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Share of records flagged, per test and rule

Source: R/methods.R
summary.occ_flags.Rd

Turns flag counts into percentages: for every rule, how many records each of its tests flags, how many it is the only reason the rule removes, and how many the rule removes in total. A record can fail several tests, so the per-test shares of a rule can add up to more than the rule's total; the only shares add up to at most that total, and the rest is records removed for more than one reason.

Usage

# S3 method for class 'occ_flags'
summary(object, ...)

# S3 method for class 'occ_flagged'
summary(object, ...)

# S3 method for class 'occ_tally'
summary(object, ...)

Arguments

object

A data frame returned by flag_occurrences() (class occ_flags), an occ_flagged object, or a table from tally_flags().

...

Passed to tally_flags(): rules, by, bins, tests.

Value

A data frame of class occ_summary, one row per group, rule and test of the rule, plus one row per group and rule with test = "(any)" for the rule as a whole. Columns: the grouping columns, rule, test, n (records in the group), flagged (records carrying the test, or removed by the rule), pct (flagged as a percentage of n), only (records whose sole flag among the rule's tests is this one) and pct_only.

Details

summary() on a flagged data frame or on on-disk flag output first calls tally_flags() with the arguments in ..., so rules, by and bins work as there; on an occ_tally it reshapes the counts already made.

See also

plot.occ_summary() to draw it.

Examples

x <- data.frame(species = c("a", "a", "b", "c", "c"),
                kingdom = c("P", "P", "A", "A", "A"),
                decimalLongitude = c(12.58, 0, 16.37, 2.35, 2.35),
                decimalLatitude = c(55.67, 0, 48.21, 48.85, 48.85))
f <- flag_occurrences(x)
summary(f)
summary(f, rules = list(strict = c("zero", "capital", "duplicate")), by = "kingdom")