SSplotRecdevs {r4ss}

Plot recruitment deviations

Description

Plot recruitment deviations and associated quantities including derived measures related to bias adjustment.

Usage

SSplotRecdevs(
  replist,
  subplots = 1:3,
  plot = TRUE,
  print = FALSE,
  add = FALSE,
  uncertainty = TRUE,
  minyr = -Inf,
  maxyr = Inf,
  forecastplot = FALSE,
  col1 = "black",
  col2 = "blue",
  col3 = "green3",
  col4 = "red",
  legendloc = "topleft",
  labels = c("Year", "Asymptotic standard error estimate", "Log recruitment deviation",
    "Bias adjustment fraction, 1 - stddev^2 / sigmaR^2"),
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = "default",
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

subplots

vector controlling which subplots to create

plot

plot to active plot device?

print

print to PNG files?

add

add to existing plot (not yet implemented)

uncertainty

include plots showing uncertainty?

minyr

optional input for minimum year to show in plots

maxyr

optional input for maximum year to show in plots

forecastplot

include points from forecast years?

col1

first color used

col2

second color used

col3

third color used

col4

fourth color used

legendloc

location of legend. see ?legend for more info

labels

vector of labels for plots (titles and axis labels)

pwidth

width of plot

pheight

height of plot

punits

units for PNG file

res

Resolution of plots printed to files. The default is res = 300.

ptsize

point size for PNG file

cex.main

character expansion for plot titles

plotdir

directory where PNG files will be written. by default it will be the directory where the model was run.

verbose

report progress to R GUI?

Author(s)

Ian Taylor, Ian Stewart

See Also

SS_plots(), SS_fitbiasramp()