update roxy

Author: divine7022

R/data.R

@@ -1,218 +1,144 @@
 # Dataset documentation for betydata package
 
-#' Traits and Yields from BETYdb
+#' 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
+#' @format A data frame with trait and yield observations. 
+#'   Use `names(traitsview)` to see all columns. Key columns include
+#'   checked (quality flag), result_type, id, mean, units, trait, and scientificname.
+#' @source <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)
-#' }
+#' names(traitsview)
 "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}
+#' Taxonomic information for plant species in BETYdb including USDA PLANTS
+#' database attributes.
+#'
+#' @format A data frame. Key columns include id, genus, species, scientificname,
+#'   commonname. See `names(species)` for all columns.
+#' @source <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}
+#' @format A data frame. Key columns include id, sitename, city, state, country.
+#'   See `names(sites)` for all columns.
+#' @source <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}
+#' @format A data frame. Key columns include id, name, description, units.
+#'   See `names(variables)` for all columns.
+#' @source <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}
+#' @format A data frame. Key columns include id, author, year, title, journal, doi.
+#'   See `names(citations)` for all columns.
+#' @source <https://betydb.org>
 "citations"
 
 #' Plant cultivars from BETYdb
+#'
 #' @format A data frame with cultivar information.
-#' @source \url{https://betydb.org}
+#'   See `names(cultivars)` for all columns.
+#' @source <https://betydb.org>
 "cultivars"
 
 #' Measurement methods from BETYdb
+#'
 #' @format A data frame with method descriptions.
-#' @source \url{https://betydb.org}
+#'   See `names(methods)` for all columns.
+#' @source <https://betydb.org>
 "methods"
 
 #' Experimental treatments from BETYdb
+#'
 #' @format A data frame with treatment definitions.
-#' @source \url{https://betydb.org}
+#'   See `names(treatments)` for all columns.
+#' @source <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}
+#' @format A data frame. Key columns include id, name, definition.
+#'   See `names(pfts)` for all columns.
+#' @source <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}
+#' @format A data frame. Key columns include id, variable_id, distn, parama, paramb.
+#'   See `names(priors)` for all columns.
+#' @source <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}
+#'   See `names(managements)` for all columns.
+#' @source <https://betydb.org>
 "managements"
 
 #' Entities from BETYdb
+#'
 #' @format A data frame with entity (individual/plot) information.
-#' @source \url{https://betydb.org}
+#'   See `names(entities)` for all columns.
+#' @source <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}
+#' @format A data frame with columns pft_id and specie_id (plus metadata).
+#'   See `names(pfts_species)` for all columns.
+#' @source <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}
+#' @format A data frame with columns pft_id and prior_id (plus metadata).
+#'   See `names(pfts_priors)` for all columns.
+#' @source <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}
+#' @format A data frame with columns management_id and treatment_id (plus metadata).
+#'   See `names(managements_treatments)` for all columns.
+#' @source <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}
+#' @format A data frame with columns cultivar_id and pft_id (plus metadata).
+#'   See `names(cultivars_pfts)` for all columns.
+#' @source <https://betydb.org>
 "cultivars_pfts"