lhPar: Generates life history parameters

In flr/FLife: Methods for Modelling Life History Traits

Generates life history parameters

Description

Uses life history theory to derive parameters for biological relationships, i.e. or growth, maturity, natural mortality. Selectivity by default is set so age at peak selectivity is the same as age at 50% mature (a50) As a minimum all 'lhPar' requires is 'linf' the asymptotic length of the von Bertalannfy growth equation.

Uses life history theory to derive parameters for biological relationships, i.e. or growth, maturity, natural mortality. Selectivity by default is set so age at peak selectivity is the same as age at 50% mature (a50) As a minimum all 'lhPar' requires is 'linf' the asymptotic length of the von Bertalannfy growth equation.

Usage

lhPar(
  ...,
  m = list(model = "gislason", params = c(m1 = 0.55, m2 = -1.61, m3 = 1.44)),
  k = function(params, a = 3.15, b = -0.64) a * params["linf"]^b,
  t0 = function(params, a = -0.3922, b = -0.2752, c = -1.038) -exp(a - b *
    log(params$linf) %-% (c * log(params$k))),
  l50 = function(params, a = 0.72, b = 0.93) a * params["linf"]^b
)

lhStk(
  ...,
  k = function(params, a = 3.15, b = -0.64) a * params["linf"]^b,
  t0 = function(params, a = -0.3922, b = -0.2752, c = -1.038) -exp(a - b *
    log(params$linf) %-% (c * log(params$k))),
  l50 = function(params, a = 0.72, b = 0.93) a * params["linf"]^b,
  gowth = vonB,
  mat = logistic,
  sel = dnormal,
  sr = "bevholt",
  m = list(model = "gislason", params = c(m1 = 0.55, m2 = -1.61, m3 = 1.44)),
  fmult = function(x) refpts(x)["msy", "harvest"] %*% FLQuant(seq(0, 2, length.out =
    100)),
  range = c(min = 0, max = 40, minfbar = 1, maxfbar = 40, plusgroup = 40),
  spwn = 0,
  fish = 0.5,
  midyear = 0.5
)

Arguments

t0	of von Bertalanffy. This is a default that isnt normally derived from life history theory, as are the following args.
sr	obsolete now replaced by sel3
params	FLPar object with parameters for life history equations and selection pattern. Need Linfinity to estimate other parameters, if any other parameters supplied in code then these are not provided by the algorithm
a	coefficient of length weight relationship
b	exponent of length weight relationship
ato95	age at which 95% of fish are mature, offset to age at which 50% are mature
s	steepness of stock recruitment relationship
v	virgin biomass
sel1	selectivity-at-age parameter for double normal, age at maximum selectivity by default set to same as age at 100% mature
sel2	selectivity-at-age parameter for double normal, standard deviation of lefthand limb of double normal, by default 5
sel3	selectivity-at-age parameter for double normal, standard deviation of righthand limb of double normal, by default 5000
sl	obsolete now replaced by sel2
m1	m-at-age parameter by default for Gislason empirical relationship
m2	m-at-age parameter, by default for Gislason empirical relationship
m3	m-at-age parameter, by default for Gislason empirical relationship

Value

object of class FLPar with missing parameters calculated from life history theory

object of class FLPar with missing parameters calculated from life history theory

See Also

loptAge, lhRef, lhPar, lhEql

loptAge, lhRef, lhPar, lhEql

Examples

## Not run: 
#COMPARE with output of FLife::lhPar

x <- as(lhpar(linf=100), 'list')
x <- x[sort(names(x))]
y <- as(lhPar(FLPar(linf=100)), 'list')
y <- y[sort(names(y))]

all.equal(x,y)

for(i in seq(length(x)))
   cat(names(x[i]), ":", unlist(x[i]), "-", names(y[i]), ":", unlist(y[i]), "\n")
   
 # CALL with iters
 lhpar(FLPar(linf=100), v=rnorm(100, 300, 200))
 
 lhPar(FLPar(linf=rnorm(100, 80, 10)))
 lhPar(FLPar(linf=100, v=rnorm(100, 300, 200)))
 lhPar(FLPar(linf=100), FLPar(v=rnorm(100, 300, 200)))
 lhPar(FLPar(linf=100, v=rnorm(100, 300, 200)), t0=-1, data.frame(a=1,b=7))
 
 attributes(lhpar(FLPar(linf=100), v=rnorm(100, 300, 200)))$mmodel

## End(Not run)

## Not run: 

flr/FLife documentation built on March 29, 2024, 5:50 p.m.