atlantistools (version 0.4.3)

plot_spatial_box: Visualize the spatial distribution per species and stanza combination.

Description

Visualize the spatial distribution per species and stanza combination.

Usage

plot_spatial_box(bio_spatial, bgm_as_df, select_species = NULL,
  timesteps = 2, polygon_overview = 0.2)

Arguments

bio_spatial

Biomass per group and stanza in tonnes for each timestep, layer and polygon. This dataframe should be generated with calculate_biomass_spatial. The columns of the dataframe have to be 'species', 'species_stanza', 'polygon', 'layer', 'time' and 'atoutput'. Column 'atoutput' is the biomass in tonnes. Please use combine_ages to transform an age-based dataframe to a stanza based dataframe.

bgm_as_df

*.bgm file converted to a dataframe. Please use convert_bgm to convert your bgm-file to a dataframe with columns 'lat', 'long', 'inside_lat', 'inside_long' and 'polygon'.

select_species

Character vector listing the species to plot. If no species are selected NULL (default) all available species are plotted.

timesteps

Integer giving the number of timesteps to visualize. Default is 2. By default the start and end of the simulation is shown. In case timesteps > 2 equally spaced timesteps are added.

polygon_overview

numeric value between 0 and 1 indicating the size used to plot the polygon overview in the upper right corner of the plot. Default is 0.2.

Value

grob of 3 ggplot2 plots.

Examples

# NOT RUN {
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")

bgm_as_df <- convert_bgm(file.path(d, "VMPA_setas.bgm"))

# Spatial distribution in Atlantis is based on adu- and juv stanzas.
# Therefore, we need to aggregate the age-based biomass to
# stanzas with \code{\link{combine_ages}}.
bio_spatial <- combine_ages(ref_bio_sp, grp_col = "species", agemat = ref_agemat)

# }
# NOT RUN {
# Apply \code{\link{plot_spatial_box}}
grobs <- plot_spatial_box(bio_spatial, bgm_as_df, timesteps = 3)
gridExtra::grid.arrange(grobs[[1]])
gridExtra::grid.arrange(grobs[[9]])

# use names() to select specific plots
names(grobs)
# }
# NOT RUN {
# Plot specific species
grobs <- plot_spatial_box(bio_spatial, bgm_as_df,
                          select_species = "Shallow piscivorous fish", timesteps = 3)
gridExtra::grid.arrange(grobs[[1]])
# }