pubmedtk (version 1.0.4)

get_pmids_from_searches: Downloads PMID results for a column of Pubmed search queries in a data frame

Description

Downloads PMID results for a column of Pubmed search queries in a data frame

Usage

get_pmids_from_searches(df, column, api_key, quiet = FALSE)

Value

A data frame containing the original columns as well as three additional columns:

The `pubmed_search_success` column is TRUE in the case that the
search rcesults were successfully obtained from Pubmed; FALSE
in the case that an error occurred in search (e.g. due to a
search query that is not well-formed).
The `n_results` column contains the number of research results
for the query provided.
The `pmids` column returns a JSON-encoded list of PMID's for
the search query provided.

Arguments

df

A dataframe containing a column of Pubmed search queries. This data frame cannot have columns with the following names: pubmed_search_success, pmids.

column

The name of the column containing Pubmed search queries

api_key

A valid Pubmed API key

quiet

A boolean TRUE or FALSE. If TRUE, no progress messages will be printed during download. FALSE by default, messages printed for every version downloaded showing progress.

Examples

if (FALSE) {
## Read in API key
ak <- readLines("api_key.txt")

## Example Pubmed searches, some valid, some not, some with more
## than 10k results
searches <- tribble(
  ~terms,
  "Carlisle B[Author]",
  "NCT00267865",
  "(Clinical Trial[Publication Type])",
  ""
)

## Download search results
results <- get_pmids_from_searches(searches, "terms", ak)
}