plot.pacea_index: Plot a pacea climatic or oceanographic index

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

Plot a pacea climatic or oceanographic index

Description

Temporal plot for a pacea index ('pacea_index') object, with options for display style, and adding in times of other events (to ask questions such as 'does this rare event coincide with El Niño?'). See examples and vignette.

Usage

## S3 method for class 'pacea_index'
plot(
  obj,
  value = "anomaly",
  xlab = "Date",
  ylab = attr(obj, "axis_name"),
  smooth_over_year = FALSE,
  type = "l",
  style = "red_blue_bar",
  y_tick_by = 0.25,
  y_tick_start = NULL,
  y_tick_end = NULL,
  y_tick_max_number = 50,
  x_tick_extra_years = 200,
  start_decade_ticks = lubridate::ymd("1800-01-01", truncated = 2),
  event_years = NULL,
  event_lub = NULL,
  event_pch = 20,
  event_cex = 3,
  event_col = "grey",
  ...
)

Arguments

obj	a 'pacea_index' object, which is a time series.
value	which column of 'obj' to plot
xlab	x-axis label
ylab	y-axis label, the default is an attribute of the 'pacea_index' object.
smooth_over_year	logical to smooth monthly values over each calendar year (as per Tetjana Ross' plots, see '?oni' for reference). Note that the corresponding 'date' is for 1st January of each year.
type	usual argument for 'plot()'
style	what style of plot: "red_blue_bar": for red bars above 0 and blue bars below 0, but may need to manually adjust the thickness 'lwd' for width of bars to look good for your specific plot "red_blue": for a line with filled in colouring for red above 0 and blue below 0 "goa": TODO (not implemented yet) for Gulf of Alaska Ecosystem Report style plots "plain": just a plain line
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)'.
y_tick_start	where to start y-axis tickmarks, set automatically if not specified (may need to occasionally specify)
y_tick_end	where to end y-axis tickmars, as for 'y_tick_start'
y_tick_max_number	maximum number of y tickmarks.
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)
event_years	years of the event occurring (e.g. sighting of a rare shark) to add to the plot (sensible for rare-ish events, to quickly see if they coincide with the values of the index); points will be shown for 1st July (Oh Canada!) of the given year, and at the value of the index to make it easy to quickly spot any correlation. Assumes 'event_years' values are unique. For more control instead use 'event_lub'.
event_lub	dates of events as lubridate objects (only 'event_years' or 'event_lub' can be specified). Assumes 'event_lub' values are unique.
event_pch	'pch' for events
event_cex	'cex' for events
event_col	'col' for events
...	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 to the current device (returns nothing)

Author(s)

Andrew Edwards

Examples

## Not run: 
plot(oni)
plot(oni,
     xlim = c(lubridate::dmy(01011950),
     lubridate::dmy(01012040))) # to expand x-axis
plot(npi_monthly,
     value = "value")

# The overlaying of events idea was inspired from a lunchtime conversation regarding a
# rare sighting of a Bluntnose Sixgill Shark by divers in Port Alberni, that garnered
# [media attention](https://www.timescolonist.com/local-news/divers-encounter-deep-water-shark-in-alberni-inlet-7102038).
# A lunchtime conversation with Maxime Veilleux led to the question of whether catches
# f these sharks in BC waters are related to El Niño. Specifically, as the data from
# the International Pacific Halibut Commission annual longline survey are
# readily available in the [gfiphc](https://github.com/pbs-assess/gfiphc)
# package, we looked at years which caught a Bluntnose Sixgill Shark (at a
# standard station, outside of the Strait of Georgia).

library(gfiphc)
sp_set_counts <- iphc_get_calc_plot_full("bluntnose sixgill shark")   # Need
  access to DFO Groundfish database
bluntnose_caught_years <- unique(filter(sp_set_counts$set_counts, N_it > 0, standard == "Y")$year)
plot(oni,
     event_years = bluntnose_caught_years,
     xlim = c(lubridate::dmy(01011995), lubridate::dmy(01012024)),
     lwd = 2)
# This is not meant to be a definitive analysis, but a demonstration of the plotting options in pacea.

## End(Not run)

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