easyPubMed (version 2.3)

articles_to_list: Cast PubMed Data into a List of Articles

Description

Convert an XML object of PubMed records into a list of strings (character vector of length 1) corresponding to individual PubMed articles. PubMed records are identified by a "/PubmedArticle" XML tag. This automatically cast all the content of each PubMed record to a character-class object without removing XML tags.

Usage

articles_to_list(pubmed_data)

Arguments

pubmed_data

String corresponding to the name of an XML file (typically, the result of a batch_pubmed_download() call). Alternatively, an XML Object, such as the result of a fetch_pubmed_data() call.

Value

List of character elements including the all records from the original XML object. Elements in the list are not named and are only accessible via the numeric index.

Details

The input is an XML object or an XML file, typically the result of a fetch_pubmed_data() call or a batch_pubmed_download() call. The function returns a list where each element is a different PubMed record.

References

http://www.biotechworld.it/bioinf/2016/01/05/querying-pubmed-via-the-easypubmed-package-in-r/

Examples

# NOT RUN {
#
# retrieve PubMed data and return a list ot articles
dami_query <- "Damiano Fantini[AU]"
outfile <- batch_pubmed_download(dami_query, dest_file_prefix = "easyPM_ex001_")
listed_articles <- articles_to_list(pubmed_data = outfile)
listed_articles[[3]]
# }