plot.predict_mod: Plotting prediction models yield per recruit and Thompson &...
In TropFishR: Tropical Fisheries Analysis

Description Usage Arguments References Examples

This function plots objects of the class "predict_mod", which are results of the function predict_mod.

## S3 method for class 'predict_mod'
plot(
  x,
  type = "ypr",
  xaxis1 = "FM",
  yaxis1 = "Y_R.rel",
  yaxis2 = "B_R.rel",
  yaxis_iso = "Lc",
  identify = FALSE,
  mark = FALSE,
  contour = TRUE,
  xlab = NA,
  ylab1 = NA,
  ylab2 = NA,
  ylab3 = NA,
  plot_refs = c("F01", "Fmax", "F05", "F04"),
  cols_refs = c("goldenrod2", "darkred", "darkgreen", "darkorange"),
  ...
)

`x`	a object of the class 'predict_mod'
`type`	a character indicating, which type of plot should be displayed in case of Beverton and Holt's yield per recurit model. Options are either "ypr" (default) for line plot or "Isopleth" for isopleth plot.
`xaxis1`	which x-axis should be plotted? Either "FM" (fishing mortality; default) or "E" (exploitation rate).
`yaxis1`	which (first) y-axis should be plotted? "Y_R" (yield per recruit; default) or "Y_R.rel" (relative yield per recruit) for type = "ypr". For "Isopleth" in addition: "B_R" (biomass per recruit) and "B_R.rel" (relative yield per recruit). For Thompson and Bell model in addition also "value" or "catch" possible.
`yaxis2`	which second y-axis should be plotted for type = "ypr"? Either "B_R" (biomass per recruit; default), "B_R.rel" (relative biomass per recruit), or "B_R.percent" (percentage biomass per recruit)
`yaxis_iso`	determines label and scale of y axis of Isopleth graph. Either "Lc" (default) for length at first capture or "Lc/Linf" for the relation of length at first capture to the infinite length
`identify`	logical; indicating whether points in the graph are supposed to be identified by clicking on them (uses `locator` function). To stop press right mouse click. (default: TRUE).
`mark`	logical; if value of choosen points should be displayed in graph (default: TRUE)
`contour`	used in combination with the Isopleth graph. Usage can be logical (e.g. TRUE) or providing a numeric which indicates the number of levels (`nlevels` in `contour`). By default TRUE.
`xlab`	Label of x-axis. If set to NA, then default "Fishing mortality", or "Exploitation rate" is used.
`ylab1`	Label of y-axis. If set to NA, then default "Yield" is used for the Thompson and Bell model, "Lc" is used for the Isopleth graph, and "Y/R" is used for ypr.
`ylab2`	Label of second y-axis. If set to NA, then default "Biomass" is used for the Thompson and Bell model and "B/R" for ypr.
`ylab3`	Label of third y-axis. If set to NA, then default "Value" is used for the Thompson and Bell model.
`plot_refs`	Define reference points to be plotted. Default: c("F01","Fmax","F05","F04")
`cols_refs`	Define colours for reference points. Default: c("goldenrod2","darkred","darkgreen","darkorange")
`...`	optional parameters of plot function

Sparre, P., Venema, S.C., 1998. Introduction to tropical fish stock assessment. Part 1. Manual. FAO Fisheries Technical Paper, (306.1, Rev. 2). 407 p.

## Not run: 
# Nemipterus marginatus - age structured data
threadfin <- list(Winf = 286,K = 0.37, t0 = -0.2, M = 1.1, tr = 0.4)

output <- predict_mod(threadfin, FM_change = seq(0,6,0.1),
   tc_change = seq(0.2,1,0.2), type = 'ypr')
plot(output)

# hake - length structured data
data(hake)
hake$Lr <- 35
select.list <- list(selecType = 'trawl_ogive', L50 = 20, L75 = 24)
output <- predict_mod(param = hake, FM_change = seq(0,0.4,0.05),
                      curr.E = 0.4, curr.Lc = 40,
                      Lc_change = seq(5,80,1), s_list = select.list,
                      type = 'ypr', plot = FALSE)
plot(output, type = "Isopleth", xaxis1 = "FM", yaxis1 = "Y_R.rel",
   identify = FALSE)


## End(Not run)