Which tests run on an input

Without tests, flag_occurrences() runs every test whose inputs are available: the columns the test reads (the needs column of flag_tests(), named through occ_columns()) and, for range, species range polygons in gazetteers. Running a test only adds its flags, so which records to exclude is decided afterwards by a cleaning rule (see has_flag() and tally_flags()).

Usage

test_plan(x, columns = occ_columns(), gazetteers = NULL)

Arguments

x

Input to flag_occurrences(): a data frame, or a path to a file or directory. Or its output: an occ_flags data frame, an occ_flagged object, or the output directory.

columns, gazetteers

As in flag_occurrences(); used for input only.

Value

A data frame with one row per test in layout order: test, run (logical), missing (the input the test lacks: column names, "range polygons", or "a path" for a grouped test given a single-run vectra_node; NA when it runs or was not requested) and reason (why the test does not run, NA when it runs).

Details

For input, test_plan() lists the tests that would run and the reason each other test would not. For flag output, it lists the tests that ran and the reason each other test did not: a missing input, or "not requested" when tests named the tests to run.

Examples

x <- data.frame(species = c("a", "a", "b"),
                decimalLongitude = c(12.58, 0, 16.37),
                decimalLatitude = c(55.67, 0, 48.21))
p <- test_plan(x)
p[p$run, "test"]
p[!p$run, ]