Plot IAMSE diagnostic / uncertainty quantities
plotiamse.quant.Rd`plotiamse.quant()` visualises selected diagnostic or uncertainty-related quantities computed from an IAMSE management strategy evaluation. Typical examples include the variability of biomass and fishing mortality relative to reference points, or the variability of catch over time.
Usage
plotiamse.quant(
dat,
set,
resMSE,
hcrs = NULL,
quants = c("bpbmsy.sd", "fmfmsy.sd", "cp.sd"),
hline = NULL,
plot.legend = TRUE
)Arguments
- dat
Data object as returned by [check.dat()], containing life-history and reference-point information used in the MSE.
- set
Settings list as returned by [check.set()] and modified for the MSE run (e.g. containing `nysim`, `nrep`, and `hcr`).
- resMSE
Result object returned by [run.mse()], containing simulated time series for each HCR and replicate.
- hcrs
Optional character vector or numeric indices specifying which HCRs to include in the plot. If `NULL` (default), all HCRs present in `set$hcr` (and `resMSE`) are used.
- quants
Character vector specifying the names of the quantities to plot. Defaults to `c("bpbmsy.sd", "fmfmsy.sd", "cp.sd")`, which typically correspond to the standard deviation of biomass relative to B\(_{MSY}\), fishing mortality relative to F\(_{MSY}\), and catch performance (or a related quantity). The available names depend on how summary statistics were computed upstream.
- hline
Optional numeric value or vector giving horizontal reference line(s) to be added to the plot (e.g. a threshold or target level). If `NULL` (default), no reference lines are drawn.
- plot.legend
Logical; if `TRUE` (default), add a legend identifying the plotted HCRs.