parse_doc: Read and parse doc of PubMed records and extract specified...

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

Description

Read and parse doc of PubMed records and extract specified datatypes as csv's

Usage

parse_doc(
  doc,
  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

doc	Filepath of doc of 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	and @param suffix If both are equal to default, doc is checked against filename patterns of files generated by fetch_batch (either "YYYY-MM-DD_FILENAME_SUFFIX.txt" or "YYYY-MM-DD_FILENAME.txt"). Available values are extracted.
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.