Check measured values against the registry's declared bounds

The standard bounds check for an ingest notebook and for the release. Compares every value in a long-format measurement table against valid_min / valid_max from metadata/measurement_type.csv, and reports the types that violate a bound alongside the types that declare none — see the note in R/bounds.R for why the second matters at least as much as the first.

Usage

check_measurement_bounds(
  con,
  tbl = "obs",
  mt = NULL,
  dataset_key = NULL,
  type_col = "measurement_type",
  value_col = "measurement_value",
  depth_col = NULL,
  include_undeclared = TRUE
)

Arguments

con

DuckDB connection

tbl

table or view to check (default "obs"). Works on any long-format table: the per-dataset {dataset}_measurement during wrangling, the emitted obs, or sample_measurement.

mt

the measurement registry: a data.frame, a path to measurement_type.csv, or NULL (default) to read a measurement_type table from con.

dataset_key

optional dataset_key to filter to, when tbl holds more than one dataset. Ignored if tbl has no dataset_key column.

type_col, value_col

column names (default measurement_type / measurement_value)

depth_col

optional depth column enabling the depth-window check against valid_depth_min_m / valid_depth_max_m — the depth over which a type is defined. A non-null value outside that window is a finding: it means the type was emitted where the registry says it does not exist.

include_undeclared

report types with no declared bound (default TRUE). Set FALSE for a violations-only view.

Value

A tibble, one row per measurement type present, ordered worst-first (violations by count, then undeclared by count):

status

out_of_range (declared and violated), undeclared (nothing declared), ok (declared and respected)

n_total, n_bad, pct_bad

rows checked, rows outside, percent

n_low, n_high

split by which bound was broken

v_min, v_max

observed range, for proposing a bound

valid_min, valid_max

what the registry declares

n_outside_depth

present only when depth_col is given

finding

a one-line summary, ready to paste into the context column of a questions.csv row

Details

Read-only: it deletes and rewrites nothing. Enforce with drop_out_of_bounds(), and only once the bound is agreed.

Bounds may be one-sided. valid_min = 0 with no valid_max is the useful case for abundances and counts — "never negative" is agreeable without knowing the ceiling — and a type is undeclared only when both are missing.

See also

drop_out_of_bounds() to enforce, bounds_datatable() to render, read_measurement_type() for the registry, register_measurement_types() to declare a new bound.

Examples

if (FALSE) { # \dontrun{
b <- check_measurement_bounds(
  con, "ctd_measurement",
  mt = here::here("metadata/measurement_type.csv"))
bounds_datatable(b)
} # }