This function's main goal is to merge and standardize different datasets into a new dataset with column names following the Darwin Core terminology. All the process is based on a metadata file provided by the user.
bdc_standardize_datasets( metadata, format = "csv", overwrite = FALSE, save_database = FALSE )
A data frame with metadata containing information about the name, path, and columns of the original data set which need to be renamed. See @details.
a character setting the output file type. Option available are "csv" and "qs" (recommenced to save large datasets). Default == "csv".
A logical vector indicating whether the final merged dataset should be overwritten. The default is FALSE.
logical. Should the standardized database be locally saved? Default = FALSE.
A merged data.frame with column names following Darwin Core terminology.
bdc_standardize_datasets() facilitate the standardization of datasets with
different column names by converting them into a new dataset following the
Darwin Core terminology. The standardization process relies on a metadata
file containing the name, path, and columns that need to be renamed. The
metadata file can be constructed using built-in functions (e.g.,
data.frame()) or storing the information in a CSV file and importing it
into R. Regardless of the method chosen, the data frame with metadata needs
to contain the following column names (this is a list of required column
names; for a comprehensive list of column names following Darwin Core
datasetName: A short name identifying the dataset (e.g., GBIF)
fileName: The relative path containing the name of the input dataset
scientificName: Name of the column in the original database presenting
the taxon scientific names with or without authorship information, depending
on the format of the source dataset (e.g., Myrcia acuminata)
decimalLatitude: Name of the column in the original database presenting
the geographic latitude in decimal degrees (e.g., -6.370833)
decimalLongitude: Name of the column in the original database presenting
the geographic longitude in decimal degrees (e.g., -3.25500)