Convert flags to CoordinateCleaner's spatialvalid format

Returns flagged records in the layout that CoordinateCleaner's clean_coordinates() and clean_fossils() return with value = "spatialvalid", so code written for that object (its summary() and plot() methods, filters on .summary) runs unchanged. The record columns come first, then one logical column per test, TRUE when the record passes, then .summary, TRUE when it passes every test given.

Usage

as_spatialvalid(x, tests = NULL)

Arguments

x

A flagged data frame (occ_flags) from flag_occurrences(), or flags written to disk (an occ_flagged object or its directory). Flags on disk are read into memory with their keep columns as the record columns.

tests

Tests to include, from those x was flagged with; default all of them. .summary is then the complement of the rule made of these tests.

Value

A data frame of class c("spatialvalid", "data.frame"), carrying the reference and layout version of the flags as attributes occ_reference and occ_layout_version.

Details

Each test takes the column name CoordinateCleaner uses for it (.cap for capital, .otl for outlier, see the spatialvalid column of flag_tests()); a test without one there is written as .<test>, for example .issue_coordinate. The columns are decoded from the flags word, so a record whose flag word is NA is NA in every column.

See also

flag_occurrences(), has_flag()

Examples

x <- data.frame(species = c("a", "a", "b"),
                decimalLongitude = c(0, 16.37, 10),
                decimalLatitude = c(0, 48.21, 50))
sv <- as_spatialvalid(flag_occurrences(x))
sv
sv[sv$.summary, ]