plot.pacea_harbour_seals: Plot the Pacific Harbour Seals abundance estimates

In pbs-assess/PACea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management

Plot the Pacific Harbour Seals abundance estimates

Description

Default is to plot all seven regions plus the coastwide estimate, to mostly replicate Figure 3 of DFO (2022; see '?harbour_seals') in a 'ggplot' style. If a single region is indicated then a time series plot is shown, in the same style as plots of object class 'pacea_biomass' (such as 'hake_biomass'). Note that the values are means and confidence intervals (not medians and confidence intervals like other objects); see '?harbour_seals'.

Usage

## S3 method for class 'pacea_harbour_seals'
plot(
  obj,
  region = NULL,
  value = "mean",
  include_coastwide = TRUE,
  xlab = "Year",
  ylab = attr(obj, "axis_name"),
  y_tick_by = 1000,
  x_tick_extra_years = 20,
  start_decade_ticks = lubridate::ymd("1800-01-01", truncated = 2),
  y_max = NULL,
  uncertainty_shade_col = rgb(0, 0, 1, 0.1),
  uncertainty_line_col = "blue",
  uncertainty_line_lty = 3,
  median_type = "l",
  median_pch = 16,
  median_line_col = "black",
  median_line_lty = 1,
  median_line_lwd = 2,
  ...
)

Arguments

obj	'pacea_harbour_seals', as this is of class 'pacea_harbour_seals' and the plotting is tailored for this data set.
region	which region to plot for a single plot; must be one of SOG, WCVI, QCS, DP, CMC, NMC, HG, or coastwide. If 'NULL' (the default) then do a panel plot showing all seven regions.
value	the column to plot as a solid line, in this case always the default 'mean'
include_coastwide	logical, whether to include the coastwide population in the eight panel plot (keep 'region = NULL').
xlab	x-axis label
ylab	y-axis label, the default is an attribute of the 'pacea_index' object.
y_tick_by	increment for y-axis ticks; gets overwritten in 'add_tickmarks()' if this yields more than 'y_tick_max_number' tickmarks. If using [plot.pacea_biomass()] the default of 1 gets automatically changed to 0.25 for 'plot(hake_biomass)'.
x_tick_extra_years	number of extra years to expand around the range of data for which to add annual tick marks (does not expand the axis); in hindsight could have simplified this in 'add_tickmarks()', but just made the default big here.
start_decade_ticks	where to start tickmarks for decades (defaults to 1800 as hard to automate)
y_max	maximum y value for certain types of plot (use this if you get an error when specifying 'ylim')
uncertainty_shade_col	colour of shading for uncertainty
uncertainty_line_col	colour of line for uncertainty
uncertainty_line_lty	lty of line for uncertainty
median_type	'type' of plot ("o", "p", etc.) for means (note: we have used median elsewhere so kept with that name, but the seal estimates are means not medians)
median_pch	pch for median
median_line_col	col for median
median_line_lty	lty for median
median_line_lwd	lwd for median
...	optional arguments passed onto 'plot()'. Note that the x-axis is constructed using a lubridate 'date' object, so 'xlim' needs to be a 'date' object (see example).

Value

plot of the time series as median with bars showing uncertainty (if 'low' and 'high' are columns of 'obj) to the current device; returns nothing.

Author(s)

Andrew Edwards

Examples

## Not run: 
plot(harbour_seals)
plot(harbour_seals, region = "SOG")
plot(harbour_seals, include_coastwide = FALSE)

## End(Not run)

pbs-assess/PACea documentation built on April 17, 2025, 11:36 p.m.