easyPubMed (version 3.1.6)

EPM_validate_parse_params: Validate Parameters of a PubMed Record Parsing Job.

Description

Check and correct (if needed) the parameters of an easyPubMed Record Parsing job.

Usage

EPM_validate_parse_params(params)

Value

list including the vetted parameters.

Arguments

params

list of user-provided parameters.

Author

Damiano Fantini,

Details

The following elements are expected and/or parsed from the `params` list:

• `max_authors`. Numeric, maximum number of authors to retrieve. If this is set to -1, only the last author is extracted. If this is set to 1, only the first author is returned. If this is set to 2, the first and the last authors are extracted. If this is set to any other positive number (i), up to the leading (i-1) authors are retrieved together with the last author. If this is set to a number larger than the number of authors in a record, all authors are returned. Note that at least 1 author has to be retrieved, therefore a value of 0 is not accepted (coerced to -1).

• `autofill_address`. Logical, shall author affiliations be propagated within each record to fill missing values.

• `compact_output`. Logical, shall record data be returned in a compact format where each row is a single record and author names are collapsed together. If `FALSE`, each row corresponds to a single author of the publication and the record-specific data are recycled for all included authors.

• `include_abstract`. Logical, shall abstract text be included in the output `data.frame`.

• `max_references`. Numeric, maximum number of references to return (from each PubMed record).

• `ref_id_type`. String, must be one of the following values: `c('pmid', 'doi')`.

• `verbose`. Logical, shall details about the progress of the operation be printed to console.

References

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

Examples

prms <- list(
  max_authors  = 12, 
  autofill_address = TRUE, 
  compact_output = FALSE,
  include_abstract = TRUE, 
  max_references = 100, 
  ref_id_type = 'doi',
  verbose = TRUE)
easyPubMed:::EPM_validate_parse_params(prms)