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

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

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 [e-mail] (ORCID)

Authors:

• S. G. Roy

• S. D. Snyder

• J. D. Zydlewski

See Also

Useful links:

• https://danstich.github.io/anadrofish/

danStich/anadrofish documentation built on Jan. 17, 2025, 9:46 a.m.