gnomonicStochastic {gnomonicM}

Gnomonic stochastic

Description

Estimate natural mortality based on gnomonic interval approach with different distribution in fecundity.

Usage

gnomonicStochastic(
  nInterval,
  eggDuration,
  addInfo = NULL,
  longevity,
  fecundity = NULL,
  sd_fecundity = NULL,
  min_fecundity = NULL,
  max_fecundity = NULL,
  distr = "uniform",
  a_init = 2,
  niter = 999,
  seed = 7388
)

Arguments

nInterval

a numeric value that represents the number of gnomonic intervals.

eggDuration

a numeric value with the egg stage (first gnomonic interval) duration in days.

addInfo

a numeric vector with additional information related to the observed duration of the other gnomonic intervals different than the first interval (egg stage duration). Write addInfo = NULL if you do not provide additional information.

longevity

a numeric value indicating the lifespan of the species in days.

fecundity

a numeric value indicating the mean or the mode of the fecundity as the number of eggs produced for a female if a normal or triangular distribution is assumed, respectively.

sd_fecundity

a numeric value indicating the standard deviation of fecundity if a normal distribution is assumed.

min_fecundity

a numeric value indicating the minimum range of fecundity if a uniform or triangle distribution is assumed.

max_fecundity

a numeric value indicating the maximum range of fecundity if a uniform or triangle distribution is assumed.

distr

a character string indicating the distribution to be applied: "uniform", "triangle" or "normal"

a_init

a numeric value indicating the initial parameter related to the proportionality constant optimized by iterative solution via univariate (1-dim.) minimization. a_init = 2 as default value.

niter

a single numeric value representing the number of iterations.

seed

a single value, interpreted as an integer.

Details

Estimate natural mortality (M) based on gnomonic interval approach .

The argument nInterval is NULL by default. If you have -at least- one observed value for the duration of the other gnomonic intervals you should provide this as a vector which length must be nInterval - 1, for example addInfo = c(3, NA, NA, NA, NA, NA)) for a nInterval = 7.

The argument fecundity requires a character string indicating the name of the distribution of fecundity values to be used in the analysis (i.e. fecundity = "uniform").

The argument niter requires a number which is related with the number of observations. If length(n) > 1, the length is taken to be the number required. can be calculated from each bootstrap sample (median and confidence intervals).

Value

A list of class 'gnomosBoot'.

a the proportionality constant.

G the 'n' iter values of constant proportion of the overall natural death rate.

mean_G the mean of constant proportion of the overall natural death rate,

M a dataframe with the M values for each gnomonic intervals for each 'n' iteration.

fecundity the 'n' iter values of fecundity based on the distribution assumed.

results a dataframe with the duration ("interval_duration_day"), mean, confidence interval and standard deviation of natural mortality ("M_lower", "M", "M_upper", "M_sd") for each gnomonic interval.

Examples

#The values are based on Caddy (1996).
modelBoot <- gnomonicStochastic(nInterval = 7, eggDuration = 2, addInfo = NULL, longevity = 365,
distr = "uniform", min_fecundity = 100000, max_fecundity = 300000, niter = 999, a_init = 2)

# 'niter' parameters:
modelBoot$a
modelBoot$G
modelBoot$mean_G
modelBoot$M
modelBoot$fecundity
modelBoot$results