anadrofish-package: anadrofish: Anadromous Fish Population Responses to Habitat...

anadrofish-packageR Documentation

anadrofish: Anadromous Fish Population Responses to Habitat Changes

Description

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.

Functions called directly

The following functions can be called directly from anadrofish:

sim_pop

main function used to simulate populations

add_unequal_vectors

add vectors of unequal length

beverton_holt

Beverton-Holt recruitment with density dependence

custom_habitat_template

make custom habitat for an existing river or a template for a new river of interest

get_dams

get dams for specified river from American shad habitat data

get_govt

get governmental unit for specified river by species

get_region

get region for specified river by species

get_rivers

find out which rivers are available

make_downstream

river-specific, catchment-wide downstream survival through dams

make_eggs

simulate eggs per female by species and river

make_habitat

subset of habitat dataset for selected river

make_iteroparity

predict iteroparity from latitude based on reported relationships

make_lat

get latitude for specified river

make_maxage

get region-specific maximum age for specified population

make_mortality

calculate natural, instantaneous mortality by river

make_pop

simulate starting population

make_postspawn

predict post-spawning survival based on natural mortality and iteroparity

make_recruits

predict recruits from number of adults, fecundity, sex ratio, and juvenile survival

make_spawners

draw spawners from age-specific spawn recruitment probabilities

make_spawnrecruit

get region- and age-specific probabilities of recruitment to spawn

project_pop

project population to next time step without reproduction

sim_juvenile_s

simulate juvenile survival based on reported rates

lower95

convenience function for calculating upper 95% CI

upper95

convenience function for calculating lower 95% CI

Data

The following built-in datasets are included:

crecco_1983

Regression parameters for latitude-iteroparity relationship in American shad

fl_tl_conversions

Fork length - total length conversions for river herring

habitat

American shad habitat data

habitat_ale

Alewife habitat data

habitat_bbh

Blueback herring habitat data

jessop_1993

Fork length-fecundity relationships for alewife

length_weight

Regional length-weight regression parameters for American shad

lw_pars_rh

Regional length-weight regression parameters for river herring

maki_pars

Regional spawner recruitment parameters for river herring

maturity

Regional spawner recruitment probabilities for American shad

max_ages

Regional maximum ages by sex and species

mortality

Regional mortality estimates for American shad by sex

mortality_rh

Regional mortality estimates for river herring by sex

olney_mcbride

Regression parameters for weight-batch fecundity relationships

vbgf_ale

von Bertalanffy growth parameters for alewife

vbgf_bbh

von Bertalanffy growth parameters for blueback herring

vbgf_NI

von Bertalanffy growth parameters for NI American shad

vbgf_SI

von Bertalanffy growth parameters for SI American shad

vbgf_SP

von Bertalanffy growth parameters for SP American shad

Author(s)

Maintainer: Daniel S. Stich daniel.stich@oneonta.edu (ORCID)

Authors:

See Also

Useful links:


danStich/anadrofish documentation built on June 11, 2025, 11:25 p.m.