spict: Stochastic production in continuous time (spict)

In DLMtool/DLMextra: Additional OMs, Data, and Assessment functions for DLMtool and MSEtool

Description

A state-space surplus production model that uses a time-series of catches and a relative abundance index and coded in TMB (Pedersen and Berg 2017). This is a wrapper assessment function for the MSEtool package, which calls the model from the spict package. There are a multitude of possible configurations for spict. Here, the default is to use n = 2 (symmetric yield curve), dep = 1 (unfished stock in year 1 of model), and alpha, beta = 1 (equal observation and process standard deviations). These can be changed in the function arguments below.

Usage

spict(
  x = 1,
  Data,
  start = NULL,
  fix_dep = TRUE,
  fix_n = TRUE,
  fix_sigma = FALSE,
  fix_omega = FALSE,
  fix_alpha = TRUE,
  fix_beta = TRUE,
  n_seas = 4L,
  inp_args = list(),
  ...
)

Arguments

x	An index for the objects in Data when running in runMSE. Otherwise, equals to 1 when running an assessment interactively.
Data	An object of class Data.
start	Optional list of starting values. See details.
fix_dep	Logical, whether to fix the initial depletion (ratio of biomass to carrying capacity in the first year of the model). If TRUE, uses the value in start, otherwise equal to 1 (assumes unfished conditions).
fix_n	Logical, whether to fix the exponent of the production function. If TRUE, uses the value in start, otherwise equal to n = 2, where the biomass at MSY is half of carrying capacity.
fix_sigma	Logical, whether the standard deviation of the index is fixed. If TRUE, sigma is fixed to value provided in start (if provided), otherwise, value based on Data@CV_Ind.
fix_omega	Logical, whether the standard deviation of the catch is fixed. If TRUE, omega is fixed to value provided in start (if provided), otherwise, value based on Data@CV_Cat.
fix_alpha	Logical, whether the ratio of index and biomass standard deviations is fixed. If TRUE, alpha is fixed to value provided in start (if provided), otherwise, equal to 1.
fix_beta	Logical, whether the ratio of catch and F standard deviations is fixed. If TRUE, tau is fixed to value provided in start (if provided), otherwise, equal to 1.
n_seas	Integer, the number of sub-annual time steps in the model, i.e. the inverse of the Euler time step. Defaults to 4 (seasonal time steps).
inp_args	A named of list of additional variables for the inp list to pass to check.inp.
...	Additional arguments (not currently used).

Details

To provide starting values, a named list can be provided for MSY, K, n, omega, and sigma via the start argument. Otherwise, the defaults from the spict package are used.

Value

An object of Assessment containing assessment output.

Required Data

• spict: Cat, Ind

Optional Data

• spict: CV_Cat, CV_Ind

Note

This is a wrapper function intended for a DLMtool Data object. The spict package can be downloaded from Github with devtools::install_github("DTUAqua/spict/spict").

The full spict model also accommodates time-varying reference points and seasonal data among other things, but these features are currently not used here. Additional diagnostics and plotting functions are also available in the spict package.

Author(s)

Q. Huynh

References

Pedersen, M. W. and Berg, C. W. 2017. A stochastic surplus production model in continuous time. Fish and Fisheries. 18:226-243.

See Also

SP_production plot.Assessment summary.Assessment make_MP

Examples

library(MSEtool)
data(swordfish)

res <- spict(Data = swordfish)
plot(res)
summary(res)

## Use additional spict-package functions
spict_output <- res@info
library(spict)
summary(spict_output)
plot(spict_output)
spict_retro <- retro(spict_output)
plotspict.retro(spict_retro)

DLMtool/DLMextra documentation built on May 19, 2020, 12:49 p.m.