EchogramCurtain: Create echogram curtain plot from interval-layer data.

In dmwarn/EchoNet2FishnO: Estimate Fish Abundance from Acoustic Echoes and Net Catch

Description

Create echogram curtain plot from interval-layer data.

Usage

EchogramCurtain(
  the.dir,
  d.units,
  spgrp = c("X106.L0", "X106.L100", "X109.L0", "X109.L90", "X204.L0", "X204.L120"),
  QuantileFilter = FALSE,
  Quantile = 0.99
)

Arguments

the.dir	Character, the directory containing the data that will be used to make the plots.
d.units	Character, either "nph" or "gph".
spgrp	Character vector listing the species groups that should be plotted. Must be entered in the form "X106.L100", for example, for alewife (species code = 106) that are >= 100 mm long. These names are in the form generated by the estimateLake() function.
QuantileFilter	Logical scalar indicating whether or not the user wants to plot all values as they are or if the user wants to assign the values above a particulare percentile the value of the chosen percentile. The intent of this parameter is to allow one to choose to use the plots to find acoustic cells that might have unreasonable density and need to be checked or, instead to plot distribution after confirming that any really high values appear to be real. This allows one to reduce the influence of a few very high values on distribution patterns.
Percentile	Numeric scalar. The data values that are equal to or greater than this percentile will be assigned the value of this percentile.

Details

This function is intended to build on the plots in exploreACMT(). The plots provide a view of the data that is not possible when looking at just Sv or TS/sigma, as these two can interact in such a way as to generate fish density that might be higher than expected given the appearance of the Sv data.One key use for this sort of plot is to look for analysis cells that have density that is higher than expected because of low numbers of targets.

Value

This function generates curtain plots for each species group listed and every acoustic transect. The transects are facets, the vertical axis is depth, and the horizontal axis is transect interval number.

dmwarn/EchoNet2FishnO documentation built on March 4, 2021, 12:49 a.m.