## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>" ,fig.width = 8, fig.height = 8,fig.align="center")
library(LeMANS)
## ----run1, echo=TRUE-----------------------------------------------------
results <- key_run(Ffull=0.4, nYrs=50, rochet_GB_modelSetup, rochet_GB_parameterValues, rochet_GB_initialValues, rochet_GB_foodweb, rochet_GB_species)
## ----run2, echo=TRUE-----------------------------------------------------
str(results)
## ----plot_c, echo = TRUE-------------------------------------------------
plot_key_run(results$catch/1E6, ylabel = "Catch (millions individuals)", speciesNames=rochet_GB_species, scales="free")
## ----plot_n, echo = TRUE-------------------------------------------------
plot_key_run(results$N/1E6, ylabel = "Abundance (millions individuals)", is.aggregated=T, speciesNames=rochet_GB_species, scales="free")
## ----plot_m2, echo = TRUE------------------------------------------------
plot_key_run(results$M2, ylabel = "Predation mortality", speciesNames=rochet_GB_species, scales="fixed")
## ----plot_suit, echo = TRUE----------------------------------------------
plot_key_run(results$suitability, ylabel = "Suitability", speciesNames = rochet_GB_species, scales="free",speciesSuitability = "Forage fish",predOrPrey = "prey")
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