plot_param_density: Create a plot showing the density of the posterior for the...
In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

plot_param_density

R Documentation

Create a plot showing the density of the posterior for the catch forecast for a given year

Description

Create a plot showing the density of the posterior for the catch forecast for a given year

Usage

plot_param_density(
  model,
  param_nm,
  prob_vec = probs,
  scale = 1000,
  x_lab = "",
  y_lab = "Density",
  x_lim = c(0, 3000),
  y_lim = c(0, 1e-04),
  expand_vec = c(0, 0),
  x_breaks = seq(x_lim[1], x_lim[2], by = (x_lim[2] - x_lim[1])/6),
  fill_color = ts_single_model_ribbon_fill,
  fill_alpha_tail = 0.3,
  fill_alpha_main = 0.7,
  show_y_labels = TRUE,
  show_med_label = TRUE,
  med_label_units = "kt",
  med_label_digits = 3,
  arrow_obj = arrow(length = unit(0.5, "cm"), angle = 20, type = "closed"),
  label_x_offset = 500,
  label_y_offset = 1e-04,
  ...
)

Arguments

`model`	The model output from Stock Synthesis as loaded by `create_rds_file()`
`param_nm`	A parameter name present in `names(model$mcmc)`
`prob_vec`	A vector of probabilities to use in the `quantile()` calculation
`scale`	A value to divide the parameter values by
`x_lab`	The x-axis label
`y_lab`	The y-axis label. Only shown if `show_y_labels` is `TRUE`
`x_lim`	A vector of two values. The x-axis minimum and maximum values
`expand_vec`	A vector to pass to the `expand` argument of the `ggplot2::scale_x_continuous()` function. Default is `c(0, 0)`
`fill_color`	The color used to fill under the density curve
`fill_alpha_tail`	The transparency used for the color of the tails
`fill_alpha_main`	The transparency used for the color of the main part of the curve (-1SD - 1SD)
`show_y_labels`	Logical. If `TRUE`, show the y-axis label , ticks, and tick labels
`show_med_label`	Logical. If `TRUE`, show the median label with arrow
`med_label_units`	Units (as text) to place in the label showing the median. Only used if `show_med_label` is `TRUE`
`label_x_offset`	An x-axis offset to move the median label to, Positive means move right. Only used if `show_med_label` is `TRUE`
`label_y_offset`	A y-axis offset to move the median label to, Positive means move up. Only used if `show_med_label` is 'TRUE
`...`	Arguments to pass to `theme_axis_text()`
`show_med_digits`	Number of decimal places to show in the median label. Only used if `show_med_label` is `TRUE`