Reference

Tutorials
tutorial()	Open tutorials
New plotting functions
plotCalibration()	Summary function bundling helpful plots during calibration.
plotDiet2()	Function showing the diet proportion of predators
plotFeedingLevel2()	Plot ....
plotFmsy()	A function plotting the fisheries effort versus yield of a species.
plotGrowthCurves2()	Plot growth curves giving weight as a function of age
plotPredObsYield()	A function that plots the predicted yield versus observed yield.
plotSummary()	Summary plot displaying 8 differents plots useful to assess the state of a mizerSim object.
Other functions
getError()	Compares modelled and empirical output
getDietComp()	Get the diet composition
getBiomassFrame2()	Plot ....
Data
nsParams	Species specific parameters for the North Sea
interNS	Interaction matrix for the North Sea
catchAvg	averaged catch in the North Sea 2014 - 2019
Fmat	ICES fisheries mortality
FmatWeightedInterpolated	ICES fisheries mortality processed On the ICES database, some species have multiple entries and some have none. Fisheries mortality is weighted by the species abundance to be able to take into account multiple database entries Gurnard data is extrapolated from whiting (same gear and physiology) ....
HTM1_sim	HTM1 final simulation saved (sim_guessed) Used at the beginning of HTM2
HTM2_Fmsy1	HTM2 Fmsy plot file (step 2 - Fmsy1 plot_dat) plotFmsy() runs slowly so saving the result for fast kniting
HTM2_Fmsy2	HTM2 Fmsy plot file (step 2 - Fmsy2 plot_dat) plotFmsy() runs slowly so saving the result for fast knitting
HTM2_optimParallel_Rmax1	HTM2 optim parallel output (step 1 - optim_result) The Rmax vector output of optim parallel is saved for fast knitting ....
HTM2_optimParallel_Rmax2	HTM2 optim parallel output (step 2 - optim_loop) The Rmax vector output of optim parallel is saved for fast knitting ....
HTM2_sim_optim1	HTM2 saved simulation (step 1 - results) Used as checkpoint/kick start if .rmd are not run from the beginning ....
HTM2_sim_optim2	HTM2 saved simulation (step 2 - tweaked erepro) Used as checkpoint/kick start if .rmd are not run from the beginning ....
HTM2_sim_optim3	HTM2 saved simulation (step 2 - sim_loop) Used as checkpoint/kick start if .rmd are not run from the beginning ....
Shiny apps
shiny_erepro()	shiny app to tweak erepro
shiny_fmsy()	shiny app to tweak erepro per species and see the effects on Fmsy
shiny_gamma()	shiny app to tweak gamma per species and see the effects on growth
shiny_kappa()	shiny app to tweak gamma per species and see the effects on growth