spmMult | R Documentation |
spmMult 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.
spmMult(inp, indat, schaefer = TRUE)
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 |
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
## 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)
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