plot.pacea_zooplankton: Plot the one of the zooplankton anomalies.

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

Plot the one of the zooplankton anomalies.

Description

Temporal plot for one of the columns of a pacea zooplankton ('pacea_zooplankton') object, as defined in '?zooplankton_sog'. The specified 'species_group' gets passed onto 'plot.pacea_index()' as the anomaly to be plotted, and yields a correctly automated y-axis label (that can be user-specified if desired). Other options specified here also get passed onto 'plot.pacea_index()' and 'plot()', such as for display style, adding in times of other events, etc. See examples and zooplankton vignette, as well as the climatic and oceanographic indices vignette.

Usage

## S3 method for class 'pacea_zooplankton'
plot(
  obj,
  species_group = "total_biomass",
  xlab = "Year",
  ylab = NULL,
  lwd = 15,
  mgp_val = c(2.5, 1, 0),
  ...
)

Arguments

obj	a 'pacea_zooplankton' object, which is a tibble with columns giving 'year', 'num_samples' (number of samples), 'volume_filtered', 'total_biomass', and then 24 species groups of zooplankton (see '?zooplankton_sog', currently the only zooplankton data in pacea).
species_group	which column of 'obj' to plot, either 'total_biomass' (the default) or one of the 24 species groups described in '?zooplankton_sog'.
xlab	x-axis label, defaults to 'Year'
ylab	y-axis label, if 'NULL' (the default) then automatically selects the 'axis_name' corresponding to 'species_group' in the object 'zooplankton_sog_axis_names'. User can also just provide their own label.
lwd	line thickness to plot the anomalies, defaults to 15 since these are annual; likely needs tweaking depending on the size of the final figure.
mgp_val	mgp value for 'par()', first value is slightly less than the default to fit the superscripts in okay. Resets to existing value after plotting.
...	optional arguments passed onto 'plot.pacea_index()' and 'plot()'. Note that the x-axis is constructed using a lubridate 'date' object, so 'xlim' needs to be a 'date' object (see 'plot.pacea_index()' example).

Value

plot of the time series to the current device (returns nothing)

Author(s)

Andrew Edwards

Examples

## Not run: 
# Also see zooplankton vignette
plot(zooplankton_sog)    # Default is total_biomass, calls plot.pacea_zooplankton()
plot(zooplankton_sog, species_group = "cladocera")  # y-axis name is automated

## End(Not run)

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