easyPubMed (version 2.3)

table_articles_byAuth: Extract Publication and Affiliation Data from PubMed Records

Description

Extract Publication Info from PubMed records and cast data into a data.frame where each row corresponds to a different author. It is possible to retrieve data from first authors or last authors only as well as information from all authors of each PubMed record.

Usage

table_articles_byAuth(pubmed_data, 
                      included_authors = "all", 
                      max_chars = 500, 
                      autofill = TRUE, 
                      dest_file = NULL)

Arguments

pubmed_data

PubMed Data in XML format: typically, an XML file resulting from a batch_pubmed_download() call or an XML object, result of a fetch_pubmed_data() call.

included_authors

Character: c("first", "last", "all"). Only includes information from the first, the last or all authors of a PubMed record.

max_chars

Numeric: maximum number of chars to extract from the AbstractText field.

autofill

Logical. If TRUE, missing affiliations are imputed according to the available values (from the same article)

dest_file

String (character of length 1). Name of the file that will be written for storing the output. If NULL, no file will be saved.

Value

Data frame including the following fields: c("article.title","article.abstract", "date.year","date.month","date.day", "journal.abbrv","journal.title", "auth.last","auth.fore","auth.address", "auth.email").

Details

Retrieve publiccation and author information from PubMed data in the form of a data frame.

References

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

Examples

# NOT RUN {
#
#
dami_query <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query)
dami_abstracts_xml <- fetch_pubmed_data(dami_on_pubmed)
table_articles_byAuth(pubmed_data = dami_abstracts_xml, 
                      included_authors = "first", 
                      max_chars = 100, 
                      autofill = TRUE)[1:2,]
#
#
dami_query <- "Damiano Fantini[AU]"
curr.file <- batch_pubmed_download(dami_query, dest_file_prefix = "test_bpd_")
table_articles_byAuth(pubmed_data = curr.file[1], 
                      included_authors = "all", 
                      max_chars = 20, 
                      autofill =FALSE)
# }