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Plot movement rates from model output

Source: R/SSplotMovementRates.R
SSplotMovementRates.Rd

Plots estimated movement rates in final year for each area/season with movement as reported in Report.sso. If movement is time-varying, an additional figure shows pattern across years (if the MGparm_By_Year_after_adjustments table (report:7) is available in the Report.sso file)

Usage

SSplotMovementRates(
  replist,
  plot = TRUE,
  print = FALSE,
  subplots = 1:2,
  plotdir = "default",
  colvec = "default",
  ylim = "default",
  legend = TRUE,
  legendloc = "topleft",
  moveseas = "all",
  min.move.age = 0.5,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

plot

Plot to active plot device?

print

Print to PNG files?

subplots

which subplots to create.

plotdir

Directory where PNG files will be written.

colvec

vector of colors for each movement rate in the plot

ylim

optional input for y range of the plot. By default plot ranges from 0 to 10% above highest movement rate (not including fish staying in an area).

legend

add a legend designating which color goes with which pair of areas?

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.

moveseas

choice of season for which movement rates are shown

min.move.age

Minimum age of movement (in future will come from Report file)

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.

verbose

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

See also

SS_output(), SSplotMovementRates(),

Author

Ian Taylor

Examples

if (FALSE) { # \dontrun{
SSplotMovementRates(myreplist)
} # }