R/data.R

In ecocomDP: Tools to Create, Use, and Convert ecocomDP Data

#' Joined and flat version of EDI data package knb-lter-hfr.118.33
#'
#' A fully joined and flat version of EDI data package knb-lter-hfr.118.33 (Ant Assemblages in Hemlock Removal Experiment at Harvard Forest since 2003) with all relevant ecocomDP L1 identifiers and content added. Use this dataset as an input to the \code{L0_flat} argument of the "create" functions.
#'
#' @format A data frame with 2931 rows and 45 variables:
#' \describe{
#'   \item{datetime}{dates}
#'   \item{block}{block}
#'   \item{plot}{plot number}
#'   \item{treatment}{treatment type}
#'   \item{moose.cage}{location of grid with respect to moose exclosure}
#'   \item{trap.type}{trap type}
#'   \item{trap.num}{applies only to pitfall cups}
#'   \item{subfamily}{ant subfamily}
#'   \item{hl}{head length. We used trait definitions from Del Toro et al. (2015) and filled in missing species' data with information from Ellison et al.}
#'   \item{rel}{eye length relative to body size}
#'   \item{rll}{femur length relative to body size}
#'   \item{colony.size}{size of colony for each species}
#'   \item{feeding.preference}{feeding preference for each species}
#'   \item{nest.substrate}{nest substrate}
#'   \item{primary.habitat}{primary habitat}
#'   \item{secondary.habitat}{secondary habitat associations}
#'   \item{seed.disperser}{whether or not a seed dispersing species}
#'   \item{slavemaker.sp}{whether or not a slavemaking species}
#'   \item{behavior}{classifications based on behavioral interactions with other ants}
#'   \item{biogeographic.affinity}{biogeographic affinity based on available occurrence records}
#'   \item{source}{where trait information was found. Full citations for literature are as follows: Del Toro, I., R.R. Silva, and A.M. Ellison. 2015. Predicated impacts of climatic change on ant functional diversity and distributions in eastern North American forests. Diversity and Distributions 21:781-791; Ellison, A.M., N.J. Gotelli, G. Alpert, and E.J. Farnsworth. 2012. A field guide to the ants of New England. Yale University Press, New Haven, Connecticut, USA.}
#'   \item{unit_hl}{units for "hl" variable}
#'   \item{unit_rel}{units for "rel" variable}
#'   \item{unit_rll}{units for "rll" variable}
#'   \item{variable_name}{variables of the primary observation table}
#'   \item{value}{values of variable_name}
#'   \item{unit}{units of variable_name}
#'   \item{observation_id}{the observation id}
#'   \item{location_id}{the location id}
#'   \item{event_id}{the event id}
#'   \item{latitude}{approximate latitude of study area}
#'   \item{longitude}{approximate longitude of study area}
#'   \item{elevation}{approximate elevation of study area}
#'   \item{taxon_name}{name of organism}
#'   \item{taxon_id}{the taxon id}
#'   \item{taxon_rank}{the taxon rank}
#'   \item{authority_system}{the authority system taxon_name was resolved to}
#'   \item{authority_taxon_id}{the id of taxon_name in authority_system}
#'   \item{package_id}{the identifier of this ecocomDP dataset}
#'   \item{original_package_id}{the identifier of the source dataset}
#'   \item{length_of_survey_years}{number of years the survey has been ongoing}
#'   \item{number_of_years_sampled}{number of years during the survey that samples were taken}
#'   \item{std_dev_interval_betw_years}{the standard deviation between surveys in years}
#'   \item{max_num_taxa}{number of unique taxa in this dataset}
#'   \item{geo_extent_bounding_box_m2}{the study area in meters squared}
#' }
#' @source \url{https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hfr&identifier=118&revision=33}
"ants_L0_flat"








#' The ecocomDP (L1) version of EDI data package knb-lter-hfr.118.33
#'
#' The the ecocomDP (L1) formatted version of EDI data package knb-lter-hfr.118.33 (Ant Assemblages in Hemlock Removal Experiment at Harvard Forest since 2003) read from the EDI API with \code{read_data(id = "edi.193.5")}. Use this dataset as an input to data "use" functions.
#'
#' @format A list of:
#' \describe{
#'   \item{id}{The dataset identifier}
#'   \item{metadata}{See source url for metadata}
#'   \item{tables}{A list of data frames, each an ecocomDP table}
#'   \item{validation_issues}{Is NULL because there are no validation issues for this dataset}
#' }
#' @source \url{https://portal.edirepository.org/nis/mapbrowse?scope=edi&identifier=193&revision=5}
"ants_L1"