add dataset doc

Author: divine7022

R/betydata-package.R

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+#' betydata: Public Data from the BETYdb Database
+#'
+#' Offline access to plant trait and yield data from BETYdb.
+#' Load datasets with `data(traitsview)`, `data(species)`, etc.
+#'
+#' @seealso [traitsview], [species], [sites], [variables], [pfts], [priors]
+#' @keywords internal
+"_PACKAGE"

R/data.R

@@ -0,0 +1,218 @@
+# Dataset documentation for betydata package
+
+#' Traits and Yields from BETYdb
+#'
+#' A denormalized view combining plant trait measurements and crop yield data
+#' from the BETYdb database. This is the primary dataset for offline analysis.
+#'
+#' @format A data frame with 43,532 rows and 36 columns:
+#' \describe{
+#'   \item{checked}{Data quality flag: 0 = unchecked, 1 = verified, -1 = flagged (excluded)}
+#'   \item{result_type}{Type of measurement: "traits" or "yields"}
+#'   \item{id}{Unique identifier for the trait or yield record}
+#'   \item{citation_id}{Foreign key to citations table}
+#'   \item{site_id}{Foreign key to sites table}
+#'   \item{treatment_id}{Foreign key to treatments table}
+#'   \item{sitename}{Name of the research site}
+#'   \item{city}{City or region where site is located}
+#'   \item{lat, lon}{Site coordinates (decimal degrees)}
+#'   \item{scientificname}{Species scientific name (Genus species)}
+#'   \item{commonname}{Species common name}
+#'   \item{genus}{Taxonomic genus}
+#'   \item{species_id}{Foreign key to species table}
+#'   \item{cultivar_id}{Foreign key to cultivars table (may be NA)}
+#'   \item{author}{Citation author(s)}
+#'   \item{citation_year}{Year of publication}
+#'   \item{treatment}{Experimental treatment name}
+#'   \item{date}{Formatted measurement date (human-readable)}
+#'   \item{time}{Time of measurement or confidence indicator}
+#'   \item{raw_date}{Raw timestamp from database}
+#'   \item{month, year}{Extracted month and year}
+#'   \item{dateloc}{Date location confidence (1-9 scale)}
+#'   \item{trait}{Variable/trait name (e.g. "SLA", "Vcmax", "Ayield")}
+#'   \item{trait_description}{Description of the trait/variable}
+#'   \item{mean}{Mean value of the measurement}
+#'   \item{units}{Units of measurement}
+#'   \item{n}{Sample size}
+#'   \item{statname}{Type of uncertainty statistic (SE, SD, etc.)}
+#'   \item{stat}{Value of the uncertainty statistic}
+#'   \item{notes}{Additional notes}
+#'   \item{access_level}{Data access level (4 = public)}
+#'   \item{cultivar}{Cultivar name if applicable}
+#'   \item{entity}{Entity name (for repeated measures)}
+#'   \item{method_name}{Measurement method name}
+#' }
+#' @source \url{https://betydb.org}, exported from traits_and_yields_view
+#' @seealso [species], [sites], [variables], [citations]
+#' @examples
+#' head(traitsview)
+#' 
+#' # Count by trait
+#' if (requireNamespace("dplyr", quietly = TRUE)) {
+#'   dplyr::count(traitsview, trait, sort = TRUE)
+#' }
+"traitsview"
+
+#' Species taxonomy from BETYdb
+#'
+#' Taxonomic information for plant species in BETYdb.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{Species identifier}
+#'   \item{spcd}{Species code}
+#'   \item{genus}{Taxonomic genus}
+#'   \item{species}{Specific epithet}
+#'   \item{scientificname}{Full scientific name}
+#'   \item{commonname}{Common name(s)}
+#' }
+#' @source \url{https://betydb.org}
+"species"
+
+#' Research sites from BETYdb
+#'
+#' Geographic and metadata for research sites.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{Site identifier}
+#'   \item{sitename}{Site name}
+#'   \item{city, state, country}{Location}
+#'   \item{lat, lon}{Coordinates (decimal degrees)}
