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Salmon-coho-Oregon-Coast-ESU-OCcoho2020.R
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Salmon-coho-Oregon-Coast-ESU-OCcoho2020.R
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#' Salmon-coho-Oregon-Coast-ESU-OCcoho2020
#'
#'
#' @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: Coho salmon. Method: Survey. \href{../data/Salmon-coho-Oregon-Coast-ESU-OCcoho2020.html}{View raw data} or \href{../data/Salmon-coho-Oregon-Coast-ESU-OCcoho2020.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:
#' * Alsea River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Beaver Creek: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Coos Bay: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Coquille River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Floras Creek: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Lower Umpqua: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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 Umpqua: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Necanicum River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Nehalem River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Nestucca River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * North Umpqua: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Salmon River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Siletz River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Siltcoos River (Lake): Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Siuslaw River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Sixes River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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 Umpqua: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Tahkenitch Lake: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Tenmile Lake: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Tillamook Bay: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Yaquina River: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (1994-2018). 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.
#' * Oregon Mid-Coast Coho dependent population group: Oregon Coast Coho 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.
#' * Oregon North Coast Coho dependent population group: Oregon Coast Coho 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.
#' * Oregon Mid-South Coast Coho dependent population group: Oregon Coast Coho Natural Origin Spawner Abundance Dataset (2010-2018). 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-coho-Oregon-Coast-ESU-OCcoho2020
#' @docType data
#' @examples
#' data('Salmon-coho-Oregon-Coast-ESU-OCcoho2020')
#' 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-coho-Oregon-Coast-ESU-OCcoho2020') +
#' 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