Skip to contents

R6 Class Representing a Fish

Source: R/fish_class.R
Fish.Rd

A fish object has all the life history data needed to model a finfish population

Details

Fish like to swim

Methods

Public methods

Method new()

Used to store parameters describing the behavior of an object of class Fish

Usage

Fish$new(
  common_name = NA,
  scientific_name = NA,
  linf = NA,
  vbk = NA,
  t0 = -0.5,
  cv_len = 0.1,
  l0 = 18.85,
  rmax = 37.24,
  k = 0.89,
  t50 = 4.57,
  length_a = 0.1,
  length_b = 3,
  length_units = "cm",
  length_bin_width = 1,
  growth_model = "von_bertalanffy",
  min_age = 0,
  max_age = NA,
  weight_a = NA,
  weight_b = NA,
  pups = 10,
  weight_units = "kg",
  fec_form = "weight",
  fec_expo = 1,
  fec_at_age = NULL,
  length_50_mature = NA,
  length_95_mature = NA,
  delta_mature = 0.1,
  age_50_mature = NA,
  age_95_mature = NA,
  age_mature = NA,
  semelparous = FALSE,
  m = NA,
  m_at_age = NULL,
  steepness = 0.8,
  r0 = 10000,
  ssb0 = NA,
  b0 = NA,
  popsize_measure = "b0",
  density_dependence = "global_habitat",
  adult_diffusion = 4,
  recruit_diffusion = 10,
  adult_home_range = NULL,
  recruit_home_range = NULL,
  query_fishlife = T,
  sigma_rec = 0,
  ac_rec = 0,
  cores = 4,
  mat_mode = "age",
  default_wb = 2.8,
  tune_weight = FALSE,
  linf_buffer = 1.2,
  resolution = NULL,
  patch_area = 1,
  habitat = list(),
  season_blocks = list(),
  recruit_habitat = NA,
  depletion = 1,
  burn_years = 50,
  seasons = 1,
  explt_type = "f",
  init_explt = 0.1,
  get_common_name = FALSE,
  spawning_seasons = NA,
  max_hab_mult = 2,
  lorenzen_m = TRUE,
  lorenzen_c = -1
)

Arguments

common_name

common name of the species (can be used to lookup information using taxize and fishlife)

scientific_name

common name of the species (can be used to lookup information in fishlife)

linf

asymptotic length of the species in a von Bertalanffy growth function

vbk

growth parameter k of the species in a von Bertalanffy growth function

t0

hypothetical age at which the fish would have length 0 (e.g. -0.5 years)

cv_len

coefficient of variation around the length at age relationship (in log space)

l0

length at age 0 in growth cessation model

rmax

related to maximum growth rate in growth cessation model

k

steepness of the logistic function in the growth cessation model >=0

t50

age at the logistic function midpoint in the growth cessation model

length_a

a coefficient in power function growth

length_b

b power coefficient in power function growth

length_units

units of the length at age function (arbitrary)

length_bin_width

the width of the length bins in the length-at-age key, defaults to 1cm

growth_model

one of "von_bertalanffy" or "power"

min_age

minimum age tracked in the model. Best to leave at 0, as the model does not explicitly track delays for recruitment

max_age

maximum age tracked by the model (individuals this age or older are tracked in the plus group)

weight_a

alpha parameter in the allometric weight function alpha x length ^ beta

weight_b

beta parameter in the allometric weight function alpha x length ^ beta

pups

number of pups per individual for animals with pups rather than larvae

weight_units

units of the allometric weight function (defaults to kg)

fec_form

one of of "weight" (default) or "pups". When "weight", fecundity is a function of weight. When "pups", constant number of pups per individual produced

fec_expo

exponent for fecundity at weight relationship, 1 = isometric > 1 hyperallometric

fec_at_age

manual vector of fecundity at age

length_50_mature

length at 50% maturity in a logistic maturity ogive

length_95_mature

length at 95% maturity in a logistic maturity ogive

delta_mature

as an alternative, the different in units of length between length_50_mature and length_95_mature

age_50_mature

age at 50% maturity in a logistic maturity ogive if maturity is age based

age_95_mature

age at 95% maturity in a logistic maturity ogive if maturity is age based

age_mature

an alternative option to just set one age mature, which ends up as the age_50_mature

semelparous

TRUE or FALSE. When FALSE (default), individuals can reproduce multiple times. When TRUE, individuals can only spawn once, so mortality at increase increases as a function of maturity at age

m

instantaneous natural mortality rate. When lorenzen_m = TRUE, this is the average natural mortality across all ages

