R/data.R

In forestgeo/allodb: Tree Biomass Estimation at Extra-Tropical Forest Plots

#' Tables of allometric equations and associated metadata
#'
#' A compilation of best available allometry equations to calculate tree
#' above-ground biomass (AGB) per species based on extratropical ForestGEO
#' sites.
#'
#' @description
#'* [equations]: Table of allometric equations.
#'* [equations_metadata]: Explanation of columns for [equations] table.
#'
#' @source See [references] for equations original sources.
#'
#' @family database datasets
#'
#' @examples
#' # preview the datasets
#' print(head(equations))
#' print(head(equations_metadata))
"equations"
#' @rdname equations
"equations_metadata"

#' Explanations of missing values codes
#'
#' Explanation of the codes used to indicate missing information in equation
#' table.
#'
#' @family database datasets
#'
#' @examples
#' # preview the dataset
#' print(head(missing_values))
"missing_values"

#' Sites and tree species used in allodb and associated metadata
#'
#' * [sitespecies]: Table of extratropical ForestGEO sites in allodb (n=24) and
#' their tree species.
#' * [sitespecies_metadata]: Metadata for [sitespecies] table.
#'
#' @family database datasets
#'
#' @examples
#' # preview the datasets
#' print(head(sitespecies))
#' print(head(sitespecies_metadata))
"sitespecies"
#' @rdname sitespecies
"sitespecies_metadata"

#' Equation references and associated metadata
#'
#' Bibliographical information for sourced equations. Links to the [equations]
#' table by `ref_id`.
#'
#' @description
#' * [references]: A data frame listing all references used in `equation` table.
#' * [references_metadata]: Metadata for `reference` table.
#'
#' @family database datasets
#'
#' @examples
#' # preview the datasets
#' print(head(references))
#' print(head(references_metadata))
"references"
#' @rdname references
"references_metadata"

#' ForestGEO sites used in allodb
#'
#' Table with geographical information for extratropical ForestGEO sites used in
#' allodb (n=24).
#'
#' More details on geographical aspects of these ForestGEO sites can be found in
#' the accompanying manuscript.
#'
#' @family database datasets
#'
#' @examples
#' # preview the datasets
#' print(head(sites_info))
"sites_info"

#' Tree census data from SCBI ForestGEO plot
#'
#' A table with tree data from the Smithsonian Conservation Biology Institute,
#' USA (SCBI) ForestGEO dynamics plot. This dataset is an extract from the first
#' tree census in 2008, only covering 1 hectare (SCBI plot is 25.6 ha). DBH in
#' cm.
#'
#' @source Full datasets for tree census data at SCBI can be requested through
#'   the ForestGEO portal (<https://forestgeo.si.edu/>). Census 1, 2, and 3 can
#'   also be accessed at the public GitHub repository for SCBI-ForestGEO Data
#'   (<https://github.com/SCBI-ForestGEO>).
#'
#' @family datasets
#'
#' @examples
#' # preview the datasets
#' print(head(scbi_stem1))
"scbi_stem1"

#' Genus and family table for selected ForestGEO sites
#'
#' Genus and their associated family identified in the extratropical ForestGEO
#' sites used in allodb.
#'
#' @family datasets
#'
#' @examples
#' # preview the dataset
#' print(head(genus_family))
"genus_family"

#' Gymnosperms identified in selected ForestGEO sites
#'
#' Table with genus and their associated family for Gymnosperms identified in
#' the ForestGEO sites used in allodb.
#'
#' @family datasets
#'
#' @examples
#' # preview the dataset
#' print(head(gymno_genus))
"gymno_genus"

#' Shrub species identified in selected ForestGEO sites
#'
#' Genus and species of shrubby plants identified in the 24 extratropical
#' ForestGEO sites used in allodb.
#'
#' @family datasets
#'
#' @examples
#' # preview the dataset
#' print(head(shrub_species))
"shrub_species"

#' Koppen climate classification matrix
#'
#' A table built to facilitate the comparison between the Koppen climate of a
#' site and the allometric equation in question.
#'
#' The value of column `we` is the weight given to the combination of Koppen
#' climates in columns `zone1` and `zone2`; the table is symmetric: `zone1` and
#' `zone2` can be interchanged. This weight is calculated in 3 steps: (1) if the
#' main climate group (first letter) is the same, the climate weight starts at
#' 0.4; if one of the groups is "C" (temperate climate) and the other is "D"
#' (continental climate), the climate weight starts at 0.2 because the 2 groups
#' are considered similar enough; otherwise, the weight is 0; (2) if the
#' equation and site belong to the same group, the weight is incremented by an
#' additional value between 0 and 0.3 based on precipitation pattern similarity
#' (second letter of the Koppen zone), and (3) by an additional value between 0
#' and 0.3 based on temperature pattern similarity (third letter of the Koppen
#' zone). The resulting weight has a value between 0 (different climate groups)
#' and 1 (exactly the same climate classification).
#'
#' @family datasets
#'
#' @examples
#' # preview the dataset
#' print(head(koppenMatrix))
"koppenMatrix"