R/shadia.R

In danStich/shadia: American shad dam passage performance standard model for R

#' shadia: American shad dam passage performance standard models for R
#'
#' The shadia package provides an interface for running
#' the American shad dam passage performance standard
#' model. It includes a limited number of functions intended to
#' be called directly by the user, and a large number of
#' supporting internal functions that are visible to promote
#' transparency in the model.
#'
#' @section Functions called directly:
#'   \describe{
#'     \code{\link{connecticutRiverModel}} \cr
#'     \code{\link{kennebecRiverModel}} \cr
#'     \code{\link{merrimackRiverModel}} \cr
#'     \code{\link{mohawkHudsonRiverModel}} \cr
#'     \code{\link{penobscotRiverModel}} \cr
#'     \code{\link{sacoRiverModel}} \cr
#'     \code{\link{susquehannaRiverModel}} \cr
#'     \code{\link{addStochList}} \cr
#'     \code{\link{CI}} \cr
#'     \code{\link{invlogit}} \cr
#'     \code{\link{substrRight}}
#'   }
#'
#' @section Internal functions:
#'  \describe{
#'    \code{\link{annualUpstream}} \cr
#'    \code{\link{additionalEggsProcessing}} \cr
#'    \code{\link{annualUpstream}} \cr
#'    \code{\link{assignFishToRoutes}} \cr
#'    \code{\link{assignFishToRoutes}} \cr
#'    \code{\link{createPUMatrix}} \cr
#'    \code{\link{defineHabitat}} \cr
#'    \code{\link{defineHydroSystem}} \cr
#'    \code{\link{defineOutputVectors}} \cr
#'    \code{\link{definePassageRates}} \cr
#'    \code{\link{downstreamMigration}} \cr
#'    \code{\link{fillOutputVectors}} \cr
#'    \code{\link{fwFishingMort}} \cr
#'    \code{\link{innerLoopSampling}} \cr
#'    \code{\link{nextGeneration}} \cr
#'    \code{\link{populationMatrices}} \cr
#'    \code{\link{postSpawnMortality}} \cr
#'    \code{\link{processCohorts}} \cr
#'    \code{\link{processPopulation}} \cr
#'    \code{\link{scalePop}} \cr
#'    \code{\link{setScalar}} \cr
#'    \code{\link{writeData}} \cr
#'  }
#'
#' @section Data:
#'   \describe{
#'
#'   }
#'
#'
#' @docType package
#'
#' @name shadia
#'
#' @importFrom graphics abline lines par plot
#' @importFrom stats aggregate nls quantile runif var
#' @importFrom geosphere daylength
#' @importFrom lubridate year yday
#' @importFrom MASS mvrnorm rnegbin
#' @importFrom zoo na.spline
#' @importFrom magrittr %>%
#' @importFrom dplyr summarize group_by filter
#' @import Rcpp
#'
#' @useDynLib shadia
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