SSTfuncDM: Original dynamic model

In eeholmes/DM: Dynamic Model

Description

Implements the DM model from the original RER process. Estimates escapement by year using escapement data from previous years, maturation rates, harvest rates, and rates of natural mortality. The estimated escapement is log transformed and subtracted from the log transformed values of observed escapement. These differences are then squared and summed to get the sum of squares residual which is returned by the function. This function can be used to estimated the spawner-recruit parameters through the use of an optimization function.

Usage

SSTfuncDM(p, SRfunc, dat, input, returnAll = FALSE)

Arguments

p	The values of the SR function parameters. p[1] and p[2] are logged to keep them positive. p[1]=log(prod), p[2]=log(cap). The other p depend on what covariates are in the model. These are unlogged as they could be positive or negative depending on the covariate.. The length of p is 2 + number of covariates. If there are 2 covariates, then p[3]= msCoef and p[4]=flowCoef.
SRfunc	a SR function: ricker, bevertonHolt, hockeyStick, as returned by selectSR()
dat	data from the A & P file
input	a list with the other values needed for a DM run. The following are examples naturalMort, analysisType = "DM", SRfunction, covariates, includeMarineSurvival, includeFlow
returnAll	(TRUE/FALSE)

Value

Returns the sum of squares residuals between the observed and estimated escapement. If returnAll is true, the estimated and observed escapement are also returned.

eeholmes/DM documentation built on May 26, 2019, 3:36 p.m.