+#'   \item{mat, map}{Mean annual temperature and precipitation}
+#' }
+#' @source \url{https://betydb.org}
+"sites"
+
+#' Variable definitions from BETYdb
+#'
+#' Definitions and metadata for measured variables/traits.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{Variable identifier}
+#'   \item{name}{Variable name (e.g., "SLA", "Vcmax")}
+#'   \item{description}{Full description}
+#'   \item{units}{Standard units}
+#'   \item{min, max}{Valid range}
+#' }
+#' @source \url{https://betydb.org}
+"variables"
+
+#' Literature citations from BETYdb
+#'
+#' Bibliographic references for data sources.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{Citation identifier}
+#'   \item{author}{Author(s)}
+#'   \item{year}{Publication year}
+#'   \item{title}{Article/book title}
+#'   \item{journal}{Journal name}
+#'   \item{doi}{Digital Object Identifier}
+#' }
+#' @source \url{https://betydb.org}
+"citations"
+
+#' Plant cultivars from BETYdb
+#' @format A data frame with cultivar information.
+#' @source \url{https://betydb.org}
+"cultivars"
+
+#' Measurement methods from BETYdb
+#' @format A data frame with method descriptions.
+#' @source \url{https://betydb.org}
+"methods"
+
+#' Experimental treatments from BETYdb
+#' @format A data frame with treatment definitions.
+#' @source \url{https://betydb.org}
+"treatments"
+
+#' Plant Functional Types (PFTs) from BETYdb
+#'
+#' PFT definitions used for grouping species for modeling.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{PFT identifier}
+#'   \item{name}{PFT name (e.g. "temperate.deciduous")}
+#'   \item{definition}{Full definition}
+#' }
+#' @source \url{https://betydb.org}
+#' @seealso [pfts_species], [pfts_priors]
+"pfts"
+
+#' Prior distributions from BETYdb
+#'
+#' Prior probability distributions for Bayesian analysis.
+#'
+#' @format A data frame with columns including:
+#' \describe{
+#'   \item{id}{Prior identifier}
+#'   \item{variable_id}{Associated variable}
+#'   \item{distn}{Distribution type (e.g. "norm", "gamma")}
+#'   \item{parama, paramb, paramc}{Distribution parameters}
+#' }
+#' @source \url{https://betydb.org}
+#' @seealso [pfts_priors], [variables]
+"priors"
+
+#' Management practices from BETYdb
+#' @format A data frame with management event data.
+#' @source \url{https://betydb.org}
+"managements"
+
+#' Entities from BETYdb
+#' @format A data frame with entity (individual/plot) information.
+#' @source \url{https://betydb.org}
+"entities"
+
+#' PFT-Species mapping from BETYdb
+#'
+#' Many-to-many relationship linking PFTs to species.
+#'
+#' @format A data frame with columns:
+#' \describe{
+#'   \item{pft_id}{Foreign key to pfts}
+#'   \item{specie_id}{Foreign key to species}
+#' }
+#' @source \url{https://betydb.org}
+"pfts_species"
+
+#' PFT-Prior mapping from BETYdb
+#'
+#' Many-to-many relationship linking PFTs to priors.
+#'
+#' @format A data frame with columns:
+#' \describe{
+#'   \item{pft_id}{Foreign key to pfts}
+#'   \item{prior_id}{Foreign key to priors}
+#' }
+#' @source \url{https://betydb.org}
+"pfts_priors"
+
+#' Management-Treatment mapping from BETYdb
+#'
+#' Many-to-many relationship linking managements to treatments.
+#'
+#' @format A data frame with columns:
+#' \describe{
+#'   \item{management_id}{Foreign key to managements}
+#'   \item{treatment_id}{Foreign key to treatments}
+#' }
+#' @source \url{https://betydb.org}
+"managements_treatments"
+
+#' Cultivar-PFT mapping from BETYdb
+#'
+#' Many-to-many relationship linking cultivars to PFTs.
+#'
+#' @format A data frame with columns:
+#' \describe{
+#'   \item{cultivar_id}{Foreign key to cultivars}
+#'   \item{pft_id}{Foreign key to pfts}
+#' }
+#' @source \url{https://betydb.org}
+"cultivars_pfts"