Description Usage Arguments Value Author(s) References Examples
View source: R/StochasticSRA.R
Specify an operating model, using catch composition data and a historical catch series. Returns and operating model with depletion (D), selectivity parameters (L5, LFS) and effort trajectory (Effyears, EffLower, EffUpper) filled. Modified version using cpp code.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | StochasticSRAcpp(
OM,
CAA,
Chist,
Ind,
Cobs = 0.1,
sigmaR = 0.5,
Umax = 0.9,
nsim = 48,
proyears = 50,
Jump_fac = 1,
nits = 20000,
burnin = 1000,
thin = 50,
ESS = 300,
ploty = T,
nplot = 6,
SRAdir = NA
)
|
OM |
An operating model object with M, growth, stock-recruitment and maturity parameters specified. |
CAA |
A matrix nyears (rows) by nages (columns) of catch at age (age 1 to maxage in length) |
Chist |
A vector of historical catch observations (nyears long) going back to unfished conditions |
Ind |
A vector of historical index observations (nyears long, may be patchy with NAs) going back to unfished conditions. |
Cobs |
A numeric value representing catch observation error as a log normal sd |
sigmaR |
A numeric value representing the prior standard deviation of log space recruitment deviations |
Umax |
A numeric value representing the maximum harvest rate for any age class (rejection of sims where this occurs) |
nsim |
The number desired draws of parameters / effort trajectories |
proyears |
The number of projected MSE years |
Jump_fac |
A multiplier of the jumping distribution variance to increase acceptance (lower Jump_fac) or decrease acceptance rate (higher Jump_fac) |
nits |
The number of MCMC iterations |
burnin |
The number of initial MCMC iterations to discard |
thin |
The interval over which MCMC samples are extracted for use in graphing / statistics |
ESS |
Effective sample size - the weighting of the catch at age data |
ploty |
Do you want to see diagnostics plotted? |
nplot |
how many MCMC samples should be plotted in convergence plots? |
SRAdir |
A directory where the SRA diagnostics / fit are stored |
A list with three positions. Position 1 is the filled OM object, position 2 is the custompars data.frame that may be submitted as an argument to runMSE() and position 3 is the matrix of effort histories [nyears x nsim]
vector of objects of classclassy
T. Carruthers (Canadian DFO grant)
Walters, C.J., Martell, S.J.D., Korman, J. 2006. A stochastic approach to stock reduction analysis. Can. J. Fish. Aqua. Sci. 63:212-213.
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