Simple plotting functions — plot

These are simple plotting helpers to quickly visualize outputs from sim_abundance(), sim_distribution(), and related simulation functions.

plot_trend(sim, sum_ages = sim$ages, col = viridis::viridis(1), ...)

plot_surface(sim, mat = "N", xlab = "Age", ylab = "Year", zlab = mat, ...)

plot_grid(grid, ...)

plot_distribution(
  sim,
  ages = sim$ages,
  years = sim$years,
  type = "contour",
  scale = "natural",
  ...
)

plot_survey(sim, which_year = 1, which_sim = 1)

plot_total_strat_fan(sim, surveys = 1:5, quants = seq(90, 10, by = -10), ...)

plot_length_strat_fan(
  sim,
  surveys = 1:5,
  years = 1:10,
  lengths = 1:50,
  select_by = "year",
  quants = seq(90, 10, by = -10),
  ...
)

plot_age_strat_fan(
  sim,
  surveys = 1:5,
  years = 1:10,
  ages = 1:10,
  select_by = "year",
  quants = seq(90, 10, by = -10),
  ...
)

plot_error_surface(sim, plot_by = "rule")

plot_survey_rank(sim, which_strat = "age")

Arguments

sim: Object returned by sim_abundance(), sim_distribution(), etc.
sum_ages: Vector of ages to sum across.
col: Plot color.
...: Additional arguments passed to plotly::plot_ly().
mat: Name of the matrix in the sim list to plot.
xlab, ylab, zlab: Axis labels.
grid: Grid produced by make_grid().
ages: Subset the data to one or more ages.
years: Subset the data to one or more years.
type: Plot type: "contour" or "heatmap".
scale: Plot response on "natural" or "log" scale.
which_year: Subset to a specific year.
which_sim: Subset to a specific simulation replicate.
surveys: Subset the data to one or more surveys.
quants: Quantile intervals to display on the fan plot.
lengths: Subset the data to one or more length groups.
select_by: Select plot by "age", "length", or "year".
plot_by: Plot error surface by "rule" or "samples".
which_strat: Stratification focus: "total", "length", or "age".

Value

A plot of class plotly.