Export classified records to compressed CSV files

Writes the results of detect_native_coord() and/or detect_native_country() to disk as gzip-compressed CSV files. Each classification supplied produces two files: all of its classified records and the native subset.

Usage

export_records(
  native_detected_coord = NA,
  native_detected_country = NA,
  export_path = NA
)

Arguments

native_detected_coord

A nativeDetected object returned by detect_native_coord(), containing records with validated coordinates. It must carry gbifID, native_status, decimalLongitude and decimalLatitude, and none of its coordinates may be missing. Optional, but at least one of native_detected_coord and native_detected_country must be supplied.

native_detected_country

A nativeDetected object returned by detect_native_country(), containing the records classified through their countryCode. It must carry gbifID and native_status; missing coordinates are allowed. Optional, but at least one of the two classification arguments must be supplied.

export_path

Directory where the compressed CSV files should be written.

Value

Called for its side effect of writing files to export_path. Returns NULL invisibly.

Details

Each classification supplied is written as its own pair of files, so the two sets never overwrite each other:

• all_records_coord.csv.gz: every record classified by detect_native_coord(), with all its columns and its native status

• native_records_coord.csv.gz: the subset of those records classified as "native"

• all_records_country.csv.gz: every record classified by detect_native_country(), with all its columns and its native status

• native_records_country.csv.gz: the subset of those records classified as "native"

Only the pair belonging to a supplied argument is written, so supplying one argument leaves the files of the other untouched. The two sets are exported separately rather than bound together: this function never writes a combined table.

The two all_records_* files are likewise not a partition of a single input and cannot be row-bound with each other. They carry different columns - the coordinate result comes from CoordinateCleaned, whereas the country-code result comes from CoordinateProblematic, which keeps its per-test verdict columns - and detect_native_country() classifies only the records it receives with a usable countryCode.

Both arguments already carry every column of the input records, so no join is performed here: each table is written straight from the object.

native_detected_coord must carry coordinates for every record: it is the spatial output of detect_native_coord(), which only classifies records with validated coordinates. The function stops if decimalLongitude or decimalLatitude is missing for any of its records, which catches the two arguments being swapped. native_detected_country carries no such requirement, because detect_native_country() classifies the records that failed coordinate validation - including records whose coordinates are entirely absent.

Files are written with fwrite(encoding = "UTF-8"). export_path is validated before writing: if it is not a single character path or exists as a file (not a directory), the function stops with an error; if it does not exist, a warning is emitted and the directory is created automatically.

See also

detect_native_coord(), detect_native_country(), par_clean_coordinates()