plot: Plot 'sspm' objects

In pedersen-fisheries-lab/spaspm: Spatial Surplus Production Model Framework for Northern Shrimp Populations

Plot sspm objects

Description

Plot methods for a range of sspm objects.

Usage

## S4 method for signature 'sspm_boundary,missing'
plot(x, y, ...)

## S4 method for signature 'sspm_dataset,missing'
plot(
  x,
  y,
  ...,
  var = NULL,
  point_size = 1,
  line_size = 1,
  use_sf = FALSE,
  interval = FALSE,
  page = "first",
  nrow = 2,
  ncol = 2,
  log = FALSE,
  scales = "fixed",
  show_PI = TRUE,
  show_CI = TRUE
)

## S4 method for signature 'sspm_fit,missing'
plot(
  x,
  y,
  ...,
  point_size = 1,
  line_size = 1,
  train_test = FALSE,
  biomass = NULL,
  next_ts = FALSE,
  smoothed_biomass = FALSE,
  aggregate = FALSE,
  interval = FALSE,
  biomass_origin = NULL,
  use_sf = FALSE,
  page = "first",
  nrow = 2,
  ncol = 2,
  log = FALSE,
  scales = "fixed",
  show_PI = TRUE,
  show_CI = TRUE
)

Arguments

x	[sspm_...] An object from this package.
y	NOT USED (from generic).
...	NOT USED (from generic).
var	[character] (For sspm_dataset) Variable to plot.
point_size	[numeric] Passed on to ggplot size parameter for point size.
line_size	[numeric] Passed on to ggplot size parameter for line size.
use_sf	[logical] Whether to produce a spatial plot.
interval	[logical] (For sspm_fit & sspm_dataset) Whether to plot CI and PI intervals.
page	The page to draw
nrow	Number of rows per page
ncol	Number of columns per page
log	[logical] For productivity, whether to plot log productivity, (default to FALSE) for others, whether to plot on a log scale (default to TRUE).
scales	Are scales shared across all facets (the default, "fixed"), or do they vary across rows ("free_x"), columns ("free_y"), or both rows and columns ("free")?
show_PI	[character] Whether to show the PIs.
show_CI	[character] Whether to show the CIs.
train_test	[logical] (For sspm_fit) Whether to plot a train/test pair plot.
biomass	[character] (For sspm_fit) The biomass variable for predictions.
next_ts	[logical] (For sspm_fit) Whether to plot a predictions for next timestep.
smoothed_biomass	[logical] (For sspm_fit) Whether to plot a the smoothed biomass used for predictions.
aggregate	[logical] (For sspm_fit) For biomass predictions only, whether to aggregate the data to the boundary level. Default to FALSE.
biomass_origin	[character] Biomass variable to plot (from original dataset, optionnal).

Value

A ggplot2 plot object.

Examples

## Not run: 
# To plot a boundary object and visualize patches/points
plot(sspm_boundary)
# To plot a dataset variable
plot(biomass_smooth, var = "weight_per_km2", log = FALSE)
plot(biomass_smooth, var = "weight_per_km2", use_sf = TRUE)
# To plot a fitted model
# Test-train plot
plot(sspm_model_fit, train_test = TRUE, scales = "free")
# Timeseries plot
plot(sspm_model_fit, log = T, scales = 'free')
plot(sspm_model_fit, log = T, use_sf = TRUE)
plot(sspm_model_fit, biomass = "weight_per_km2_borealis",  scales = "free")
plot(sspm_model_fit, biomass = "weight_per_km2_borealis", use_sf = TRUE)
plot(sspm_model_fit, biomass = "weight_per_km2_borealis",
     next_ts = TRUE, aggregate = TRUE, scales = "free", interval = T)

## End(Not run)

pedersen-fisheries-lab/spaspm documentation built on Feb. 16, 2025, 7:39 p.m.