plot_pairs: Create a pairs plot showing correlations among key parameters...
In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

plot_pairs

R Documentation

Create a pairs plot showing correlations among key parameters or recruitment deviations against the R0 parameter

Description

Create a pairs plot showing correlations among key parameters or recruitment deviations against the R0 parameter

Usage

plot_pairs(
  model,
  type = c("key", "devs"),
  key_posteriors = NULL,
  key_posteriors_titles = NULL,
  recr = NULL,
  bratio = NULL,
  forecatch = NULL,
  point_color = "royalblue",
  point_alpha = 0.3,
  point_size = 0.05,
  lm_color = "black",
  lm_linetype = "solid",
  lm_linewidth = 1,
  strip_fill_color = "transparent",
  strip_fill_alpha = 0.3
)

Arguments

`model`	The model output from Stock Synthesis as loaded by `create_rds_file()`.
`type`	Either "key" or "devs", which describe the type of pairs plot to create. If this is "key", all parameters listed in the `key_posteriors` argument will be plotted as well as the objective function and recruitment parameters for years listed in `recr`. If this is "devs", The R0 parameter will be plotted against the recruitment deviation parameters for the years listed in `recr`
`key_posteriors`	A list of key posterior names (as regular expressions)
`key_posteriors_titles`	A list of key posterior titles (pretty names which are meant to be shown on plots)
`recr`	A vector of the recruitment parameter years to include.
`bratio`	A vector of years to plot the relative spawning biomass for
`forecatch`	A vector of years to plot the default harvest catch for. There are forecasts, hence the name
`point_color`	The color of the scatter plot points
`point_alpha`	The transparency of the scatter plot points
`point_size`	Th size of the scatter plot points
`lm_color`	The color of the regression line found on the scatter plot panels
`lm_linetype`	The type of the regression line found on the scatter plot panels
`lm_linewidth`	The width of the regression line found on the scatter plot panels
`strip_fill_color`	The color to fill in the strip labels (facet labels)
`strip_fill_alpha`	The transparency for the strip labels (facet labels)