plot_output: plot LIME output

In merrillrudd/LIME: Length-based Integrated Mixed Effects (LIME) assessment method

Description

plot_output plot output from LIME or LB-SPR

Usage

plot_output(
  Inputs = NULL,
  Report = NULL,
  Sdreport = NULL,
  LBSPR = NULL,
  lh,
  true_years = NULL,
  True = NULL,
  plot = c("Fish", "Rec", "SPR", "ML", "SB", "Selex"),
  set_ylim = list(SPR = c(0, 1)),
  legend = FALSE
)

Arguments

Inputs	LIME input file
Report	LIME report file
Sdreport	LIME standard error file
LBSPR	LBSPR results - either straight from LBSPR output or LIME-edited
lh	life history list
true_years	vector of true years (in case all_years and lc_years are 1:20 instead of 1998:2017)
True	default=NULL, possible to specify true list from generated data if simulation
plot	options for plotting include "Fish"=fishing mortality, "Rec"=recruitment (LIME only), "SPR"=spawning potential ratio, "ML"=mean length (including observed values; LIME only), "SB"=spawning biomass (LIME only), "Selex"=selectivity-at-length
set_ylim	list to set ylim for each of the 'plot' arguments

Value

figure with length composition data and model fits if Report or LBSPR are specified

Author(s)

M.B. Rudd

merrillrudd/LIME documentation built on June 20, 2020, 2:58 p.m.