Plot composition data and fits.

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", "(t)",
    "(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 plot for marginal data with Dirichlet-Multinomial and no Francis adjustment
9 TA1.8 Francis weighting plot for marginal data
10 TA1.8 Francis plot for conditional data with Dirichlet-Multinomial and no Francis adjustment
11 TA1.8 Francis weighting plot for conditional data
12 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

Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.

fleetnames

Optional replacement for fleetnames used in data file.

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 labels.

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.

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.

cex.main

Character expansion for plot titles. The default is cex.main=1.

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

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

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 should be included at the top (not yet implemented for all plots).

...

additional arguments that will be passed to the par command in the make_multifig() function.

Author

Ian Taylor

Usage

Arguments

See also

Author