sscom: SSCOM model

In datalimited/datalimited: Stock Assessment Methods for Data-limited Fisheries

Description

State-space catch-only model from Thorson et al. (2013).

Usage

sscom(yr, ct, start_r = resilience("unknown"), NburninPrelim = 1000,
  NiterPrelim = 2000, NthinPrelim = 1, NchainsPrelim = 100,
  NburninJags = 1e+06, NiterJags = 2e+06, NthinJags = 1000, Nchains = 3,
  return_jags = FALSE)

Arguments

yr	Years
ct	Catch time series
start_r	Lower and upper intrinsic population growth rates
NburninPrelim	Number of warmup iterations during the preliminary phase
NiterPrelim	Number of preliminary iterations
NthinPrelim	Thinning of preliminary iterations
NchainsPrelim	Number of chains for preliminary iterations
NburninJags	Number of warmup iterations for main sampling phase
NiterJags	Number of sampling iterations for main sampling phase
NthinJags	Thining for main sampling phase
Nchains	Number of chains for the main sampling phase
return_jags	Logical: should the JAGS output object be returned at the end as well. If TRUE then a list with elements jags and output will be returned with the JAGS and SSCOM output, respectively.

References

Thorson, J. T., C. Minto, C. V. Minte-Vera, K. M. Kleisner and C. Longo, 2013. A new role for effort dynamics in the theory of harvested populations and data-poor stock assessment. Can. J. Fish. Aquat. Sci. 70(12):1829-1844.

Examples

## Not run: 
x <- sscom(blue_gren$yr, blue_gren$ct,
 NburninPrelim = 1e3,
 NiterPrelim = 2e3,
 NthinPrelim = 1,
 NchainsPrelim = 20,
 NburninJags = 1e3,
 NiterJags = 3e3,
 NthinJags = 2,
 Nchains = 3, return_jags = TRUE)
 
## End(Not run)

datalimited/datalimited documentation built on May 14, 2019, 7:44 p.m.