Generate Key Projection Quantities and Table Plot
get_key_quants.Rd
Calculates biological and fishery reference points and performs population projections to estimate terminal spawning biomass, catch advice, and reference point values by model and region. Also returns a formatted table plot of key quantities.
Arguments
- data
A list of model input data objects, one for each model (i.e., a list of SPoRC-formatted data lists). Each element should contain information on regions, years, ages, fleets, and biological inputs (e.g., weight-at-age, maturity, mortality).
- rep
A list of model output objects, one for each model (i.e., a list of SPoRC-formatted report lists). Each element must include recruitment, selectivity, mortality, and numbers-at-age.
- reference_points_opt
A named list specifying options for reference point calculations. See
Get_Reference_Points
for more details. Must include:- SPR_x
Spawning potential ratio (e.g., 0.4) for calculating F reference points. May be
NULL
if usingbh_rec
.- t_spwn
Fraction of year when spawning occurs (e.g., 0.5).
- sex_ratio_f
Proportion of recruits that are female.
- calc_rec_st_yr
Start year for averaging recruitment.
- rec_age
Recruitment age.
- type
Reference point calculation method (e.g., "multi_region").
- what
Type of output requested from the reference point function.
- proj_model_opt
A named list of projection settings. See
Do_Population_Projection
for details. Must include:- n_proj_yrs
Number of years to project forward.
- HCR_function
Harvest control rule function to use.
- recruitment_opt
Recruitment assumption (e.g., "mean_rec", "bh_rec", "inv_gauss").
- fmort_opt
Fishing mortality assumption (e.g., "input", "HCR").
- n_avg_yrs
Number of years to average over for projection inputs.
- model_names
A character vector of model identifiers (e.g., c("Base", "Alt1", "Alt2")), one for each element in
data
andrep
.
Value
A list with two elements:
[[1]]
A data.frame of key quantities by model and region, including terminal SSB, catch advice, and reference points.
[[2]]
A cowplot table plot (ggdraw object) of the same key quantities.
Details
This function checks input list completeness, calculates reference points using Get_Reference_Points()
, performs population projections with Do_Population_Projection()
, and assembles both tabular and visual summaries.
If recruitment_opt
is set to "inv_gauss", a warning is issued since only a single simulation will be run. This is typically not appropriate and an alternative assumption is recommended.
Examples
if (FALSE) { # \dontrun{
reference_points_opt <- list(SPR_x = 0.4,
t_spwn = 0,
sex_ratio_f = 0.5,
calc_rec_st_yr = 20,
rec_age = 2,
type = "multi_region",
what = "global_SPR")
proj_model_opt <- list(
n_proj_yrs = 2,
n_avg_yrs = 1,
HCR_function = function(x, frp, brp, alpha = 0.05) {
stock_status <- x / brp
if (stock_status >= 1) f <- frp
if (stock_status > alpha && stock_status < 1) f <- frp * (stock_status - alpha) / (1 - alpha)
if (stock_status < alpha) f <- 0
return(f)
},
recruitment_opt = "mean_rec",
fmort_opt = "HCR"
)
out <- get_key_quants(list(mlt_rg_sable_data),
list(mlt_rg_sable_rep),
reference_points_opt,
proj_model_opt,
"Model 1")
out[[1]] # key quantities data.frame
out[[2]] # table plot
} # }