Package index • anadrofish

All functions

add_unequal_vectors(): Add vectors of unequal length

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

beverton_holt(): Beverton-Holt stock recruit curve

crecco_1983: Daily mortality of juvenile American shad

custom_habitat_template(): Make custom habitat for an existing river or a template for a new river of interest

fill_output(): Fill output vectors

fl_tl_conversions: Fork length - total length conversions for river herring

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(): Rivers included in habitat data by species

habitat: American shad habitat

habitat_ale: Alewife habitat

habitat_bbh: Blueback herring habitat

jessop_1993: Fork length-fecundity relationships for alewife

length_weight: Length-weight regression coefficients for American shad

lower95(): Calculate lower 95 % confidence limit

lw_pars_rh: Length-weight regression coefficients for river herring

make_downstream(): Calculate downstream survival given dam passage scenario.

make_eggs(): Simulate number of eggs per fish

make_eggs_rh(): Simulate number of eggs per fish for river herring

make_habitat(): Make cumulative habitat for river

make_iteroparity(): Estimate rate of iteroparity for American shad from latitude based on Leggett and Cascardden (1978) and Bailey and Zydlewski (2013).

make_lat(): Retrieve latitude for American shad rivers.

make_maxage(): Make maximum age for population using built-in data sets.

make_mortality(): Make instantaneous natural mortality.

make_output(): Make output vectors

make_pop(): Make population

make_postspawn(): Post-spawning survival

make_recruits(): Make recruits

make_s_spawn(): Make total spawning migration mortality

make_spawners(): Make spawning population

make_spawnrecruit(): Make age-specific proportion of spawners in population

make_spawnrecruit_rh(): Make spawnrecruit vectors for river herring

maki_pars: Sex-specific maturity schedules for River Herring

maturity: Sex-specific maturity schedules for American shad

max_ages: Sex-specific maximum ages of American shad

mortality: Sex-specific instantaneous mortality of American shad

mortality_rh: Sex-specific instantaneous natural mortality of river herring

olney_mcbride: Weight-batch fecundity relationships for American Shad

project_pop(): Project population

rtrunc_norm(): Simulate random samples from truncated normal distribution

sim_juvenile_s(): Juvenile (hatch-to-outmigrant) survival

sim_pop(): Simulate population dynamics through time.

upper95(): Calculate upper 95 % confidence limit

vbgf_NI: Sex-aggregate von Bertalanffy growth parameters for Northern Iteroparous American shad

vbgf_SI: Sex-aggregate von Bertalanffy growth parameters for Southern Iteroparous American shad

vbgf_SP: Sex-aggregate von Bertalanffy growth parameters for Semelparous American shad

vbgf_ale: Sex-specific von Bertalanffy growth parameters for alewife

vbgf_bbh: Sex-specific von Bertalanffy growth parameters for blueback herring

write_output(): Write simulation results