multiplot_proj: multiplot.proj

In mcsiple/mmrefpoints: Project Marine Mammal Populations and Calculate Reference Points

multiplot.proj

Description

plots outputs from several projections that result from projections(), with multiple depletion levels.

Usage

multiplot_proj(
  high.d1,
  med.d1,
  low.d1,
  high.d2,
  med.d2,
  low.d2,
  high.d3,
  med.d3,
  low.d3,
  spaghetti = FALSE,
  years.to.plot = 50,
  color.palette = c("forestgreen", "darkorange", "red"),
  lang = "en"
)

Arguments

high.d1	a list containing output from projections() (including a matrix of simulation trajectories) - this corresponds to the highest bycatch level (thus "high") and the depletion level ( d1 indicates the lowest starting depletion level)
med.d1	a list containing the middle bycatch value and lowest starting depletion
low.d1	a list containing the lowest bycatch value and lowest starting depletion
high.d2	a list containing the highest bycatch value and middle starting depletion
med.d2	a list containing the middle bycatch value and middle starting depletion
low.d2	a list containing the lowest bycatch value and middle starting depletion
high.d3	a list containing the highest bycatch value and highest starting depletion
med.d3	a list containing the middle bycatch value and highest starting depletion
low.d3	a list containing the lowest bycatch value and highest starting depletion
spaghetti	either FALSE or a number, where the number is how many simulations to show from the same scenario
years.to.plot	How many years to plot on the x axis
color.palette	A vector of length 3 giving the color values for low, medium, and high bycatch mortality or bycatch mortality rate
lang	language to use. "en" = English; "es" = Spanish; "fr" = French.

Value

A plot of 50 percent and 90 percent confidence intervals of population projections if spaghetti == FALSE or a spaghetti plot with n individual projections if spaghetti == n , from projections().

Examples

parms <- list(
  S0 = 0.944, S1plus = 0.99,
  K1plus = 9000,
  AgeMat = 18, nages = 20,
  z = 2.39, lambdaMax = 1.02
)
InitDepl.vec <- c(0.1, 0.5, 0.9)
BycatchCV <- 0.2
nyears <- 100

high.list <- lapply(
  X = InitDepl.vec,
  function(x) {
    projections(
      NOut = 50,
      ConstantRateBycatch = list(Rate = 0.3, CV = BycatchCV),
      InitDepl = x,
      lh.params = parms,
      nyears = nyears,
      obs_CV = 0.2
    )
  }
)

med.list <- lapply(
  X = InitDepl.vec,
  function(x) {
    projections(
      NOut = 50,
      ConstantRateBycatch = list(Rate = 0.02, CV = BycatchCV),
      InitDepl = x,
      lh.params = parms,
      nyears = nyears,
      obs_CV = 0.2
    )
  }
)
low.list <- lapply(
  X = InitDepl.vec,
  function(x) {
    projections(
      NOut = 50,
      ConstantRateBycatch = list(Rate = 0.001, CV = BycatchCV),
      InitDepl = x,
      lh.params = parms,
      nyears = nyears,
      obs_CV = 0.2
    )
  }
)
multiplot_proj(
  high.d1 = high.list[[1]], # d1 is the lowest depletion
  med.d1 = med.list[[1]],
  low.d1 = low.list[[1]],
  high.d2 = high.list[[2]],
  med.d2 = med.list[[2]],
  low.d2 = low.list[[2]],
  high.d3 = high.list[[3]],
  med.d3 = med.list[[3]],
  low.d3 = low.list[[3]],
  years.to.plot = nyears
)

mcsiple/mmrefpoints documentation built on June 17, 2022, 8:41 p.m.