inst/doc/model-comparison.R

In atlantistools: Process and Visualise Output from Atlantis Models

## ------------------------------------------------------------------------
library("atlantistools")
library("ggplot2")
library("gridExtra")

gen_labels <- list(x = "Time [years]", y = "Biomass [t]")

# You should be able to build the vignette either by clicking on "Knit PDF" in RStudio or with
# rmarkdown::render("model-comparison.Rmd")

## ------------------------------------------------------------------------
result <- preprocess

dummy_setas <- function(list, mult) {
  for (i in seq_along(list)) {
    if (is.data.frame(list[[i]])) {
          mult <- rep_len(mult, length.out = nrow(list[[i]]))
          list[[i]][, ncol(list[[i]])] <- list[[i]][, ncol(list[[i]])] * mult
    }
  }
  return(list)
}

store_data <- list(result, 
                   dummy_setas(result, mult = c(1, 1.2)),
                   dummy_setas(result, mult = c(2, 2.2)))

result <- combine_runs(outs = store_data, runs = c("run1", "run2", "run3"))

## ---- fig.width = 14, fig.height = 8-------------------------------------
sum_bio <- agg_data(result$biomass, groups = c("time", "run"), fun = sum)
plot <- plot_line(sum_bio, wrap = NULL, col = "run")
update_labels(plot, gen_labels)

## ------------------------------------------------------------------------
plot_line(result$biomass, col = "run", ncol = 4) %>% update_labels(gen_labels)

## ------------------------------------------------------------------------
df <- convert_relative_initial(result$biomass)
plot <- plot_line(df, col = "run", ncol = 4)
plot <- plot_add_box(plot)
update_labels(plot, labels = list(x = "Time [year]", y = expression(Biomass/Biomass[initial])))

## ---- fig.width = 30, fig.height = 12------------------------------------
plot <- plot_line(result$physics, wrap = NULL, col = "run")
custom_grid(plot, grid_x = "polygon", grid_y = "variable")