Plot tagging data and fits

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.
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".
ptsize: Point size for plotted text in plots printed to files (see help("png") in R for details).
res: Resolution of plots printed to files. The default is res = 300.
cex.main: Character expansion for plot titles. The default is cex.main=1.
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.
verbose: A logical value specifying if output should be printed to the screen.

Author

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

Usage

Arguments

See also

Author