PlotPresenceAbsence.fn: Plot showing presence and absence per haul by depth,...

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

Plot showing presence and absence per haul by depth, latitude, or sex bin

Description

This function was deprecated in nwfsc version 2.1. Please use plot_proportion() instead.

Usage

PlotPresenceAbsence.fn(
  data,
  dim = c("depth", "lat", "sex"),
  dir = NULL,
  dopng = lifecycle::deprecated(),
  plot_type = c("proportion", "total"),
  depth_min = 50,
  depth_max = NULL,
  depth_bin_width = 25,
  lat_min = 32,
  lat_max = 49,
  lat_bin_width = 1,
  add_range_to_main = TRUE,
  xlab = NULL
)

Arguments

data	Data frame containing data per haul created by pull_catch() or biological data created by pull_bio() where the dim = "sex" must be true for the latter.
dim	Dimension of interest, either "depth", "lat", or "sex".
dir	Directory where output will be saved. The directory where the file should be saved. If dir = NULL no output will be saved.
dopng	Deprecated with nwfscSurvey 2.1 because providing a non-NULL value to dir can serve the same purpose as dopng = TRUE without the potential for errors when dopng = TRUE and dir = NULL. Thus, users no longer have to specify dopng to save the plot as a png.
plot_type	Two options area available "proportion" or "total" where the default, "proportion", plot the proportion by depth/latitude with equal bar widths and the "total" option plot the numbers by depth/latitude were the bar widths in a production of sampling by depth/latitude.
depth_min	Minimum depth (in meters).
depth_max	Maximum depth (in meters). A NULL value will cause the function to automatically set depth_max to the multiple of depth_bin_width beyond the 99.9 percentile of the observations.
depth_bin_width	Width of each depth bin (in meters).
lat_min	Minimum latitute (in decimal degrees).
lat_max	Maximum latitute (in decimal degrees).
lat_bin_width	Width of each latitude bin (in decimal degrees).
add_range_to_main	Add the range of latitude or depth by which the data are filtered.
xlab	Label for x-axis. A NULL value will cause the function to choose either "Depth (m)" or "Latitude (°N)".

Author(s)

Ian G. Taylor and Chantel Wetzel

Examples

## Not run: 
# load WCGBTS data data
data.WCGBTS.ling <- nwfscSurvey::PullCatch.fn(
  Name = "lingcod",
  SurveyName = "NWFSC.Combo"
)
bio.WCGBTS.ling <- nwfscSurvey::PullBio.fn(
  Name = "lingcod",
  SurveyName = "NWFSC.Combo"
)
PlotPresenceAbsence.fn(data = data.WCGBTS.ling, dim = "lat")
PlotPresenceAbsence.fn(data = data.WCGBTS.ling, dim = "depth")
PlotPresenceAbsence.fn(data = bio.WCGBTS.ling, dim = "sex")

# Plot with package data
PlotPresenceAbsence.fn(catch_nwfsc_combo)

## End(Not run)

nwfsc-assess/nwfscSurvey documentation built on Nov. 12, 2024, 8:14 p.m.