easyPubMed: table_articles_byAuth – R documentation

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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 limit data extraction to first authors or last authors only, or get information about all authors of each PubMed record.

Usage

table_articles_byAuth(pubmed_data, 
                             included_authors = "all", 
                             max_chars = 500, 
                             autofill = TRUE, 
                             dest_file = NULL, 
                             getKeywords = TRUE, 
                             encoding = "UTF8")

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.
`getKeywords`	Logical. If TRUE, the operation will attempt to extract PubMed record keywords (MESH topics, keywords).
`encoding`	The encoding of an input/output connection can be specified by name (for example, "ASCII", or "UTF-8", in the same way as it would be given to the function base::iconv(). See iconv() help page for how to find out more about encodings that can be used on your platform. Here, we recommend using "UTF-8".

Details

Retrieve publication and author information from PubMed data, and cast them as a data.frame.

Value

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

Author(s)

Damiano Fantini damiano.fantini@gmail.com

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

## Not run: 
## Cast PubMed record info into a data.frame

dami_query <- "Damiano Fantini[AU]"
dami_on_pubmed <- get_pubmed_ids(dami_query)
dami_abstracts_xml <- fetch_pubmed_data(dami_on_pubmed, encoding = "ASCII")
xx <- table_articles_byAuth(pubmed_data = dami_abstracts_xml, 
                            included_authors = "first", 
                            max_chars = 100, 
                            autofill = TRUE)

print(xx[1:5, c("pmid", "lastname", "jabbrv")])
#
## Download records first
## Also, auto-fill disabled
dami_query <- "Damiano Fantini[AU]"
curr.file <- batch_pubmed_download(dami_query, dest_file_prefix = "test_bpd_", encoding = "ASCII")
xx <- table_articles_byAuth(pubmed_data = curr.file[1], 
                            included_authors = "all", 
                            max_chars = 20, 
                            autofill = FALSE)
print(xx[1:5, c("pmid", "lastname", "jabbrv")])


## End(Not run)

easyPubMed

Search and Retrieve Scientific Publication Records from PubMed

v2.13

GPL-2

Authors

Damiano Fantini

Initial release

2019-03-25