R/Steelhead-Lower-Columbia-River-DPS-LCsthd2020.R

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

#' Steelhead-Lower-Columbia-River-DPS-LCsthd2020
#' 

#' 
#' @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-Lower-Columbia-River-DPS-LCsthd2020.html}{View raw data} or \href{../data/Steelhead-Lower-Columbia-River-DPS-LCsthd2020.csv}{Download raw data}
#' 
#' 
#' @source

#' * Coweeman Winter Steelhead: Washington Department of Fish and Wildlife
#' * North Fork Toutle Winter Steelhead: Washington Department of Fish and Wildlife
#' * South Fork Toutle Winter Steelhead: Washington Department of Fish and Wildlife
#' * Upper Cowlitz and Cispus Winter Steelhead: Washington Department of Fish and Wildlife
#' * Tilton Winter Steelhead: Washington Department of Fish and Wildlife
#' * Kalama Winter Steelhead: Washington Department of Fish and Wildlife
#' * East Fork Lewis Winter Steelhead: Washington Department of Fish and Wildlife
#' * Clackamas River: Oregon Department of Fish and Wildlife
#' * Sandy River: Oregon Department of Fish and Wildlife
#' * Washougal Winter Steelhead: Washington Department of Fish and Wildlife
#' * Upper Gorge (Columbia) Winter Steelhead: Washington Department of Fish and Wildlife
#' * Hood River: Oregon Department of Fish and Wildlife
#' * Kalama Summer Steelhead: Washington Department of Fish and Wildlife
#' * East Fork Lewis Summer Steelhead: Washington Department of Fish and Wildlife
#' * Washougal Summer Steelhead: Washington Department of Fish and Wildlife
#' * Wind River (Upper Gorge) Summer Steelhead: 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: 
#' * Coweeman Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1987-2019). 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 Toutle Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2005-2019). 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.
#' * South Fork Toutle Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1981-2019). 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.
#' * Upper Cowlitz and Cispus Winter Steelhead: Lower Columbia River Steelhead 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.
#' * Tilton Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1999-2018). 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 Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1977-2019). 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.
#' * East Fork Lewis Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1986-2019). 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.
#' * Clackamas River: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1974-2019). 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/PSMFC.
#' * Sandy River: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2010-2019). 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/PSMFC.
#' * Washougal Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1991-2019). 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.
#' * Upper Gorge (Columbia) Winter Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2000-2019). 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.
#' * Hood River: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (2011-2018). 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.
#' * Kalama Summer Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1977-2019). 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.
#' * East Fork Lewis Summer Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1996-2019). 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.
#' * Washougal Summer Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1953-2019). 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.
#' * Wind River (Upper Gorge) Summer Steelhead: Lower Columbia River Steelhead Natural Origin Spawner Abundance Dataset (1989-2019). 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.
#' 
#' @name Steelhead-Lower-Columbia-River-DPS-LCsthd2020
#' @docType data
#' @examples
#' data('Steelhead-Lower-Columbia-River-DPS-LCsthd2020')
#' 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-Lower-Columbia-River-DPS-LCsthd2020') +
#'   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