SSplotTags {r4ss}

Plot tagging data and fits

Description

Plot observed and expected tag recaptures in aggregate and by tag group.

Usage

SSplotTags(
  replist = replist,
  subplots = 1:10,
  latency = NULL,
  taggroups = NULL,
  rows = 1,
  cols = 1,
  tagrows = 3,
  tagcols = 3,
  plot = TRUE,
  print = FALSE,
  pntscalar = 2.6,
  minnbubble = 8,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  ptsize = 10,
  res = 300,
  cex.main = 1,
  col1 = rgb(0, 0, 1, 0.7),
  col2 = "red",
  col3 = "grey95",
  col4 = "grey70",
  labels = c("Year", "Frequency", "Tag Group", "Fit to tag recaptures by tag group",
    "Post-latency tag recaptures aggregated across tag groups",
    "Observed tag recaptures by year and tag group",
    "Residuals for post-latency tag recaptures: (obs-exp)/sqrt(exp)",
    "Observed and expected post-latency tag recaptures by year and tag group",
    "Summarized observed and expected numbers of recaptures by fleet",
    "Pearson residuals by tag group"),
  plotdir = "default",
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

subplots

vector controlling which subplots to create

latency

period of tag mixing to exclude from plots (in future could be included in SS output)

taggroups

which tag groups to include in the plots. Default=NULL causes all groups to be included.

rows

number or rows of panels for regular plots

cols

number or columns of panels for regular plots

tagrows

number or rows of panels for multi-panel plots

tagcols

number or columns of panels for multi-panel plots

plot

plot to active plot device?

print

print to PNG files?

pntscalar

maximum bubble size for balloon plots; each plot scaled independently based on this maximum size and the values plotted. Often some plots look better with one value and others with a larger or smaller value. Default=2.6

minnbubble

minimum number of years below which blank years will be added to bubble plots to avoid cropping

pwidth

default width of plots printed to files in units of punits. Default=7.

pheight

default height width of plots printed to files in units of punits. Default=7.

punits

units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".

ptsize

point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.

res

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

cex.main

character expansion parameter for plot titles

col1

color for bubbles

col2

color for lines with expected values

col3

shading color for observations within latency period

col4

shading color for observations after latency period

labels

vector of labels for plots (titles and axis labels)

plotdir

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

verbose

return updates of function progress to the R GUI?

Author(s)

Andre E. Punt, Ian G. Taylor, Ashleigh J. Novak

See Also

SS_plots(), SS_output()