Usage
SSplotComps(replist, subplots = 1:8, kind = "LEN", aalyear =
-1, aalbin = -1, plot = TRUE, print = FALSE, fleets = "all",
datonly = FALSE, samplesizeplots = TRUE, compresidplots = TRUE,
bub = FALSE, showsampsize = TRUE, showeffN = TRUE, minnbubble = 8, pntscalar =
2.6, pwidth = 7, pheight = 7, punits = "in", ptsize = 12, res = 300,
plotdir = "default",
cex.main = 1, linepos = 1, fitbar = FALSE, maxsize = 3, do.sqrt = TRUE,
smooth = TRUE, cohortlines = c(), labels = c("Length (cm)", "Age (yr)",
"Year", "Observed sample size", "Effective sample size", "Proportion",
"cm", "Frequency", "Weight (lbs)", "(mt)", "(numbers x1000)",
"Stdev (Age) (yr)", "Andre's conditional AAL plot, "), printmkt = TRUE,
printsex = TRUE, maxrows = 6, maxcols = 6, maxrows2 = 2, maxcols2 = 4,
rows = 1, cols = 1,
fixdims = TRUE, maxneff = 5000, verbose = TRUE, ...)Arguments
replist
list created by SSoutput
subplots
vector controlling which subplots to create
kind
indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE",
"L@A", or "W@A".
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. Defa
plot
plot to active plot device?
fleets
optional vector to subset fleets for which plots will be made
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?
showsampsize
add sample sizes to plot
showeffN
add effective sample sizes to plot
minnbubble
number of unique x values before adding buffer. see ?bubble3 for more info.
pntscalar
maximum bubble size for bubble 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
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. 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
maxsize
maximum size of bubble plots
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 gender 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
fixdims
fix the dimensions at maxrows by maxcols or resize based on number of
years of data
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?
...
additional arguments that will be passed to the plotting.