plot_spatial_ts: Visualize the spatial distribution per species and stanza...

In alketh/atlantistools: Process and Visualise Output from Atlantis Models

Description

Visualize the spatial distribution per species and stanza combination.

Usage

plot_spatial_ts(
  bio_spatial,
  bgm_as_df,
  vol,
  select_species = NULL,
  ncol = 7,
  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'.
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 NULL (default) all available species are plotted.
ncol	Number of columns in final plot. Default is 7.
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

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]])

alketh/atlantistools documentation built on Oct. 30, 2021, 5:46 a.m.