parse_batch: Parse batch of PubMed records and extract specified datatypes...

In maia-sh/pubmedparser: Fetch and Parse PubMed Records

Description

Parse batch of PubMed records and extract specified datatypes as csv's

Usage

parse_batch(
  batch,
  pmids = NULL,
  datatypes = c("table", "abstract", "databanks", "authors", "mesh", "keywords",
    "pubtypes"),
  file_name = "pubmed",
  suffix = NULL,
  dir = here::here(),
  subdir = dir,
  quiet = FALSE,
  return = TRUE
)

Arguments

batch	Batch of unparsed PubMed records, such as the output of fetch_batch.
pmids	Vector of pmids. If pmids not user-provided, pmids will be saved as .rds.
datatypes	Types of data to extract from xml for which there is a corresponding "pubmed_" function ("table", "abstract", "databanks", "authors", "mesh", "keywords", "pubtypes")
file_name	Root for file names. Defaults to "pubmed".
suffix	Suffix for file names. For example, record numbers. Defaults to NULL.
dir	Directory for saving files (log file and pmids.rds, and extracted csv's, depending on subdir). Defaults to project root (here::here())
subdir	Directory for saving extracted csv's. Defaults to dir.
quiet	Whether to silence messages in console. Defaults to FALSE.
return	Whether to return parsed xml. Defaults to TRUE. Set to FALSE if interested in only side-effect csv's.

Value

Parsed xml with names = pmids. Also, side-effect of specified datatypes as csv's.

maia-sh/pubmedparser documentation built on Feb. 18, 2021, 11:44 a.m.