SSplotTags: Plot tagging data and fits

In r4ss: R Code for Stock Synthesis

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()

r4ss documentation built on May 28, 2022, 1:11 a.m.