atlantistools (version 0.4.3)

plot_diet_bec_dev: Plot contribution of diet contents for each functional group.

Description

Visualize diet proportions form predator and prey perspective. The upper panel plot shows the predator perspective while the lower panel plot shows the prey perspective for a given group. Please note that this function uses the SpecPredMort.txt file to visualize feeding interactions and therefore is only an indication of the realized true diet within the model. Please use plot_diet instead.

Usage

plot_diet_bec_dev(data, species = NULL, wrap_col, combine_thresh = 15)

Arguments

data

SpecPredMort.txt read in with load_spec_mort.

species

Character string giving the acronyms of the species you aim to plot. Default is NULL resulting in all available species being ploted.

wrap_col

Character specifying the column of the dataframe to be used as multipanel plot. In case you aim to plot SpecMort.txt data use either "agecl" or "stanza".

combine_thresh

Number of different categories to plot. Lets say predator X has eaten 20 different prey items. If you only want to show the 3 most important prey items set combine_thresh to 3. As rule of thumb values < 10 are useful otherwise to many colors are used in the plots. Default is 15.

Value

List of ggplot2 objects.

See Also

Other plot functions: plot_bar, plot_boxes, plot_diet, plot_line, plot_rec, plot_species

Examples

# NOT RUN {
# Plot SpecMort.txt per ageclass.
plots <- plot_diet_bec_dev(preprocess_setas$diet_specmort, wrap_col = "agecl")
gridExtra::grid.arrange(plots[[1]])

# Only plot specific species
plots <- plot_diet_bec_dev(preprocess_setas$diet_specmort, species = "CEP", wrap_col = "agecl")
gridExtra::grid.arrange(plots[[1]])

# Plot SpecMort.txt per stanza First we need to transform the ageclasses to stanzas.
d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
diet_stanza <- combine_ages(dir = d,
                            data = preprocess_setas$diet_specmort,
                            col = "pred",
                            prm_biol = "VMPA_setas_biol_fishing_New.prm")
plots <- plot_diet_bec_dev(diet_stanza, wrap_col = "stanza")
gridExtra::grid.arrange(plots[[1]])
# }