get_pmids_from_searches {pubmedtk} | R Documentation |
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)
Arguments
df |
A dataframe containing a column of Pubmed search
queries. This data frame cannot have columns with the following
names: |
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. |
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.
Examples
## Not run:
## 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)
## End(Not run)
[Package pubmedtk version 1.0.4 Index]