negLLM: negLLM -ve log-normal likelihoods for multiple index...

In MQMF: Modelling and Quantitative Methods in Fisheries

negLLM -ve log-normal likelihoods for multiple index time-series

Description

negLLM we have negLL and negLL1 for use when using -ve log-likelihoods to fit surplus production models that only have a single index of relative abundance, but there are many fisheries that have more than one index of relative abundance. negLLM is for those cases that have multiple (M) time-series of such indices. It is used in conjunction with simpspmM and spmCE.

Usage

negLLM(pars, funk, logobs, indat, index = "cpue", harvpen = TRUE, ...)

Arguments

pars	the log-transformed parameter starting points. For a surplus production model these are r, K, Binit (if initial depletion is likely, otherwise omit this and it will be set =K inside the function), then as many sigma values as there are time-series of abundance indices; these are the associated standard deviations of the log-normal residuals.
funk	the function that generates the predicted cpue values. for multiple time-series in a SPM use simpspmM
logobs	the log-transformed observed cpue columns in indat, the data needed by funk, transferred inside the ...
indat	the fisheries data used in the analysis
index	the prefix of the columns of each of the indices, defaults to cpue
harvpen	default = TRUE, which sets a penalty1 on each of the implied harvest rates to ensure we do not get harvest rates > 1.0
...	the continuation ellipsis to allow the transfer of other arguments required by funk. The argument 'schaefer' in the example below illustrates such usage.

Value

a single scalar as the -ve log-likelihood of the input data

Examples

 data(twoindex)
 fish <- as.matrix(twoindex)
 pars <- log(c(0.04,155000,0.4,0.3))
 bestSP <- nlm(f=negLLM,p=pars,funk=simpspmM,indat=fish,
             schaefer=TRUE,logobs=log(fish[,c("cpue1","cpue2")]),
             steptol=1e-06,harvpen=TRUE)
 outfit(bestSP,digits=5,title="negLLM example") #optimum solution
 answer <- plotspmmod(bestSP$estimate,indat=fish,
                      plotprod=TRUE,maxy=3.4)

MQMF documentation built on Sept. 8, 2023, 5:14 p.m.