MQMF (version 0.1.1)

plotspmmod: plotspmmod plots an spm model fit given parameters and data

Description

plotspmmod takes a parameter set and the spmdat matrix and plots the predicted depletion, catch, the CPUE and the model fit to CPUE. If plotprod=TRUE, it also plots the productivity curves

Usage

plotspmmod(
  inp,
  indat,
  schaefer = TRUE,
  limit = 0.2,
  target = 0.48,
  addrmse = FALSE,
  fnt = 7,
  plotout = TRUE,
  vline = 0,
  plotprod = FALSE,
  maxy = 0
)

Arguments

inp

a vector of model parameters at least (r,K,B0)

indat

a matrix with at least columns 'year', 'catch', and 'cpue'

schaefer

if TRUE, the default, then the Schaefer SPM is used. If FALSE then an approximate Fox SPM would be used

limit

defaults to the Commonwealth limit of 0.2B0.

target

defaults to the Commonwealth target of 0.48B0. Determines the green line plotted on the exploitable biomass plot.

addrmse

default is FALSE but if set TRUE this will add the loess curve to the CPUE trend for comparison with the fitted line

fnt

the font used in the plot and axes. Default=7, bold Times. Using 6 gives Times, 1 will give SansSerif, 2 = bold Sans

plotout

should one generate a plot or only do the calculations; default is TRUE

vline

defaults to 0 = no action but if a year is inserted, which should generally be between two years to designate some change in the time-series between two years, then a vertical line will be added on year-based plots

plotprod

if FALSE, the default, the productivity curves are not plotted. If TRUE, two extra plots are produced.

maxy

defaults to 0, if > 0 then that value will be used in the plot of CPUE

Value

invisibly a list of dynamics, production curve, MSY, and Bmsy

Examples

# NOT RUN {
data(dataspm)
pars <- log(c(0.264,4740,3064,0.2))
ans <- plotspmmod(pars,dataspm,schaefer=TRUE,plotprod=TRUE)
best <- nlm(negLL,pars,funk=simpspm,indat=dataspm,
       logobs=log(dataspm[,"cpue"]),steptol=1e-05)
outfit(best,backtran = TRUE)
ans <- plotspmmod(best$estimate,dataspm,schaefer=TRUE,plotout=TRUE,
                 plotprod=FALSE,addrmse=TRUE)
str(ans)
# }