SSplotComps: Plot composition data and fits.

In r4ss: R Code for Stock Synthesis

Plot composition data and fits.

Description

Plot composition data and fits from Stock Synthesis output. Multi-figure plots depend on make_multifig.

Usage

SSplotComps(
  replist,
  subplots = c(1:10, 21, 24),
  kind = "LEN",
  sizemethod = 1,
  aalyear = -1,
  aalbin = -1,
  plot = TRUE,
  print = FALSE,
  fleets = "all",
  fleetnames = "default",
  sexes = "all",
  yupper = 0.4,
  datonly = FALSE,
  samplesizeplots = TRUE,
  compresidplots = TRUE,
  bub = FALSE,
  showyears = TRUE,
  showsampsize = TRUE,
  showeffN = TRUE,
  aggregates_by_mkt = FALSE,
  sampsizeline = FALSE,
  effNline = FALSE,
  minnbubble = 3,
  pntscalar = NULL,
  scalebubbles = FALSE,
  cexZ1 = 1.5,
  bublegend = TRUE,
  colvec = c(rgb(1, 0, 0, 0.7), rgb(0, 0, 1, 0.7), rgb(0.1, 0.1, 0.1, 0.7)),
  linescol = c(rgb(0, 0.5, 0, 0.7), rgb(0.8, 0, 0, 0.7), rgb(0, 0, 0.8, 0.7)),
  xlas = 0,
  ylas = NULL,
  axis1 = NULL,
  axis2 = NULL,
  axis1labs = NULL,
  sizebinlabs = NULL,
  blue = rgb(0, 0, 1, 0.7),
  red = rgb(1, 0, 0, 0.7),
  pwidth = 6.5,
  pheight = 6.5,
  punits = "in",
  ptsize = 10,
  res = 300,
  plotdir = "default",
  cex.main = 1,
  linepos = 1,
  fitbar = FALSE,
  do.sqrt = TRUE,
  smooth = TRUE,
  cohortlines = c(),
  labels = c("Length (cm)", "Age (yr)", "Year", "Observed sample size",
    "Effective sample size", "Proportion", "cm", "Frequency", "Weight", "Length", "(mt)",
    "(numbers x1000)", "Stdev (Age)", "Conditional AAL plot, ", "Size bin"),
  printmkt = TRUE,
  printsex = TRUE,
  maxrows = 6,
  maxcols = 4,
  maxrows2 = 4,
  maxcols2 = 4,
  rows = 1,
  cols = 1,
  andre_oma = c(3, 0, 3, 0),
  andrerows = 4,
  fixdims = TRUE,
  fixdims2 = FALSE,
  maxneff = 5000,
  verbose = TRUE,
  scalebins = FALSE,
  addMeans = TRUE,
  mainTitle = FALSE,
  ...
)

