Description Usage Arguments Value Examples
View source: R/plot-spatial-ts.R
Visualize the spatial distribution per species and stanza combination.
1 2 | plot_spatial_ts(bio_spatial, bgm_as_df, vol, select_species = NULL,
ncol = 7, polygon_overview = 0.2)
|
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 |
vol |
Volume per polygon and timestep. See model-preprocess.Rmd for details. |
select_species |
Character vector listing the species to plot. If no species are selected
|
ncol |
Number of columns in final plot. 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 | d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
bgm_as_df <- convert_bgm(file.path(d, "VMPA_setas.bgm"))
vol <- agg_data(ref_vol, groups = c("time", "polygon"), fun = sum, out = "volume")
# 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)
# Apply \code{\link{plot_spatial_ts}}
grobs <- plot_spatial_ts(bio_spatial, bgm_as_df, vol)
gridExtra::grid.arrange(grobs[[1]])
gridExtra::grid.arrange(grobs[[7]])
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