TropFishR (version 1.6.2)

plot.VPA: VPA plot

Description

This function plots the survivors, catches, natural losses, and fishing mortality resulting from the VPA model.

Usage

# S3 method for VPA
plot(
  x,
  yaxis = "numbers",
  display_last_class = TRUE,
  xlabel = NA,
  ylabel1 = "Population",
  ylabel2 = "Fishing mortality",
  ylim = NA,
  ylim_FM = NA,
  plot.bars = TRUE,
  plot.FM = TRUE,
  plot.legend = TRUE,
  ...
)

Arguments

x

list of the class "VPA" containing the results of the VPA model.

yaxis

indicating which variable should be displayed on the y axis, either "numbers" or "biomass".

display_last_class

logical; should last age/length class be displayed in graph?

xlabel

Label of the x axis

ylabel1

Label of the first y axis

ylabel2

Label of the second y axis

ylim

limits of y axis

ylim_FM

limits of y axis of fishing mortality plot

plot.bars

logical; should the barplot of survivors, nat.losses and catch be displayed? (Default: TRUE)

plot.FM

logical; should the fishing mortality be displayed in the graph? (Default: TRUE)

plot.legend

logical; should a legend be displayed in the graph? (Default: TRUE)

...

standard parameters of barplot

References

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.

Examples

# NOT RUN {
data(whiting)
output <- VPA(whiting, terminalF = 0.5)
plot(output, display_last_class = FALSE)

data(hake)
output <- VPA(hake, terminalE = 0.5, catch_unit = "'000")
plot_mat <- output$plot_mat[,-c(1,2)]  # remove first two length classes
class(plot_mat) <- "VPA"
plot(plot_mat, xlabel = "Midlengths [cm]")

# }

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