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Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020.R
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Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020.R
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#' Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020
#'
#'
#' @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: Survey. \href{../data/Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020.html}{View raw data} or \href{../data/Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020.csv}{Download raw data}
#'
#'
#' @source
#' * Grays/Chinook Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Youngs Bay: Oregon Department of Fish and Wildlife
#' * Big Creek: Oregon Department of Fish and Wildlife
#' * Elochoman/Skamokawa Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Clatskanie River: Washington Department of Fish and Wildlife
#' * Mill/Abernathy/Germany Creeks Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Lower Cowlitz Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Coweeman Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Toutle Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Upper Cowlitz Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Kalama Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Lewis River Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Sandy River: Oregon Department of Fish and Wildlife
#' * Clackamas River: Oregon Department of Fish and Wildlife
#' * Washougal Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Lewis River Late Fall (Bright) Chinook: Washington Department of Fish and Wildlife
#' * Upper Cowlitz and Cispus Spring Chinook: Washington Department of Fish and Wildlife
#' * Kalama Spring Chinook: Washington Department of Fish and Wildlife
#' * North Fork Lewis Spring Chinook: Washington Department of Fish and Wildlife
#' * Lower Gorge (Columbia) Late Fall (Bright) Chinook: Washington Department of Fish and Wildlife
#' * Upper Gorge (Columbia) Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Big White Salmon River Fall (Tule) Chinook: Washington Department of Fish and Wildlife
#' * Big White Salmon River Spring Chinook: Washington 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:
#' * Grays/Chinook Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Youngs Bay: Lower Columbia 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/PSMFC.
#' * Big Creek: Lower Columbia 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/PSMFC.
#' * Elochoman/Skamokawa Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Clatskanie River: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (2002-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Mill/Abernathy/Germany Creeks Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1981-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Lower Cowlitz Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Coweeman Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Toutle Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Upper Cowlitz Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1996-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Kalama Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Lewis River Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1997-2019). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Sandy River: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (2009-2019). Spawner abundance data. Oregon Department of Fish and Wildlife. Protocol and Methods available at http://odfwrecoverytracker.org/metadata/. Personal Communication with Jamie Anthony by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Sandy River: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1981-2006). 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/PSMFC.
#' * Sandy River: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (2013-2018). 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/PSMFC.
#' * Clackamas River: Lower Columbia 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/PSMFC.
#' * Washougal Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Lewis River Late Fall (Bright) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1964-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Upper Cowlitz and Cispus Spring Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (2014-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Kalama Spring Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1980-2019). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * North Fork Lewis Spring Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1980-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Lower Gorge (Columbia) Late Fall (Bright) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1994-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Upper Gorge (Columbia) Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1997-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Big White Salmon River Fall (Tule) Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (1965-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Big White Salmon River Spring Chinook: Lower Columbia River Chinook Natural Origin Spawner Abundance Dataset (2013-2018). Spawner abundance data. Washington Department of Fish and Wildlife. Protocol and Methods available at https://fortress.wa.gov/dfw/score/score/. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#'
#' @name Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020
#' @docType data
#' @examples
#' data('Salmon-Chinook-Lower-Columbia-River-ESU-LCchinook2020')
#' 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-Lower-Columbia-River-ESU-LCchinook2020') +
#' facet_wrap(~COMMON_POPULATION_NAME) +
#' theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1),
#' strip.text.x = element_text(size = 6))
#'
#' 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),
#' strip.text.x = element_text(size = 6))
NULL