anadrofish: Anadromous Fish Population Responses to Habitat Changes
anadrofish-package.RdThe 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_popmain function used to simulate populations
add_unequal_vectorsadd vectors of unequal length
beverton_holtBeverton-Holt recruitment with density dependence
custom_habitat_templatemake custom habitat for an existing river or a template for a new river of interest
get_damsget dams for specified river from American shad habitat data
get_govtget governmental unit for specified river by species
get_regionget region for specified river by species
get_riversfind out which rivers are available
make_downstreamriver-specific, catchment-wide downstream survival through dams
make_eggssimulate eggs per female by species and river
make_habitatsubset of
habitatdataset for selected rivermake_iteroparitypredict iteroparity from latitude based on reported relationships
make_latget latitude for specified river
make_maxageget region-specific maximum age for specified population
make_mortalitycalculate natural, instantaneous mortality by river
make_popsimulate starting population
make_postspawnpredict post-spawning survival based on natural mortality and iteroparity
make_recruitspredict recruits from number of adults, fecundity, sex ratio, and juvenile survival
make_spawnersdraw spawners from age-specific spawn recruitment probabilities
make_spawnrecruitget region- and age-specific probabilities of recruitment to spawn
project_popproject population to next time step without reproduction
sim_juvenile_ssimulate juvenile survival based on reported rates
lower95convenience function for calculating upper 95% CI
upper95convenience function for calculating lower 95% CI
Data
The following built-in datasets are included:
crecco_1983Regression parameters for latitude-iteroparity relationship in American shad
fl_tl_conversionsFork length - total length conversions for river herring
habitatAmerican shad habitat data
habitat_aleAlewife habitat data
habitat_bbhBlueback herring habitat data
jessop_1993Fork length-fecundity relationships for alewife
length_weightRegional length-weight regression parameters for American shad
lw_pars_rhRegional length-weight regression parameters for river herring
maki_parsRegional spawner recruitment parameters for river herring
maturityRegional spawner recruitment probabilities for American shad
max_agesRegional maximum ages by sex and species
mortalityRegional mortality estimates for American shad by sex
mortality_rhRegional mortality estimates for river herring by sex
olney_mcbrideRegression parameters for weight-batch fecundity relationships
vbgf_alevon Bertalanffy growth parameters for alewife
vbgf_bbhvon Bertalanffy growth parameters for blueback herring
vbgf_NIvon Bertalanffy growth parameters for NI American shad
vbgf_SIvon Bertalanffy growth parameters for SI American shad
vbgf_SPvon Bertalanffy growth parameters for SP American shad