Description Usage Arguments Details Value Required Data Optional Data Note Author(s) References See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
x |
An index for the objects in |
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 |
fix_n |
Logical, whether to fix the exponent of the production function. If |
fix_sigma |
Logical, whether the standard deviation of the index is fixed. If |
fix_omega |
Logical, whether the standard deviation of the catch is fixed. If |
fix_alpha |
Logical, whether the ratio of index and biomass standard deviations is fixed. If |
fix_beta |
Logical, whether the ratio of catch and F standard deviations is fixed. If |
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 |
... |
Additional arguments (not currently used). |
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.
An object of Assessment
containing assessment output.
spict
: Cat, Ind
spict
: CV_Cat, CV_Ind
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.
Q. Huynh
Pedersen, M. W. and Berg, C. W. 2017. A stochastic surplus production model in continuous time. Fish and Fisheries. 18:226-243.
SP_production plot.Assessment summary.Assessment make_MP
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.