plot_survey_fit_mcmc: Creates a plot of fits to survey biomass including individual...
In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

plot_survey_fit_mcmc

R Documentation

Creates a plot of fits to survey biomass including individual posterior lines, median posterior line, observed values, and estimated values

Description

Creates a plot of fits to survey biomass including individual posterior lines, median posterior line, observed values, and estimated values

Usage

plot_survey_fit_mcmc(
  model,
  type = c("age1", "acoustic"),
  n_posts = NULL,
  show_legend = TRUE,
  x_lim = c(survey_start_yr, survey_end_yr),
  y_lim = c(0, 5),
  x_labs_mod = 5,
  y_labs_by = 0.5,
  tick_prop = 1,
  vjust_x_labels = -1.5,
  remove_yr_labels = NULL,
  post_line_width = 0.1,
  post_line_col = "black",
  post_line_alpha = 0.1,
  post_med_line_width = 1,
  post_med_line_color = "royalblue",
  post_med_line_alpha = main_alpha,
  post_med_point_size = 1.5,
  post_line_gap = ts_linegap,
  obs_line_width = 1.5,
  obs_line_color = "black",
  obs_point_color = "black",
  obs_point_size = 2.5,
  obs_alpha = 1,
  extrasd_line_width = 0.5,
  extrasd_line_color = "black",
  extrasd_point_color = "royalblue",
  extrasd_point_size = 2,
  extrasd_alpha = 1,
  glow = FALSE,
  glow_offset = 0.25,
  glow_color = "black",
  glow_alpha = 1,
  leg_ymax = y_lim[2] - 0.25,
  leg_sep = 0.6,
  leg_font_size = 10/.pt,
  ...
)

Arguments

`model`	A model object, , created by `create_rds_file()`
`type`	One of the surveys, either `age1` or `acoustic`
`n_posts`	The number of posterior lines to plot. The lines are randomly drawn from all posteriors. if this is larger than the number of posteriors, all posterior lines will be shown
`show_legend`	Logical. If `TRUE`, show the legend
`x_lim`	A vector of two for the minimum and maximum values for the x-axis on the plot
`y_lim`	A vector of two for the minimum and maximum values for the y-axis on the plot
`x_labs_mod`	How many years between year labels on the x-axis
`y_labs_by`	How often to have a label on the y-axis
`tick_prop`	A value that the length of the major tick marks are multiplied by. This proportion must be set by trial and error. Make sure to change `vjust_x_labels` so the labels are not overlapping the lines or are too far away from the lines
`vjust_x_labels`	Adjustment to move the x-axis tick labels and label up or down. Negative numbers move down
`remove_yr_labels`	A vector of years to remove the ,labels for in case they are overlapping
`post_line_width`	The width of the posterior lines
`post_line_col`	The color of the thinner individual posterior lines
`post_line_alpha`	The transparency of the thinner individual posterior lines
`post_med_line_width`	The width of the posterior median line
`post_med_line_color`	The color of the posterior median line
`post_med_line_alpha`	The transparency of the posterior median line
`post_med_point_size`	The size of the posterior median points
`post_line_gap`	The line gap value (separation between points and the line connecting them)
`obs_line_width`	The width of the error bar lines for observed values
`obs_line_color`	the color for the uncertainty bars for the observed values
`obs_point_color`	the color for the uncertainty median points for the observed values
`obs_point_size`	The size of the points on the error bars for the observed values
`obs_alpha`	The transparency of the observed lines
`extrasd_line_width`	The width of the error bar lines for the extra SD parameter estimates
`extrasd_line_color`	The color of the error bars for the extra SD parameter estimates
`extrasd_point_color`	The color of the median points for the extra SD parameter estimates
`extrasd_point_size`	The sizeof the median points for the extra SD parameter estimates
`extrasd_alpha`	The transparency of the extra SD lines
`glow`	Logical. If `TRUE`, add a glow around the lines so that they can more easily be seen in contrast to the background posterior lines
`glow_offset`	The amount to add to the lines and points to create the
`glow_color`	The color to use for the "glow" effect around lines
`glow_alpha`	The transparency to use for the "glow" effect around lines
`leg_ymax`	The top right y value for drawing the white box under the legend
`leg_sep`	The amount to seperate each entry in the legend. Needed because the legend is manually made