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Steelhead-Middle-Columbia-River-DPS-ICMC2021.R
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Steelhead-Middle-Columbia-River-DPS-ICMC2021.R
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#' Steelhead-Middle-Columbia-River-DPS-ICMC2021
#'
#'
#' @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: Steelhead. Method: Survey. \href{../data/Steelhead-Middle-Columbia-River-DPS-ICMC2021.html}{View raw data} or \href{../data/Steelhead-Middle-Columbia-River-DPS-ICMC2021.csv}{Download raw data}
#'
#'
#' @source
#' * Klickitat River: Yakama Nation Fisheries
#' * Fifteenmile Creek: Oregon Department of Fish and Wildlife
#' * Deschutes River Westside: Oregon Department of Fish and Wildlife
#' * Deschutes River Eastside: Oregon Department of Fish and Wildlife
#' * Rock Creek: Yakama Nation Fisheries
#' * John Day River Lower Mainstem Tributaries: Oregon Department of Fish and Wildlife
#' * North Fork John Day River: Oregon Department of Fish and Wildlife
#' * Middle Fork John Day River: Oregon Department of Fish and Wildlife
#' * South Fork John Day River: Oregon Department of Fish and Wildlife
#' * John Day River Upper Mainstem: Oregon Department of Fish and Wildlife
#' * Satus Creek: Yakama Nation Fisheries
#' * Toppenish Creek: Yakama Nation Fisheries
#' * Naches River: Yakama Nation Fisheries
#' * Yakima River upper mainstem: Yakama Nation Fisheries
#' * Umatilla River: Oregon Department of Fish and Wildlife
#' * Walla Walla River: Oregon Department of Fish and Wildlife
#' * Touchet River: 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:
#' * Klickitat River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2006-2019). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P148516 and https://www.cbfish.org/Document.mvc/Viewer/P160751. Accessed from www.cax.streamnet.org vers July 1, 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Fifteenmile Creek: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1985-2018). 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.
#' * Deschutes River Westside: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1978-2018). 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.
#' * Deschutes River Eastside: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1990-2018). 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.
#' * Rock Creek: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2008-2018). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P148516 and https://www.cbfish.org/Document.mvc/Viewer/P160751. Accessed from www.cax.streamnet.org vers July 1, 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * John Day River Lower Mainstem Tributaries: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1959-2019). 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.
#' * North Fork John Day River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1963-2018). 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 John Day River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1964-2019). 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 Fork John Day River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1960-2019). 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.
#' * John Day River Upper Mainstem: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1959-2018). 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.
#' * Satus Creek: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1984-2018). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P153378. Accessed from www.cax.streamnet.org vers July 1 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Toppenish Creek: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1984-2018). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P153378. Accessed from www.cax.streamnet.org vers July 1 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Naches River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1984-2018). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P153378. Accessed from www.cax.streamnet.org vers July 1 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Yakima River upper mainstem: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1984-2018). Spawner abundance data. Confederated Tribes and Bands of the Yakama Nation. Protocol and Methods available at https://www.cbfish.org/Document.mvc/Viewer/P153378. Accessed from www.cax.streamnet.org vers July 1 2020 10:00PM by Mari Williams, NOAAF NWFSC/OAI.
#' * Umatilla River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1967-2018). 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.
#' * Walla Walla River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1993-2019). 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.
#' * Touchet River: Middle Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1993-2019). 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/OAI.
#'
#' @name Steelhead-Middle-Columbia-River-DPS-ICMC2021
#' @docType data
#' @examples
#' data('Steelhead-Middle-Columbia-River-DPS-ICMC2021')
#' 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('Steelhead-Middle-Columbia-River-DPS-ICMC2021') +
#' 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