R/sockeye-data.R

In nwfsc-timeseries/atsalibrary: Packages, data and scripts for ATSA course and lab book

#' Bristol Bay Sockeye Spawner-Recruit Data
#'
#' @description Spawner-recruit data for sockeye salmon from the KVICHAK, 
#' WOOD, IGUSHIK, NAKNEK, EGEGIK, NUSHAGAK, UGASHIK,
#' TOGIAK Rivers.
#' 
#' @details Spawner-recruit data for sockeye salmon 
#' (_Oncorhynchus nerka_) from the Bristol Bay region
#'  in SW Alaska that span the years 1952-2005. The data come from a large 
#'  public database begun by Ransom Myers many years ago. The 
#'  database is now maintained as the RAM Legacy Stock Assessment Database.
#'
#'  The R script which created the data can be found in the
#'  atsalibrary GitHub site in the inst/orginal_data/sockeye folder.
#'  
#'  For convenience in the lab book, KvichakSockeye is also created
#'  which is just the Kvichak data.
#'  
#' @docType data
#' 
#' @name sockeye
#' 
#' @aliases sockeye
#'
#' @usage data(sockeye)
#' 
#' @format Object of class \code{"data.frame"}
#' \itemize{
#'   \item \strong{brood_year}  Brood year. 
#'   \item \strong{region} River. 
#'   \item \strong{spawners} Spawners (count) in thousands 
#'   \item \strong{recruits} Recruits (count) in thousands
#'   \item \strong{pdo_summer_t2} Pacific Decadal Oscillation (PDO) from Apr-Sep of brood year $t+2$ 
#'   \item \strong{pdo_winter_ts} Pacific Decadal Oscillation (PDO) from Oct (brood year $t+2$) to Mar (brood year $t+3$)
#' }
#' 
#' @keywords datasets
#'
#' @source \href{https://www.ramlegacy.org/}{RAM Legacy Stock Assessment Database v4.491}
#'
#' @references 
#' RAM Legacy Stock Assessment Database. 2018. Version 4.44-assessment-only. Released 2018-12-22. Retrieved from DOI:10.5281/zenodo.2542919.
#' 
#' Ricard, D., Minto, C., Jensen, O.P. and Baum, J.K. (2012) Evaluating the knowledge base and status of commercially exploited marine species with the RAM Legacy Stock Assessment Database. Fish and Fisheries 13 (4) 380-398. DOI: 10.1111/j.1467-2979.2011.00435.x
#'
#' Spawner escapement estimates are originally from: Bristol Bay Area Annual Management Reports from the 
#' Alaska Department of Fish and Game and are based on in river
#' spawner counts (tower counts and aerial surveys). 
#' 
#' See an example application of these data see: 
#' Rogers, L.A. and Schindler, D.E. 2008. Asynchrony in Population Dynamics of Sockeye Salmon 
#' in Southwest Alaska. Oikos 117: 1578-1586
#'  
#' @examples
#' data(sockeye)
#' 
#' a <- pivot_longer(sockeye,
#'      cols=spawners:recruits,
#'      names_to="value",
#'      values_to="count")
#'ggplot(a,aes(brood_year, count, color=value, fill=value)) +
#'    geom_area() +
#'    theme(axis.text.x = element_text(angle = 90)) +
#'      ylab("Count (thousands)") +
#'      xlab("Brood Year") +
#'    facet_wrap(~region, scales="free_y")
"sockeye"