R/pkgname.R

In nwfsc-math-bio/NWCTrends: Standardized Trend Metrics for Salmonid Populations

#' @title
#' NWFSC PNW Salmonid Viability Report Standardized Metrics
#' @description
#' This package creates the ESU/DPS tables and figures for the standardized metrics used in the
#' Northwest Fisheries Science Center's PNW Salmonid Viability Reports which support the 5-year
#' Status Review updates (prepared by WRO) for Pacific salmon and steelhead listed 
#' under the Endangered Species Act: Pacific Northwest".
#' @details
#' The 2015 NWFSC PNW Salmonid Viability Report can be viewed by typing
#' \code{RShowDoc("2015_Status_Review_Update", package="NWCTrends")}
#' at the command line. The report has a description of the
#' methods used for computing the smoothed trend lines and the status metrics. A pdf of the methods alone is also available by typing 
#' \code{RShowDoc("Methods", package="NWCTrends")}
#' at the command line.
#'
#' The default model used to fit the data is that used in the
#' 2015 Status Update. This model uses information across the
#' populations in an ESU to estimate the process variance,
#' non-process variance (residuals
#' between smoothed fits and observed spawners), covariance in
#' process errors (good and bad year correlation). However it
#' allows each population to have a different trend.  This model is
#' specified as \code{ model=list(Z="identity", R="diagonal and equal", U="unequal", Q="equalvarcov") }.
#'
#' The main function that creates the reports and plots is \link{NWCTrends_report}.
#' This calls `esu_report.Rmd` which makes the reports and figures. 
#' The data are input as a csv file and a folder is created with the name of this
#' csv file. Within that folder is  a `metadata.csv file` for the meta data from
#'  the csv file and then there are individual files for each ESU/DPS within 
#'  the csv file.
#'  
#' The look of the plots (line widths, types, colors, point types, etc) can be changed by 
#' passing in \code{\link{nwctrends.options}} to
#' \code{\link{NWCTrends_report}()}.
#' 
#' @seealso \link{data_setup}, \link{trend_15_table}, \link{trend_fits}, \link{geomean_table}.
#' @keywords internal
#' @references
#' Ford, M. J., K. Barnas, T. Cooney, L. G. Crozier, M. Diaz, J. J. Hard, E. E. Holmes, D. M. Holzer, R. G. Kope, P. W. Lawson, M. Liermann, J. M. Myers, M. Rowse, D. J. Teel, D. M. Van Doornik, T. C. Wainwright, L. A. Weitkamp, M. Williams. 2015. Status Review Update for Pacific Salmon and Steelhead Listed under the Endangered Species Act:  Pacific Northwest. National Marine Fisheries Service, Northwest Fisheries Science Center.
#' Available from the NWFSC Publications page.
"_PACKAGE"