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Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020.R
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Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020.R
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#' Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020
#'
#'
#' @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-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020.html}{View raw data} or \href{../data/Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020.csv}{Download raw data}
#'
#'
#' @source
#' * Johnson Creek: Nez Perce Tribe
#' * Secesh River: Nez Perce Tribe
#' * Tucannon River: Washington Department of Fish and Wildlife
#' * Wenaha River: Oregon Department of Fish and Wildlife
#' * Wallowa/Lostine Rivers: Oregon Department of Fish and Wildlife
#' * Minam River: Oregon Department of Fish and Wildlife
#' * Catherine Creek: Oregon Department of Fish and Wildlife
#' * Grande Ronde Upper Mainstem: Oregon Department of Fish and Wildlife
#' * Imnaha River: Oregon Department of Fish and Wildlife
#' * South Fork Salmon River: Idaho Department of Fish and Game
#' * Chamberlain Creek: Idaho Department of Fish and Game
#' * Middle Fork Salmon River Lower Mainstem: Idaho Department of Fish and Game
#' * Big Creek: Idaho Department of Fish and Game
#' * Camas Creek: Idaho Department of Fish and Game
#' * Loon Creek: Idaho Department of Fish and Game
#' * Middle Fork Salmon River Upper Mainstem: Idaho Department of Fish and Game
#' * Sulphur Creek: Idaho Department of Fish and Game
#' * Marsh Creek: Idaho Department of Fish and Game
#' * Bear Valley Creek: Idaho Department of Fish and Game
#' * North Fork Salmon River: Idaho Department of Fish and Game
#' * Lemhi River: Idaho Department of Fish and Game
#' * Salmon River Lower Mainstem: Idaho Department of Fish and Game
#' * Pahsimeroi River: Idaho Department of Fish and Game
#' * East Fork Salmon River: Idaho Department of Fish and Game
#' * Yankee Fork: Idaho Department of Fish and Game
#' * Salmon River Upper Mainstem: Idaho Department of Fish and Game
#' * Valley Creek: Idaho Department of Fish and Game
#'
#' @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:
#' * Johnson Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1987-2018). Spawner abundance data. Nez Perce Tribe. Protocol and Methods available at https://www.monitoringresources.org/Document/Protocol/Details/2246. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Secesh River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1997-2018). Spawner abundance data. Nez Perce Tribe. Protocol and Methods available at https://www.monitoringresources.org/Document/Protocol/Details/2246. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Tucannon River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1954-2019). 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.
#' * Wenaha River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1949-2018). 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.
#' * Wallowa/Lostine Rivers: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1949-2018). 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.
#' * Minam River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1954-2018). 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.
#' * Catherine Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1953-2018). 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.
#' * Grande Ronde Upper Mainstem: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1953-2018). 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.
#' * Imnaha River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1949-2018). 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.
#' * South Fork Salmon River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Chamberlain Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Middle Fork Salmon River Lower Mainstem: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Big Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Camas Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Loon Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Middle Fork Salmon River Upper Mainstem: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Sulphur Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Marsh Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Bear Valley Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * North Fork Salmon River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Lemhi River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Salmon River Lower Mainstem: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Pahsimeroi River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1980-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * East Fork Salmon River: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Yankee Fork: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Salmon River Upper Mainstem: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#' * Valley Creek: Snake River spring/summer Chinook Natural Origin Spawner Abundance Dataset (1957-2019). Spawner abundance data. Idaho Department of Fish and Game. Protocol and Methods available at https://www.monitoringmethods.org/Protocol/Details/159. Accessed from www.cax.streamnet.org vers May 26 2020 10:00PM by Mari Williams, NOAAF NWFSC/PSMFC.
#'
#' @name Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020
#' @docType data
#' @examples
#' data('Salmon-Chinook-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020')
#' 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-Snake-River-spring-summer-run-ESU-ICSRSSchinookSurvey2020') +
#' 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