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Plot recruitment deviations

Source: R/SSplotRecdevs.R
SSplotRecdevs.Rd

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. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.

labels

Vector of labels for plots (titles and axis labels).

pwidth

Default width of plots printed to files in units of punits.

pheight

Height of plots printed to png files in units of punits. Default is designed to allow two plots per page, with pheight_tall used for plots that work best with a taller format and a single plot per page.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

res

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

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

cex.main

Character expansion for plot titles. The default is cex.main=1.

plotdir

Directory where PNG files will be written.

verbose

A logical value specifying if output should be printed to the screen.

See also

SS_plots(), SS_fitbiasramp()

Author

Ian Taylor, Ian Stewart