dbparser (version 1.2.0)

drug_element: extracts the given drug elements and return data as list of tibbles.

Description

drug_element returns list of tibbles of drugs selected elements.

Usage

drug_element(
  elements_options = c("all"),
  save_table = FALSE,
  save_csv = FALSE,
  csv_path = ".",
  override_csv = FALSE,
  database_connection = NULL
)

Arguments

elements_options

list, options of elements to be parsed. default is "all"

save_table

boolean, save table in database if true.

save_csv

boolean, save csv version of parsed tibble if true

csv_path

location to save csv files into it, default is current location, save_csv must be true

override_csv

override existing csv, if any, in case it is true in the new parse operation

database_connection

DBI connection object that holds a connection to user defined database. If save_table is enabled without providing value for this function an error will be thrown. @return list of selected drug elements tibbles

Details

this functions extracts selected element of drug nodes in DrugBank xml database with the option to save it in a predefined database via passed database connection. it takes two optional arguments to save the returned tibble in the database save_table and database_connection. it must be called after read_drugbank_xml_db function like any other parser function. if read_drugbank_xml_db is called before for any reason, so no need to call it again before calling this function.

drug_element_options can be called to know the valid options for this method

See Also

Other common: drug_element_options(), run_all_parsers()

Examples

if (FALSE) {
# return only the parsed tibble
drug_element()

# will throw an error, as database_connection is NULL
drug_element(save_table = TRUE)

# save parsed tibble as csv if it does not exist in current location and
# return parsed tibble.
# if the csv exist before read it and return its data.
drug_element(save_csv = TRUE)


sqlite_con <- DBI::dbConnect(RSQLite::SQLite())
drug_element(save_table = TRUE, database_connection = sqlite_con)

# save in database, save parsed tibble as csv if it does not
# exist in current location and return parsed tibble.
# if the csv exist before read it and return its data.
drug_element(save_table = TRUE, save_csv = TRUE,
 database_connection = sqlite_con)

# save parsed tibble as csv if it does not exist in given location and
# return parsed tibble.
# if the csv exist before read it and return its data.
drug_element(save_csv = TRUE, csv_path = TRUE)

# save parsed tibble as csv if it does not exist in current
# location and return parsed tibble.
# if the csv exist override it and return it.
drug_element(save_csv = TRUE, csv_path = TRUE, override = TRUE)
drug_element(c("drug_ahfs_codes", "drug_carriers"), save_table = TRUE)
drug_element(save_table = FALSE)
drug_element(c("drug_ahfs_codes", "drug_carriers"))
}