plotPELFOSS: Plot the output from biomass2tsb() or runPelfoss().

In Sea2Data/pelfoss: Simulate acosutic-trawl surveys and produce survey estimated using Rstox

Description

Plot the output from biomass2tsb() or runPelfoss().

Usage

plotPelfoss(
  x,
  biomassthr = 1,
  NASCthr = 0.001,
  NASCexp = 2,
  NASCmax_size = 2,
  biomCol = "blue",
  biomAlpha = 0.1,
  biomShape = 20,
  biomSize = 2,
  biomThr = 1,
  trawlSize = 2,
  stratumcol = NULL,
  plot = c("biom", "nasc", "trawl", "super"),
  daysOfSurvey = NULL,
  timerange = NULL,
  show = TRUE,
  ...
)

getTSB(x, unit = "mt", digits = 4)

getAllTSB(dir, run = "Run1", outfile = NULL, copy = TRUE)

plotPelfossAll(
  dir,
  run = "Run1",
  NASCthr = 0.001,
  NASCexp = 2,
  NASCmax_size = 2,
  biomassthr = 1,
  biomCol = "blue",
  biomAlpha = 0.1,
  biomShape = 20,
  biomSize = 2,
  biomThr = 1,
  trawlSize = 2,
  stratumcol = NULL,
  plot = c("biom", "nasc", "trawl", "super"),
  daysOfSurvey = NULL,
  timerange = NULL,
  format = "png",
  show = TRUE,
  ...
)

Arguments

x	The output from biomass2tsb (containing object named report, totalBiomass, superind, transects, biomass).
NASCthr	A value below which NASC values are omitted when plotted as black dots with size proportional to NASC^NASCexp.
NASCmax_size	Maximum size of the NASC dots.
biomCol	The color of the biomass field.
trawlSize	The size to use for the red asteriks representing trawl stations.
logColscale	Logical: If TRUE, use 10 * log10 for the plotted biomass layers.
firstcol	The color to use for the first biomass level (the default, NA, omits plotting the first layer, which may include 0-values).
biomassAlpha	Transparency of the biomass layers.

Sea2Data/pelfoss documentation built on Dec. 7, 2020, 12:31 a.m.