spm: spm - calcuates the dynamics using a Schaefer or Fox model

In haddonm/datalowSA: A Package to Faciliate Application of Data poor Stock Assessments

spm - calcuates the dynamics using a Schaefer or Fox model

Description

spm calculates the dynamics using a Schaefer of Fox model. The outputs include predicted Biomass, year, catch, cpue, predicted cpue, contributions to q, ssq, and depletion levels. Generally it would be more sensible to use simpspm when fitting a Schaefer model and simpfox when fitting a Fox model as those functions are designed to generate only the predicted cpue required by the functions ssq and negLL, but the example shows how it could be used. the function spm is used inside 'displayModel' and could be used alone, to generate a fullist of model outputs after the model has been fitted.

Usage

spm(inp, indat, schaefer = TRUE)

Arguments

inp	a vector of 2 or 3 model parameters (r,K) or (r,K,Binit), you would use the latter if it was suspected that the fishery data started after some initial depletion had occurred.
indat	a matrix with at least columns 'year', 'catch', and 'cpue'
schaefer	a logical value determining whether the spm is to be a simple Schaefer model (p=1) or approximately a Fox model (p=1e-08). The default is TRUE

Value

a list of five objects; outmat the matrix with the dynamics results, q catchability, msy the maximum sustainable yield, the parameter values, and sumout, which contains r, K, B0, msy, p, q, Depl, FinalB, and InitDepl

Examples

## Not run: 
year <- 1985:2008
catch <- c(1018,742,868,715,585,532,566,611,548,499,479,428,657,481,645,961,
           940,912,955,935,940,952,1030,985)
cpue <- c(0.6008,0.6583,0.6791,0.6889,0.7134,0.7221,0.7602,0.7931,0.8582,
          0.8876,1.0126,1.1533,1.2326,1.2764,1.3307,1.3538,1.2648,1.2510,
          1.2069,1.1552,1.1238,1.1281,1.1113,1.0377)
dat <- makespmdata(cbind(year,catch,cpue))
pars <- c(0.35,7800,3500)
ans <- displayModel(pars,dat)
bestSP <- optim(par=pars,fn=ssq,callfun=simpspm,indat=dat)
bestSP
ans <- displayModel(bestSP$par,dat,schaefer=TRUE)
str(ans)

## End(Not run)

haddonm/datalowSA documentation built on Nov. 5, 2023, 6:40 p.m.