feat(tree-metrics): implement SNFI tree-level metrics and competition indices

.github/workflows/pkgdown.yaml

@@ -27,13 +27,16 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, any::quarto, local::.
           needs: website
 
       - name: Build site

DESCRIPTION

@@ -46,5 +46,5 @@ Collate:
     'treatment-thinning.R'
     'utils-assert.R'
     'zzz.R'
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0
 VignetteBuilder: quarto

NAMESPACE

@@ -16,6 +16,9 @@ export(silv_biomass)
 export(silv_density_hart)
 export(silv_density_ntrees_ha)
 export(silv_density_sdi)
+export(silv_density_sdi_auto)
+export(silv_density_sdi_class)
+export(silv_density_sdimax)
 export(silv_diametric_class)
 export(silv_dominant_height)
 export(silv_lorey_height)
@@ -30,6 +33,7 @@ export(silv_predict_snfi_volume)
 export(silv_sample_size)
 export(silv_sample_size_simple)
 export(silv_sample_size_stratified)
+export(silv_site_factor)
 export(silv_snfi_provinces)
 export(silv_snfi_species)
 export(silv_spacing_index)
@@ -41,12 +45,44 @@ export(silv_stand_lorey_height)
 export(silv_stand_qmean_diameter)
 export(silv_summary)
 export(silv_treatment_thinning)
+export(silv_tree_bal)
+export(silv_tree_bas)
 export(silv_tree_basal_area)
+export(silv_tree_basal_area_ha)
+export(silv_tree_circumference)
+export(silv_tree_coordinates)
+export(silv_tree_crown_ratio)
 export(silv_tree_dclass)
+export(silv_tree_expansion_factor)
+export(silv_tree_mean_dbh)
+export(silv_tree_slenderness)
 export(silv_tree_volume)
 export(silv_volume)
+importFrom(dplyr,
+  arrange,
+  bind_cols,
+  desc,
+  group_by,
+  left_join,
+  mutate,
+  n,
+  pull,
+  row_number,
+  select,
+  ungroup
+)
 importFrom(lifecycle,deprecated)
-importFrom(stats,qt)
-importFrom(stats,sd)
-importFrom(stats,var)
+importFrom(rlang,
+  "!!",
+  as_name,
+  enquo,
+  quo_is_null,
+  sym
+)
+importFrom(stats,
+  qt,
+  sd,
+  var
+)
+importFrom(tibble,tibble)
 importFrom(utils,tail)

R/data.R

@@ -107,3 +107,68 @@
 #' 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"
+
+
+#' SDI beta coefficients
+#'
+#' Specific beta coefficients for Reineke's Stand Density Index (SDI) per
+#' species, country, and region.
+#'
+#' @format A `tibble`
+#' \describe{
+#'   \item{article_id}{Character. Short identifier of the source article.}
+#'   \item{title}{Character. Full title of the source article.}
+#'   \item{doi_url}{Character. DOI URL of the source article.}
+#'   \item{country}{Character. Country where the study was conducted.}
+#'   \item{region}{Character. Region within the country.}
+#'   \item{species}{Character. Scientific name of the tree species.}
+#'   \item{beta}{Numeric. Beta coefficient for SDI calculation.}
+#' }
+"sdi_coefficients"
+
+
+#' Maximum stand density index (SDImax) models
+#'
+#' Coefficients for calculating maximum stand density index (SDImax) from
+#' Rodríguez de Prado (2020).
+#'
+#' @format A `tibble` with 88 rows and 13 variables:
+#' \describe{
+#'   \item{article_id}{Character. Identifier of the article.}
+#'   \item{title}{Character. Title of the article.}
+#'   \item{doi_url}{Character. DOI URL of the article.}
+#'   \item{country}{Character. Country where the study was conducted.}
+#'   \item{species}{Character. Tree species scientific name.}
+#'   \item{model_name}{Character. Name of the model/equation variant (e.g. "basic", "P1", "MXT3").}
+#'   \item{a0}{Numeric. Coeffient a0.}
+#'   \item{a1}{Numeric. Coeffient a1 (0 if not used/applicable).}
+#'   \item{b0}{Numeric. Coeffient b0.}
+#'   \item{b1}{Numeric. Coeffient b1 (0 if not used/applicable).}
+#'   \item{aic}{Numeric. Akaike Information Criterion.}
+#'   \item{pseudo_r2}{Numeric. Pseudo R-squared value.}
+#'   \item{q_index}{Numeric. Q index value.}
+#' }
+#' @references
+#' Rodríguez-de-Prado, M., et al. (2020). Potential climatic influence on maximum stand carrying capacity for 15 Mediterranean coniferous and broadleaf species. Forest Ecology and Management, 458, 117824.
+"sdimax_models"
+
+
+#' Site Factor models
+#'
+#' Coefficients for calculating the Site Factor (SF) based on Aguirre et al. (2022).
+#' The site factor is a variable that can be used in growth equations and is based on
+#' the dominant height and dominant dbh.
+#'
+#' @format A `tibble` with 24 rows and 7 variables:
+#' \describe{
+#'   \item{species}{Character. Scientific name of the tree species.}
+#'   \item{species_code}{Numeric. Species numeric code.}
+#'   \item{d_ref}{Numeric. Reference diameter (Dref).}
+#'   \item{model}{Character. Model shape and expanded parameter.}
+#'   \item{param_a}{Numeric. Parameter a.}
+#'   \item{param_b}{Numeric. Parameter b.}
+#'   \item{param_c}{Numeric. Parameter c.}
+#' }
+#' @references
+#' Aguirre, A. et al. (2022).
+"site_factor_models"