test: modularize test suite, fix S7 checks, and add comprehensive coverage (PR 7)

.Rbuildignore

@@ -16,3 +16,7 @@ internal-data/*
 ^doc$
 ^Meta$
 ^vignettes/\.quarto$
+^inst/volume/SNFI3_volume_coefficients$
+^inst/volume/SNFI4_volume_coefficients$
+^inst/volume/SFNI4_volume_equations\.py$
+^inst/volume/volume_equations\.xlsx$

DESCRIPTION

@@ -38,7 +38,9 @@ Collate:
     'metrics-stand-level.R'
     'metrics-tree-level.R'
     'predict-biomass.R'
+    'predict-carbon.R'
     'predict-height.R'
+    'predict-snfi-volume.R'
     'sample-size.R'
     'silviculture-package.R'
     'treatment-thinning.R'

NAMESPACE

@@ -21,10 +21,17 @@ export(silv_dominant_height)
 export(silv_lorey_height)
 export(silv_ntrees_ha)
 export(silv_predict_biomass)
+export(silv_predict_biomass_auto)
+export(silv_predict_biomass_components)
+export(silv_predict_carbon)
+export(silv_predict_carbon_auto)
 export(silv_predict_height)
+export(silv_predict_snfi_volume)
 export(silv_sample_size)
 export(silv_sample_size_simple)
 export(silv_sample_size_stratified)
+export(silv_snfi_provinces)
+export(silv_snfi_species)
 export(silv_spacing_index)
 export(silv_sqrmean_diameter)
 export(silv_stand_basal_area)

R/data.R

@@ -60,3 +60,50 @@
 #' Monografías INIA: Serie Forestal n.º 13. Instituto Nacional de
 #' Investigación y Tecnología Agraria y Alimentaria, Madrid.
 "carbon_models"
+
+
+#' SNFI3 tree volume coefficients
+#'
+#' Allometric equation coefficients for tree volume and increment from the 3rd
+#' Spanish National Forest Inventory (SNFI3/IFN3), as documented by MITECO.
+#'
+#' @format A `tibble` with 37,730 rows and 16 variables:
+#' \describe{
+#'   \item{Codigo_provincia}{Integer. Province numeric code.}
+#'   \item{Nombre_provincia}{Character. Province name.}
+#'   \item{Codigo_especie}{Integer. Species numeric code.}
+#'   \item{Especie}{Character. Species scientific name.}
+#'   \item{Parametro}{Character. Volume component: VCC (merchantable volume with bark), VSC (merchantable volume without bark), IAVC (annual volume increment with bark), or VLE (coarse firewood volume).}
+#'   \item{F.c.}{Integer. Tree quality class (calidad del árbol), from 1 (healthy and straight tree) to 6 (dead tree).}
+#'   \item{Par_esp}{Character. Special parameter metadata.}
+#'   \item{Modelo}{Integer. Equation model index.}
+#'   \item{a, b, c, d, p, q, r}{Numeric. Equation coefficients (NA where not applicable).}
+#'   \item{R2}{Numeric. Coefficient of determination of the model.}
+#' }
+#' @references
+#' MITECO. 3rd Spanish National Forest Inventory - SIG database codes.
+#' \url{https://www.miteco.gob.es/content/dam/miteco/es/biodiversidad/servicios/banco-datos-naturaleza/documentador_bdcampo_ifn3_tcm30-282240.pdf}
+"snfi3_volume_coefficients"
+
+
+#' SNFI4 tree volume coefficients
+#'
+#' Allometric equation coefficients for tree volume and increment from the 4th
+#' Spanish National Forest Inventory (SNFI4/IFN4), as documented by MITECO.
+#'
+#' @format A `tibble` with 20,925 rows and 15 variables:
+#' \describe{
+#'   \item{Codigo_provincia}{Integer. Province numeric code.}
+#'   \item{Nombre_provincia}{Character. Province name.}
+#'   \item{Codigo_especie}{Integer. Species numeric code.}
+#'   \item{Especie}{Character. Species scientific name.}
+#'   \item{Parametro}{Character. Volume component: VCC (merchantable volume with bark), VSC (merchantable volume without bark), IAVC (annual volume increment with bark), or VLE (coarse firewood volume).}
+#'   \item{F.c.}{Integer. Tree quality class (calidad del árbol), from 1 (healthy and straight tree) to 6 (dead tree).}
+#'   \item{Modelo}{Integer. Equation model index.}
+#'   \item{a, b, c, d, p, q, r}{Numeric. Equation coefficients (NA where not applicable).}
+#'   \item{D.n.m.}{Character. Mean plot diameter metadata (diámetro normal medio), required for IAVC equation model 13.}
+#' }
+#' @references
+#' MITECO. 4th Spanish National Forest Inventory - SIG database codes.
+#' \url{https://www.miteco.gob.es/content/dam/miteco/es/biodiversidad/temas/inventarios-nacionales/documentador_sig_tcm30-536622.pdf}
+"snfi4_volume_coefficients"

R/metrics-stand-level.R

@@ -58,10 +58,10 @@ silv_stand_basal_area <- function(
 
   # 1. Calculate basal area
   switch(units,
-    "mm" = (pi / 4) * (diameter / 1000)**2,
-    "cm" = (pi / 4) * (diameter / 100)**2,
-    "dm" = (pi / 4) * (diameter / 10)**2,
-    "m"  = (pi / 4) * diameter**2,
+    "mm" = (pi / 4) * (diameter / 1000)**2 * ntrees,
+    "cm" = (pi / 4) * (diameter / 100)**2 * ntrees,
+    "dm" = (pi / 4) * (diameter / 10)**2 * ntrees,
+    "m"  = (pi / 4) * diameter**2 * ntrees,
     cli::cli_abort("Invalid `units`. Use one of {.val {c('mm', 'cm', 'dm', 'm')}}")
   )
 
@@ -126,7 +126,7 @@ silv_stand_dominant_height <- function(
   # 0. Validate inputs
   dh_method <- match.arg(which)
   assert_positive_numeric(diameter, "diameter")
-  assert_positive_numeric(diameter, "height")
+  assert_positive_numeric(height, "height")
 
 
   # 1. Create a data frame with input variables