R/anadrofish.R

In danStich/anadrofish: Anadromous Fish Population Responses to Habitat Changes

#' anadrofish: Anadromous Fish Population Responses to Habitat Changes
#' 
#' The anadrofish package is a collection of tools for running
#' coastwide or river-specific population models for
#' anadromous fish in response to habitat change from dams.
#' 
#' @section Functions called directly:
#' The following functions can be called directly from anadrofish:
#' 
#'  \describe{
#'  
#'    \code{\link{sim_pop}}{ main function used to simulate populations} \cr
#'    
#'    \code{\link{add_unequal_vectors}}{ add vectors of unequal length} \cr
#'    \code{\link{beverton_holt}}{ Beverton-Holt recruitment with density dependence} \cr
#'    \code{\link{custom_habitat_template}}{ make custom habitat for an existing river or a template for a new river of interest} \cr
#'    \code{\link{get_dams}}{ get dams for specified river from American shad habitat data} \cr
#'    \code{\link{get_govt}}{ get governmental unit for specified river by species} \cr
#'    \code{\link{get_region}}{ get region for specified river by species} \cr
#'    \code{\link{get_rivers}}{ find out which rivers are available} \cr
#'    \code{\link{make_downstream}}{ river-specific, catchment-wide downstream survival through dams} \cr
#'    \code{\link{make_eggs}}{ simulate eggs per female by species and river} \cr
#'    \code{\link{make_habitat}}{ subset of \code{\link{habitat}} dataset for selected river} \cr
#'    \code{\link{make_iteroparity}}{ predict iteroparity from latitude based on reported relationships} \cr
#'    \code{\link{make_lat}}{ get latitude for specified river} \cr
#'    \code{\link{make_maxage}}{ get region-specific maximum age for specified population} \cr
#'    \code{\link{make_mortality}}{ calculate natural, instantaneous mortality by river} \cr
#'    \code{\link{make_pop}}{ simulate starting population} \cr
#'    \code{\link{make_postspawn}}{ predict post-spawning survival based on natural mortality and iteroparity} \cr
#'    \code{\link{make_recruits}}{ predict recruits from number of adults, fecundity, sex ratio, and juvenile survival} \cr
#'    \code{\link{make_spawners}}{ draw spawners from age-specific spawn recruitment probabilities} \cr
#'    \code{\link{make_spawnrecruit}}{ get region- and age-specific probabilities of recruitment to spawn} \cr
#'    \code{\link{project_pop}}{ project population to next time step without reproduction} \cr
#'    \code{\link{sim_juvenile_s}}{ simulate juvenile survival based on reported rates} \cr
#'    
#'    \code{\link{lower95}}{ convenience function for calculating upper 95\% CI} \cr 
#'    \code{\link{upper95}}{ convenience function for calculating lower 95\% CI} \cr
#'  }
#'  
#' @section Data:
#' The following built-in datasets are included:
#' 
#'   \describe{
#'     \code{\link{crecco_1983}}{ Regression parameters for latitude-iteroparity relationship in American shad} \cr
#'     \code{\link{fl_tl_conversions}}{ Fork length - total length conversions for river herring} \cr
#'     \code{\link{habitat}}{ American shad habitat data} \cr
#'     \code{\link{habitat_ale}}{ Alewife habitat data} \cr
#'     \code{\link{habitat_bbh}}{ Blueback herring habitat data} \cr
#'     \code{\link{jessop_1993}}{ Fork length-fecundity relationships for alewife} \cr
#'     \code{\link{length_weight}}{ Regional length-weight regression parameters for American shad} \cr
#'     \code{\link{lw_pars_rh}}{ Regional length-weight regression parameters for river herring} \cr
#'     \code{\link{maki_pars}}{ Regional spawner recruitment parameters for river herring} \cr
#'     \code{\link{maturity}}{ Regional spawner recruitment probabilities for American shad}  \cr
#'     \code{\link{max_ages}}{ Regional maximum ages by sex and species}  \cr
#'     \code{\link{mortality}}{ Regional mortality estimates for American shad by sex}  \cr
#'     \code{\link{mortality_rh}}{ Regional mortality estimates for river herring by sex}  \cr
#'     \code{\link{olney_mcbride}}{ Regression parameters for weight-batch fecundity relationships} \cr
#'     \code{\link{vbgf_ale}}{ von Bertalanffy growth parameters for alewife}  \cr
#'     \code{\link{vbgf_bbh}}{ von Bertalanffy growth parameters for blueback herring}  \cr
#'     \code{\link{vbgf_NI}}{ von Bertalanffy growth parameters for NI American shad}  \cr
#'     \code{\link{vbgf_SI}}{ von Bertalanffy growth parameters for SI American shad}  \cr
#'     \code{\link{vbgf_SP}}{ von Bertalanffy growth parameters for SP American shad}  \cr
#'   }
#'
#'
"_PACKAGE"
#' 
#' @aliases anadrofish-package
#' 
#' @importFrom truncnorm rtruncnorm
#' @importFrom stats quantile rnorm runif sd
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