extract_pubMed_fast: Quick Extraction of Data from PubMed Records

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

Description

Extract Data from PubMed Records via the alternative method.

Usage

extract_pubMed_fast(pubMed_query, 
                    batch_size = 1000, 
                    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.
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_fast(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.