plot_line: Function to plot time series of atlantis ncdf output.

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

Description

Function to plot time series of atlantis ncdf output.

Usage

plot_line(
  data,
  x = "time",
  y = "atoutput",
  wrap = "species",
  col = NULL,
  ncol = 7,
  yexpand = FALSE,
  ylim = NULL
)

Arguments

data	Dataframe to be plotted.
x	x-variable. Default is 'time'.
y	y-variable. Default is 'atoutput'.
wrap	Wraping column. Default is 'species'
col	Column to use as colour. Default is NULL.
ncol	Number of columns in multipanel plot. Default is 7.
yexpand	Expands the y axis so it always includes 0. Default is FALSE.
ylim	Numeric vector. lower and upper limits of yaxis, eg c(0,1)

Value

ggplot2 object

See Also

Other plot functions: plot_bar(), plot_boxes(), plot_diet_bec_dev(), plot_diet(), plot_rec(), plot_species()

Examples

plot_line(preprocess$biomass)
plot_line(preprocess$biomass, col = "species")
plot_line(preprocess$biomass_age, col = "agecl")
plot_line(preprocess$biomass_age, wrap = "agecl", col = "species")

# The function can also be used to compare model outoput with observed data.
d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
ex_data <- read.csv(file.path(d, "setas-bench.csv"), stringsAsFactors = FALSE)
names(ex_data)[names(ex_data) == "biomass"] <- "atoutput"

data <- preprocess$biomass
data$model <- "atlantis"
comp <- rbind(ex_data, data, stringsAsFactors = FALSE)

# Show atlantis as first factor!
lev_ord <- c("atlantis", sort(unique(comp$model))[sort(unique(comp$model)) != "atlantis"])
comp$model <- factor(comp$model, levels = lev_ord)

# Create plot
plot_line(comp, col = "model")

## Not run: 
# Use \code{\link{convert_relative_initial}} and \code{\link{plot_add_box}}
# with \code{\link{plot_line}}. Use \code{\link{convert_relative_initial}} to
# generate a relative time series first.
df <- convert_relative_initial(preprocess$structn_age)

# Create the base plot with \code{\link{plot_line}}.
plot <- plot_line(df, col = "agecl")

# Add lower and upper range.
plot_add_box(plot)

# Create spatial timeseries plots in conjuction with \code{\link{custom_grid}}.
plot <- plot_line(preprocess$physics, wrap = NULL)
custom_grid(plot, grid_x = "polygon", grid_y = "variable")

plot <- plot_line(preprocess$flux, wrap = NULL, col = "variable")
custom_grid(plot, grid_x = "polygon", grid_y = "layer")

## End(Not run)

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