plot.pacea_biomass: Plot a pacea biomass time series object (currently assumes...

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

Plot a pacea biomass time series object (currently assumes annual values)

Description

Temporal plot for a pacea biomass time series (of class 'pacea_biomass') object. The 'style' option here (unlike for 'plot.pacea_index()' defaults to 'no_uncertainty' and gets changed to 'uncertainty' if 'low' and 'high' are columns of 'obj'.

Usage

## S3 method for class 'pacea_biomass'
plot(
  obj,
  value = "median",
  xlab = "Year",
  ylab = attr(obj, "axis_name"),
  y_tick_by = 1,
  x_tick_extra_years = 20,
  start_decade_ticks = lubridate::ymd("1800-01-01", truncated = 2),
  style = "no_uncertainty",
  y_max = NULL,
  y_tick_max_number = 50,
  uncertainty_shade_col = rgb(0, 0, 1, 0.1),
  uncertainty_line_col = "blue",
  uncertainty_line_lty = 3,
  median_type = "o",
  median_pch = 16,
  median_line_col = "black",
  median_line_lty = 1,
  median_line_lwd = 2,
  ...
)

Arguments

obj	a 'pacea_biomass' object, which is a time series. Function will run on other objects (not give an error) but is not tested on those.
value	the column to plot if no uncertainties, or what to plot as dots if showing uncertainties (likely always 'median')
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)
style	'no_uncertainty' for plain time series without uncertainty, gets overridden to have uncertainty bars if 'low' and 'high' are columns of 'obj'
y_max	maximum y value for certain types of plot (use this if you get an error when specifying 'ylim')
y_tick_max_number	maximum number of y tickmarks.
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 medians
median_pch	pch for median
median_line_col	col for median
median_line_lty	lty for median
median_line_lwd	lwd for median
...	further options passed onto 'plot.default()'

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(hake_biomass)
plot(hake_biomass,
     xlim = c(lubridate::dmy(01011950),
              lubridate::dmy(01012040))) # to expand x-axis

## End(Not run)

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