Description Usage Arguments Value Examples
View source: R/plot-spatial-box.R
Visualize the spatial distribution per species and stanza combination.
1 2 | plot_spatial_box(bio_spatial, bgm_as_df, select_species = NULL,
timesteps = 2, polygon_overview = 0.2)
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bio_spatial |
Biomass per group and stanza in tonnes for each timestep,
layer and polygon. This dataframe should be generated with
|
bgm_as_df |
*.bgm file converted to a dataframe. Please use |
select_species |
Character vector listing the species to plot. If no species are selected
|
timesteps |
Integer giving the number of timesteps to visualize. Default is |
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 |
grob of 3 ggplot2 plots.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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)
## End(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]])
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