent_id'),
#    fq=list('doc_type:partial', 'doc_partial_type:Abstract'), limit=3)
# ## Return Title's only
# out <- searchplos(q='*:*', fl=c('doc_partial_body','doc_partial_parent_id'),
#    fq=list('doc_type:partial', 'doc_partial_type:Title'), limit=3)
# 
# # Remove DOIs for annotations (i.e., corrections)
# searchplos(q='*:*', fl=c('id','article_type'),
#    fq='-article_type:correction', limit=100)
# 
# # Remove DOIs for annotations (i.e., corrections) and Viewpoints articles
# searchplos(q='*:*', fl=c('id','article_type'),
#    fq=list('-article_type:correction','-article_type:viewpoints'), limit=100)
# 
# # Get eissn codes
# searchplos(q='*:*', fl=c('id','journal','eissn','cross_published_journal_eissn'),
#    fq="doc_type:full", limit = 60)
# ## End(Not run)