HUMPBACK.SIR: HUMPBACK SIR controls the sampling from the priors, the...

In antarctic-humpback-2019-assessment/HumpbackSIR: Use Sample-Importance-Resampling to Estimate Southern Humpback Abundance

HUMPBACK SIR controls the sampling from the priors, the bisection and likelihoods and the output functions

Description

HUMPBACK SIR controls the sampling from the priors, the bisection and likelihoods and the output functions

Usage

HUMPBACK.SIR(file_name = "NULL", n_resamples = 1000,
  priors = make_prior_list(),
  catch_multipliers = make_multiplier_list(),
  premodern_catch_multipliers = make_multiplier_list(),
  target.Yr = 2008, num.haplotypes = 66, output.Yrs = c(2008),
  abs.abundance = Abs.Abundance, rel.abundance = Rel.Abundance,
  rel.abundance.key = TRUE, count.data = NULL,
  count.data.key = FALSE, growth.rate.obs = c(0.074, 0.033, TRUE),
  growth.rate.Yrs = c(1995, 1996, 1997, 1998), catch.data = Catch.data,
  premodern_catch_data = NULL, realized_prior = FALSE,
  control = sir_control())

Arguments

file_name	name of a file to identified the files exported by the function
n_resamples	number of resamples to compute the marginal posterior distributions
priors	List of priors, usually generated using make_prior_list. Default is the default of make_prior_list. See details.
catch_multipliers	List of catch multipliers, generated using make_multiplier_list Can either be estimated or explicitly provided. Default is make_multiplier_list.
premodern_catch_multipliers	List of historic catch multipliers, generated using make_multiplier_list Can either be estimated or explicitly provided. Default is make_multiplier_list.
target.Yr	year of the target population estimate for the bisection method. Default is 2008
num.haplotypes	number of haplotypes to compute minimum viable population (from Jackson et al., 2006 and IWC, 2007)
output.Yrs	year for outputing the predicted abundance estimates. Default is 2008, but multiple years can be specified. For example, if outputs for 2005 and 2008 are needed, output.Yrs = c(2005, 2008)
abs.abundance	R object containing year, estimate of absolute abundance, and CV (see example)
rel.abundance	R object containing years, estimates of relative abudnance and CVs (see example)
rel.abundance.key	key to speficy if relative abundance data are used in the likelihood. Default is TRUE
count.data	R object containing years, estimates of counts and effort. NOT USED
count.data.key	key to speficy in count data are used. Default is FALSE. NOT USED
growth.rate.obs	observed growth rate (1st element) and standard error (2nd element) as in Zerbni et al. (2011). If third element is FALSE, the growth rate is not included in the likelihood
growth.rate.Yrs	Years for which the growth.rate.obs were computed (as in Zerbini et al., 2011)
catch.data	R object containing the years and catches (see example)
premodern_catch_data	R object containing the years maximum and minimum premodern catches
realized_prior	Key to specify if realized prior is to be extracted. Default is FALSE.
control	A list of control parameters, usually generated by sir_control.

Value

A list containing posterior samples and metadata

Current default prior specification: make_prior_list(r_max = make_prior(runif, 0, 0.118), K = make_prior(use = FALSE), N_obs = make_prior(runif, 500, 40000), add_CV = make_prior(use = FALSE), z = make_prior(2.39), q_IA = make_prior(use = FALSE), q_count = make_prior(use = FALSE) make_multiplier_list(c_mult_1 = make_prior(1))

Examples

## Not run: 
HUMPBACK.SIR(file_name = "test.N2005",
             n_resamples = 100,
             priors = make_prior_list(),
             catch_multipliers = make_multiplier_list(),
             premodern_catch_multipliers = make_multiplier_list(),
             Klim = c(1, 500000),
             target.Yr = 2005,
             num.haplotypes = 0,
             tolerance.for.bisection = 0.0001,
             output.Yrs = c(2005, 2006),
             abs.abundance = Abs.Abundance.2005,
             rel.abundance = Rel.Abundance,
             rel.abundance.key = TRUE,
             count.data = Count.Data,
             count.data.key = FALSE,
             growth.rate.obs = c(0.074, 0.033, TRUE),
             growth.rate.Yrs = c(1995, 1996, 1997, 1998),
             catch.data = Catch.data,
             premodern_catch_data = NULL,
             control = sir_control())

## End(Not run)

antarctic-humpback-2019-assessment/HumpbackSIR documentation built on Nov. 6, 2023, 6:07 p.m.