plotASPM: plotASPM plots catch, CPUE, Spawning Biomass and Harvest Rate

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

plotASPM plots catch, CPUE, Spawning Biomass and Harvest Rate

Description

plotASPM after running fitASPM the optimum parameters can be put through the dynamics function to generate a dataframe containing the optimum dynamics. These can be plotted using plotASPM, which plots out the catches, the Spawning Biomass, the relative CPUE and its fit to the observed CPUE, and the harvest rate. This routine is still under development to include more options.

Usage

plotASPM(infish, CI = NA, defineplot = TRUE, target = 0.48, usef = 7, png = "")

Arguments

infish	an object generated by the dynamics function
CI	defaults to NA, if confidence intervals around the cpue have been obtained using getLNCI, then the resulting matrix will generate 95pc CIs
defineplot	define the plot size and character outside the plot or automatically inside. Defaults to TRUE
target	target depletion level. Defaults to 0.48
usef	defines the font to use usef(ont),default = 7 bold times
png	save a png file with the name in 'png', default = "", which means no file produced

Value

Nothing, but it does plot six graphs in a single plot.

Examples

## Not run: 
data(dataspm)
fish <- dataspm$fish
glb <- dataspm$glb
props <- dataspm$props
pars <- c(14,0.3)
aspmLL(pars,fish,glb,props)      # should be -2.277029
bestspm <- fitASPM(pars,infish=fish,inglb=glb,inprops=props)
fishery <- dynamics(bestspm$par,fish,glb,props)
plotASPM(fishery,defineplot=TRUE)
ceCI <- getLNCI(fishery[,"PredCE"],bestspm$par[2])
plotASPM(fishery,CI=ceCI)

## End(Not run)  # infish=fishery; CI=NA; defineplot=TRUE; target=0.48; usef=7;png="test.png"

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