plot_sp_A_ts: Plot sample time series from a portfolio simulation

In metafolio: Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization

Plot sample time series from a portfolio simulation

Description

Plot sample time series from a portfolio simulation

Usage

plot_sp_A_ts(
  X,
  ylim,
  x_axis = TRUE,
  y_axis = TRUE,
  rate = FALSE,
  lwd = 1.7,
  y_axis_ticks = NULL,
  start_new_plots = 1,
  labels = NULL,
  burn = 30,
  add_lm = FALSE,
  cols,
  ...
)

Arguments

X	Object to plot. Should be a list of outputs from meta_sim.
ylim	Y axis limits.
x_axis	Should an x axis be added?
y_axis	Should a y axis be added?
rate	If TRUE then the first difference (rate of change) will be plotted. If FALSE then the raw data will be plotted.
lwd	Line width of the lines.
y_axis_ticks	Location of the y-axis tick marks, if you want to specify them.
start_new_plots	On which elements of the list X should new panels be started? A numeric vector.
labels	Labels for the panels.
burn	Burn in period to discard.
add_lm	Add a regression trend line?
cols	Colours for the lines. A vector of character.
...	Anything else to pass to plot.default

Value

A plot, possibly with multiple panels.

Examples

w_plans <- list()
w_plans[[1]] <- c(5, 1000, 5, 1000, 5, 5, 1000, 5, 1000, 5)
w_plans[[2]] <- c(5, 5, 5, 1000, 1000, 1000, 1000, 5, 5, 5)
w_plans[[3]] <- c(rep(1000, 4), rep(5, 6))
w_plans[[4]] <- rev(w_plans[[3]])
w <- list()
for(i in 1:4) { # loop over plans
 w[[i]] <- list()
 for(j in 1:2) { # loop over trials
   w[[i]][[j]] <- matrix(w_plans[[i]], nrow = 1)
 }
}

cons_arma_ts <- list()
arma_env_params <- list(mean_value = 16, ar = 0.1, sigma_env = 2, ma = 0)
for(i in 1:4) {
  use_cache <- ifelse(i == 1, FALSE, TRUE)
  cons_arma_ts[[i]] <- meta_sim(b = w[[i]][[1]], n_pop = 10, env_params =
    arma_env_params, env_type = "arma", assess_freq = 5,
    use_cache = use_cache)
}
cols <- RColorBrewer::brewer.pal(5, "Dark2")
par(mfrow = c(2, 1))
plot_sp_A_ts(cons_arma_ts, ylim = c(0000, 12400),
  start_new_plots = c(1, 3),
  labels = c("Balanced response diversity",
    "ignore", "Unbalanced response diversity", "ignore"), cols = cols)

metafolio documentation built on Oct. 21, 2023, 1:06 a.m.