Description Usage Arguments Author(s) See Also
Plot composition data and fits from Stock Synthesis output. Multifigure
plots depend on make_multifig
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23  SSplotComps(replist, subplots = c(1:21, 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)), axis1 = NULL,
axis2 = NULL, blue = rgb(0, 0, 1, 0.7), red = rgb(1, 0, 0, 0.7),
pwidth = 6.5, pheight = 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) (yr)",
"Conditional AAL plot, "), printmkt = TRUE, printsex = TRUE,
maxrows = 6, maxcols = 6, maxrows2 = 2, maxcols2 = 4, rows = 1,
cols = 1, andre_oma = c(3, 0, 3, 0), andrerows = 3,
fixdims = TRUE, fixdims2 = FALSE, maxneff = 5000, verbose = TRUE,
scalebins = FALSE, addMeans = TRUE, mainTitle = FALSE, ...)

replist 
list created by 
subplots 
vector controlling which subplots to create 
kind 
indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "L[at]A", or "W[at]A". 
sizemethod 
if kind = "SIZE" then this switch chooses which of the generalized size bin methods will be plotted. 
aalyear 
Years to plot multipanel conditional ageatlength 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 multipanel plots of the fit to conditional ageatlength 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 as well as data with 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 ageatlength plots (TRUE/FALSE, still in development) 
effNline 
show line for effective sample sizes on top of conditional ageatlength 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 dataonly 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 
axis1 
position of bottom axis values 
axis2 
position of left size axis values 
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

pheight 
default height width of plots printed to files in units of

punits 
units for 
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. Default=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 multipanel conditional ageatlength plots. 
andrerows 
Number of rows of Andre's conditional ageatlength 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 plotting. 
Ian Taylor
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