Arguments

replist	A list object created by SS_output().
subplots	vector controlling which subplots to create Numbering of subplots is as follows, where subplots 21 to 24 (aggregated across years) are provided first, and subplots 1 to 10 are all repeated for each fleet 1 index data by fleet 1 multi-panel composition plot 2 single panel bubble plot for numbers at length or age 3 multi-panel bubble plots for conditional age-at-length 4 multi-panel plot of fit to conditional age-at-length for specific years 5 Pearson residuals for A-L key 6 multi-panel plot of point and line fit to conditional age-at-length for specific length bins 7 sample size plot 8 TA1.8 Francis weighting plot 9 TA1.8 Francis weighting plot for conditional data 10 Andre's mean age and std. dev. in conditional AAL 21 composition by fleet aggregating across years 22 composition by fleet aggregating across years within each season 23 composition by fleet aggregating across seasons within a year 24 bubble plot comparison of length or age residuals
kind	indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "GSTLEN", "L@A", or "W@A".
sizemethod	if kind = "SIZE" then this switch chooses which of the generalized size bin methods will be plotted.
aalyear	Years to plot multi-panel conditional age-at-length fits for all length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking the fit of a dominant year class, critical time period, etc. Default=-1.
aalbin	The length bin for which multi-panel plots of the fit to conditional age-at-length data will be produced for all years. Useful to see if growth curves are ok, or to see the information on year classes move through the conditional data. Default=-1.
plot	plot to active plot device?
print	print to PNG files?
fleets	optional vector to subset fleets for which plots will be made
fleetnames	optional vector of fleet names to put in the labels
sexes	which sexes to show plots for. Default="all" which will include males, females, and unsexed. This option is not fully implemented for all plots.
yupper	upper limit on ymax for polygon/histogram composition plots
datonly	make plots of data without fits?
samplesizeplots	make sample size plots?
compresidplots	make plots of residuals for fit to composition data?
bub	make bubble plot for numbers at age or size?
showyears	Add labels for years to sample size plots?
showsampsize	add sample sizes to plot
showeffN	add effective sample sizes to plot
aggregates_by_mkt	separate plots of aggregates across years into different plots for each market category (retained, discarded)?
sampsizeline	show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)
effNline	show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)
minnbubble	number of unique x values before adding buffer. see ?bubble3 for more info.
pntscalar	This scalar defines the maximum bubble size for bubble plots. This option is still available but a better choice is to use cexZ1 which allow the same scaling throughout all plots.
scalebubbles	scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.
cexZ1	Character expansion (cex) for point associated with value of 1.
bublegend	Add legend with example bubble sizes to bubble plots.
colvec	Vector of length 3 with colors for females, males, unsexed fish
linescol	Color for lines on top of polygons
xlas	label style (las) input for x-axis. Default 0 has horizontal labels, input 2 would provide vertical lables.
ylas	label style (las) input for y-axis. Default NULL has horizontal labels when all labels have fewer than 6 characters and vertical otherwise. Input 0 would force vertical labels, and 1 would force horizontal.
axis1	optional position of bottom axis values
axis2	optional position of left size axis values
axis1labs	optional vector of labels for axis1 (either NULL or needs to match length of axis1)
sizebinlabs	Vector of size bin labels corresponding to the generalized size frequency method
blue	What color to use for males in bubble plots (default is slightly transparent blue)
red	What color to use for females in bubble plots (default is slightly transparent red)
pwidth	Default width of plots printed to files in units of punits. The default is pwidth=6.5.
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.
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.
cex.main	character expansion parameter for plot titles
linepos	should lines be added before points (linepos=1) or after (linepos=2)?
fitbar	show fit to bars instead of points
do.sqrt	scale bubbles based on sqrt of size vector. see ?bubble3 for more info.
smooth	add loess smoother to observed vs. expected index plots and input vs. effective sample size?
cohortlines	optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots
labels	vector of labels for plots (titles and axis labels)
printmkt	show market categories in plot titles?
printsex	show sex in plot titles?
maxrows	maximum (or fixed) number or rows of panels in the plot
maxcols	maximum (or fixed) number or columns of panels in the plot
maxrows2	maximum number of rows for conditional age at length plots
maxcols2	maximum number of columns for conditional age at length plots
rows	number or rows to return to as default for next plots to come or for single plots
cols	number or cols to return to as default for next plots to come or for single plots
andre_oma	Outer margins passed to Andre's multi-panel conditional age-at-length plots.
andrerows	Number of rows of Andre's conditional age-at-length plots within each page. Default=3.
fixdims	fix the dimensions at maxrows by maxcols or resize based on number of years of data
fixdims2	fix the dimensions at maxrows by maxcols in aggregate plots or resize based on number of fleets
maxneff	the maximum value to include on plots of input and effective sample size. Occasionally a calculation of effective N blows up to very large numbers, rendering it impossible to observe the relationship for other data. Default=5000.
verbose	return updates of function progress to the R GUI?
scalebins	Rescale expected and observed proportions by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.
addMeans	Add parameter means in addition to medians for MCMC posterior distributions in which the median and mean differ.
mainTitle	Logical indicating if a title for the plot should be produced
...	additional arguments that will be passed to the par command in the make_multifig() function.

Author(s)

Ian Taylor

See Also

SS_plots(), make_multifig()

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