displayModel: displayModel plots the model fit given the parameters and...

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

displayModel plots the model fit given the parameters and data

Description

displayModel takes a set of parameters and the spmdat matrix and plots the predicted depletion, catch, the surplus production, and the CPUE and the model fit to CPUE,

Usage

displayModel(
  inp,
  indat,
  schaefer = TRUE,
  extern = FALSE,
  limit = 0.2,
  target = 0.48,
  addrmse = FALSE,
  filename = "",
  resol = 200,
  fnt = 7,
  plotout = TRUE
)

Arguments

inp	a vector of model parameters (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
extern	defaults to FALSE, determines whether to plot the graphs in a separate window
limit	defaults to the Commonwealth limit of 0.2B0.
target	defaults to the Commonwealth target of 0.48B0. It 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
filename	default is empty. If a filename is put here a .png file with that name will be put into the working directory.
resol	the resolution of the png file, defaults to 200 dpi
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

Value

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

Examples

## Not run: 
data(dataspm)
fish <- dataspm$fish
glb <- dataspm$glb
plotfish(fish,glb) 
pars <- c(0.264,4740,3064) 
ans <- displayModel(pars,fish,schaefer=FALSE) 
bestSP <- optim(par=pars,fn=negLL,callfun=simpspm,indat=fish,schaefer=FALSE) 
outoptim(bestSP) 
ans <- displayModel(bestSP$par,fish,schaefer=FALSE) 
str(ans) 

## End(Not run)

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