Honest taxonomic-completeness report — coverage

Measures, by NAME, exactly which canonical taxa/qualifiers the package's deterministic rule base registers, replacing hand-maintained coverage claims with an auditable, reproducible diff. For "usda_subgroup" the canonical reference is the Soil Taxonomy 13th-edition subgroup set from kst13_codes; for "wrb_qualifiers" it is the WRB 2022 principal + supplementary qualifier set from wrb2022_canonical.

Usage

coverage_report(
  system = c("usda_subgroup", "usda_great_group", "usda_suborder", "wrb_qualifiers",
    "sibcs"),
  write = FALSE,
  report_dir = NULL
)

Arguments

system: Which axis to measure. USDA taxon levels against the Soil Taxonomy 13th-edition code set (kst13_codes): "usda_subgroup" (default), "usda_great_group", "usda_suborder". WRB 2022 qualifiers against wrb2022_canonical: "wrb_qualifiers" – here "covered" means the qual_* function exists and is a genuine implementation (not an unconditional passed = NA stub), and the inert ones are returned in $stubs. "sibcs" has no external canonical class list, so it honestly reports registered class counts per level only (no percentage).
write: If TRUE, also write a Markdown summary to report_dir. Default FALSE.
report_dir: Directory for the Markdown report when write = TRUE. Defaults to inst/benchmarks/reports inside the installed package.

Value

Invisibly, a list with $overall (one-row data frame: system, level, canonical_n, registered_n, covered_n, missing_n, pct), $by_group (per order, or per principal/supplementary), $missing (canonical names not registered), $extra (registered names absent from the canonical set), and – for "wrb_qualifiers" – $stubs (functions that exist but are inert). A compact summary is printed as a side effect.

Examples

cov <- coverage_report("usda_subgroup")
#> 
#> ── Coverage: usda subgroup ──
#> 
#> ℹ 2049 / 2715 canonical subgroups registered (75.5%); 666 missing.
#>        group canonical_n covered_n missing_n   pct
#>     Gelisols         129       129         0 100.0
#>    Histosols          75        75         0 100.0
#>    Spodosols         121       121         0 100.0
#>      Oxisols         213       190        23  89.2
#>     Andisols         218       189        29  86.7
#>    Vertisols         158       136        22  86.1
#>  Inceptisols         349       262        87  75.1
#>     Ultisols         215       161        54  74.9
#>     Alfisols         352       247       105  70.2
#>    Mollisols         376       257       119  68.4
#>     Entisols         239       157        82  65.7
#>    Aridisols         270       125       145  46.3
cov$overall
#>   system    level canonical_n registered_n covered_n missing_n  pct
#> 1   usda subgroup        2715         2245      2049       666 75.5
head(cov$missing)
#> [1] "Abruptic Argiaquolls"             "Abruptic Argicryolls"            
#> [3] "Abruptic Argiduridic Durixerolls" "Abruptic Argidurids"             
#> [5] "Abruptic Argiudolls"              "Abruptic Durixeralfs"