scrape2csv: Scrape PubMed, Compile information, and Export to csv

In biostatistically/PubscrapeR: Scrape PubMed, Compile, and Export to csv

Description

Queries PubMed using the extract_PubMed_data from the businessPubMed package. If a journal list is defined, the query will be performed iteratively through a loop. Results are compiled and exported to csv.

Usage

scrape2csv(
  narrow,
  broad = NULL,
  operator = NULL,
  journals = NULL,
  start,
  end = NULL,
  title = NULL,
  outpath = NULL,
  newfolder = TRUE,
  raw = TRUE,
  clist = TRUE,
  alist = FALSE,
  plist = FALSE,
  jlist = FALSE,
  report = TRUE
)

Arguments

narrow	Character vector of length 1: key search terms in double quotes using AND as the operator between terms all enclosed within parentheses
broad	Character vector of length 1: key search terms in quotes using OR as the operator between terms all enclosed within parentheses
operator	Character string: Defines the boolean operator (AND, OR, NOT) between narrow and broad (AND is default)
journals	Character vector of length j: journals to query search terms through a loop
start	Character string: start publication date for the query YYYY, or YYYY/MM, or YYYY/MM/DD format
end	Character string: end publication date for the query YYYY, or YYYY/MM, or YYYY/MM/DD format (default is 3000/12/31)
title	Character string: title of the search,'used as prefix to output
outpath	Character string: path for the output
newfolder	If 'TRUE', a new folder is created for the output (default is TRUE)
raw	If 'TRUE', raw query results are exported to csv (default is TRUE)
clist	If 'TRUE', a list of author email contacts cleaned of duplicates is exported (default is TRUE)
alist	If 'TRUE', a list of authors resulting from the query is exported (default is TRUE)
plist	If 'TRUE', a list of publication titles resulting from the query is exported (default is TRUE)
jlist	If 'TRUE', and 'journals' is not specified, a list of journals resulting from the query is exported (default is FALSE)
report	If 'TRUE', a query report is exported to csv (default is TRUE)

Examples

my.keywords = '("COVID-19" AND "coronavirus")'
my.keyphrases = '("ARDS" OR "acute respiratory distress syndrome")'
my.journals = c("JAMA Cardiol", "Allergy Asthma Clin Immunol", "N Engl J Med")
my.title = "Covid"
my.start = "2019"
scrape2csv(narrow = my.keywords, broad = my.keyphrases, operator = "OR", journals = my.journals, 
  start = my.start, title = my.title)
# searches (("COVID-19" AND "coronavirus") OR ("ARDS" OR "acute respiratory distress syndrome")) 
#   from 2019 on in 3 selected journals

biostatistically/PubscrapeR documentation built on Dec. 31, 2020, 8:55 p.m.