R/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.R

In nwfsc-math-bio/VRData: NWFSC PNW Salmonid Viability Reports Data Package

#' Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020
#' 

#' 
#' @format A csv file.
#' \describe{
#' \item{SERIES}{For certain populations, there are multiple types of spawner count data. For example survey and model counts that are based on different methods. In this case, the 'Series' column gives a name for the dataset to distinguish it from other data sets of the same population.}
#' \item{ESU}{ESU or DPS name.}
#' \item{SPECIES}{Species name.}
#' \item{METHOD}{Method for the spawner count. Survey refers to a spawning ground survey; the count itself is an expansion. See the SPS (database link in sources below) for the details for the data. LadderCount is a weir or dam count. Model  refers to the DABOM model that expands from PIT tag data. GSI is an expansion based on the BOXCAR model, which uses GSI to allocate fish sampled at Lower Granite Dam.}
#' \item{MAJOR_POPULATION_GROUP}{Major population group within the ESU or DPS.}
#' \item{NMFS_POPID}{NWFSC id for the population.}
#' \item{POPULATION_NAME}{Long population name.}
#' \item{COMMON_POPULATION_NAME}{Shorter population name used in Viability Report figures and tables.}
#' \item{RUN_TIMING}{Run timing (fall, winter, spring, etc). If missing, see the ESU/DPS name or may not be applicable for the species.}
#' \item{YEAR}{Integer in XXXX format. The year that the count was made. See details for ESU or DPS specific comments.}
#' \item{NUMBER_OF_SPAWNERS}{Total spawners or escapement count. -99 means missing count. May be integer or decimal.}
#' \item{FRACWILD}{Decimal between 0 and 1. Fraction wild or natural. -99 means missing information.}
#' \item{CONTRIBUTOR}{Data contributor. Listed under Source below.}
#' \item{COMPILER}{NWFSC staff who compiled the data file: Mari Williams}
#' \item{CITATION}{Data citation. Listed under References below.}
#' }
#' 
#' @description Spawner and fraction wild data. Species: Chinook salmon. Method: . \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: chinook. 
#' * Clackamas River: Survey. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: Chinook salmon. 
#' * Willamette Falls ESC: LadderCount. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: chinook. 
#' * North Santiam River: Survey. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: Chinook salmon. 
#' * South Santiam River: Survey. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: chinook. 
#' * McKenzie River: Survey. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' @description Spawner and fraction wild data. Species: Chinook salmon. 
#' * Middle Fork Willamette River: Survey. \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020.csv}{Download raw data}
#' 
#' 
#' @source Oregon Department of Fish and Wildlife
#' 
#' @references
 #' Ford, M.J., et al. 2022. Biological Viability Assessment Update for Pacific Salmon and Steelhead Listed Under the Endangered Species Act: Pacific Northwest. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-171. https://doi.org/10.25923/kq2n-ke70
#'
#'
#' Salmon Population Summaries (SPS) Database: \url{https://www.fisheries.noaa.gov/resource/tool-app/salmon-population-summaries-sps}
#' 
#' Original source: 
#' * Clackamas River: Upper Willamette River Chinook Natural Origin Spawner Abundance Dataset (1974-2018). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Willamette Falls ESC: Upper Willamette River Chinook Natural Origin Spawner Escapement (1946-2019). Ladder count. Personal communication from Jamie Anthony, ODFW, via Mari Williams, NOAAF NWFSC/PSMFC.
#' * North Santiam River: Upper Willamette River Chinook Natural Origin Spawner Abundance Dataset (2007-2018). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * South Santiam River: Upper Willamette River Chinook Natural Origin Spawner Abundance Dataset (2007-2018). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * McKenzie River: Upper Willamette River Chinook Natural Origin Spawner Abundance Dataset (2005-2018). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Middle Fork Willamette River: Upper Willamette River Chinook Natural Origin Spawner Abundance Dataset (2012-2018). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' 
#' @name Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020
#' @docType data
#' @examples
#' data('Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020')
#' library(ggplot2)
#' out$NUMBER_OF_SPAWNERS[out$NUMBER_OF_SPAWNERS==-99] <- NA
#' ggplot(out, aes(x=YEAR, y=NUMBER_OF_SPAWNERS)) + 
#'   geom_point(na.rm = TRUE) +
#'   ggtitle('Salmon-Chinook-Upper-Willamette-River-ESU-UWchinook2020') +
#'   facet_wrap(~COMMON_POPULATION_NAME) +
#'   theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
#' 
#' out$FRACWILD[out$FRACWILD == -99] <- NA
#' ggplot(out, aes(x=YEAR, y=FRACWILD)) +
#'   geom_point(na.rm = TRUE) +
#'   ggtitle('Fraction Wild') +
#'   ylim(0,1) +
#'   facet_wrap(~COMMON_POPULATION_NAME) +
#'   theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
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