m_at_age

a vector of natural mortality age at age in case manually specified

steepness

steepness parameter (h) in a Beverton-Holt spawner-recruit function

r0

asymptotic number of recruits under unfished conditions

ssb0

asymptotic spawning stock biomass of recruits under unfished conditions. Tunnes r0 to achieve

b0

desired level of unfished biomass

popsize_measure

whether unfished population size should be set based on biomass or spawning stock biomass

density_dependence

timing and nature of density dependence in the Beverton-Holt spawner recruit function, one of one of 'global_habitat','local_habitat','pre_dispersal','post_dispersal','global_ssb'. When 'global_habitat' density dependence is a function of the total spawning biomass across all patches, and recruits are then distributed proportional to recruit habitat quality. When 'local_habitat' density dependence is a function of the spawning biomass in each patch, and recruits are then distributed proportional to recruit habitat quality. When 'pre_dispersal', density dependence is a function of the spawning biomass in each patch, and recruits are then distributed from their home patch based on the recruit_home_range. When 'post_dispersal', larvae are distributed from their home patch based on recruit_home_range, and then density dependence happens based on spawning biomass in the settling patches. When 'global_ssb', density dependence is a function of the total spawning biomass and recruits are then distributed in space proportional to spawning biomass.

adult_diffusion

diffusion parameter D in the CTMC movement function for "adults" (not recruits). Deprecated, best to use adult_home_range

recruit_diffusion

diffusion parameter D in the CTMC movement function for recruits. Deprecated, best to use recruit_home_range

adult_home_range

the desired home range of adults. Overrides adult_diffusion if set

recruit_home_range

the desired home range of recruits Overrides recruit_diffusion if set

query_fishlife

TRUE or FALSE to query Fishlife for missing life history values. When set to FALSE all required life history values must be supplied by the user

sigma_rec

the standard deviation of recruitment deviates in log-normal space

ac_rec

the autocorrelation of recruitment deviates

cores

the number of cores used to tun the weight relationship if used (deprecated)

mat_mode

specifies whether maturity is a function of age (default) or length

default_wb

deprecated

tune_weight

deprecated

linf_buffer

multiplier around linf to create length at age key, taking into account that some fish will be larger than Linf

resolution

a vector of length two with number of patches in X and Y dimensions

patch_area

area of each patch (e.g. KM2)

habitat

a matrix with dimensions X and Y specifying quality of adult (non-recruit) habitat. Determines taxis matrix

season_blocks

list with elements indicating blocks of seasons. For example, if there are four seasons, setting season_blocks = list(c(1,2),c(3,4)) indicates that seasons 1 and 2 are one block, 3 and 4 another. Allows for the model to be run at fine time scales while allowing some processes like movement or spawning to operate at coarser scales

recruit_habitat

a matrix with dimensions X and Y with quality of recruit habitat (scales r0 in space as well as recruit diffusion under applicable forms of density dependence)

depletion

depletion (SSB/SSB0) under initial fished conditions

burn_years

number of years used to burn in the population to tune parameters without analytical solutions like SSB0

seasons

number of seasons per year. 4 would indicate quarterly time steps, 12 monthly, 365 daily.

explt_type

deprecated plot object of class fish

init_explt

instantaneous fishing mortality rate under initial fished conditions

get_common_name

TRUE or FALSE to lookup common name from scientific name. Requires internet connection

spawning_seasons

seasons in which spawning occurs

max_hab_mult

maximum value of that habitat matrix multiplier (to prevent some habitats from being >>> good, defaults to 2)

lorenzen_m

TRUE or FALSE to use the Lorenzen function to calculate natural mortality at age

lorenzen_c

the rate of the Lorenzen curve. Defaults to -1, larger values will make the difference between natural mortality at young vs old ages less pronounced

Method plot()

Usage

Fish$plot(type = 2)

Arguments

type

Returns

a plot of the life history values plot diffusion

Method plot_movement()

Usage

Fish$plot_movement()

Arguments

type

Returns

a plot of the diffusion after one year Swim

Swim advances the population one time step

Method swim()

Usage

Fish$swim(
  burn_steps = 0,
  season = 1,
  f_p_a = NULL,
  last_n_p_a = NULL,
  adult_movement = NULL,
  tune_unfished = 0,
  rec_devs = NA
)

Arguments

burn_steps

number of steps for burn in period if applicable

season

the current season

f_p_a

matrix of fishing mortality by patch and age

last_n_p_a

matrix of initial numbers by patch and age

adult_movement

the adult movement matrix

tune_unfished

boolean indicating whether to tune unfished

rec_devs

externally supplied recruitment deviates

Returns

the population in the next time step

Method clone()

The objects of this class are cloneable with this method.

Usage

Fish$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.