extract_pubMed_data: Extract Data from PubMed Records

In dami82/businessPubMed: Extract and Prepare Data from PubMer Records

Description

Extract Data from PubMed Records

Usage

extract_pubMed_data(pubMed_query, batch_size = 1000, 
                    getKeywords = FALSE, affi_regex_exclude = NULL)

Arguments

pubMed_query	String (character vector of length 1): text of the query to be submitted to pubmed
batch_size	Numeric (integer): number of the PubMed records to be downloaded in a single iteration. Cannot exceed 5000. Recommended range: 200-2000
getKeywords	Logical. If TRUE, it forces keyword exraction.
affi_regex_exclude	String (character vector of length 1): Regex expression (case-insensitive) to be applied on the results (Address field). Records matching this expression will be filtered out.

Value

List including

params	List including the parameters used for running the Data Extraction run
data	Results of the Data extracted from the PubMed Records

Author(s)

Damiano Fantini

References

http://www.biotechworld.it/bioinf/2016/01/21/scraping-pubmed-data-via-easypubmed-xml-and-regex-in-r-for-a-targeting-campaign/

Examples

## Not run: 
pubMed_query <- "OGG1 AND 2013[PDAT]"
my_result <- extract_pubMed_data(my_PM_query, 50)
#timing
my_result$params$timing
#results
KEEP <- my_result$data$firstname == "Damiano"
my_result$data[KEEP, ]
#Num of emails retrieved
sum(!is.na(my_result$data$email))

## End(Not run)

dami82/businessPubMed documentation built on May 14, 2019, 3:33 p.m.