Plot composition data and fits from Stock Synthesis output. Multi-figure
plots depend on make_multifig.
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,
...
)A list object created by SS_output().
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
indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "GSTLEN", "L@A", or "W@A".
if kind = "SIZE" then this switch chooses which of the generalized size bin methods will be plotted.
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.
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 to active plot device?
print to PNG files?
optional vector to subset fleets for which plots will be made
optional vector of fleet names to put in the labels
which sexes to show plots for. Default="all" which will include males, females, and unsexed. This option is not fully implemented for all plots.
upper limit on ymax for polygon/histogram composition plots
make plots of data without fits?
make sample size plots?
make plots of residuals for fit to composition data?
make bubble plot for numbers at age or size?
Add labels for years to sample size plots?
add sample sizes to plot
add effective sample sizes to plot
separate plots of aggregates across years into different plots for each market category (retained, discarded)?
show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)
show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)
number of unique x values before adding buffer. see ?bubble3 for more info.
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.
scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.
Character expansion (cex) for point associated with value of 1.
Add legend with example bubble sizes to bubble plots.
Vector of length 3 with colors for females, males, unsexed fish
Color for lines on top of polygons
label style (las) input for x-axis. Default 0 has horizontal labels, input 2 would provide vertical lables.
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.
optional position of bottom axis values
optional position of left size axis values
optional vector of labels for axis1 (either NULL or needs to match length of axis1)
Vector of size bin labels corresponding to the generalized size frequency method
What color to use for males in bubble plots (default is slightly transparent blue)
What color to use for females in bubble plots (default is slightly transparent red)
Default width of plots printed to files in units of
punits. The default is pwidth=6.5.
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.
Units for pwidth and pheight. Can be "px"
(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).
The default is punits="in".
Point size for plotted text in plots printed to files (see
help("png") in R for details).
Resolution of plots printed to files.
The default is res = 300.
directory where PNG files will be written. by default it will be the directory where the model was run.
character expansion parameter for plot titles
should lines be added before points (linepos=1) or after (linepos=2)?
show fit to bars instead of points
scale bubbles based on sqrt of size vector. see ?bubble3 for more info.
add loess smoother to observed vs. expected index plots and input vs. effective sample size?
optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots
vector of labels for plots (titles and axis labels)
show market categories in plot titles?
show sex in plot titles?
maximum (or fixed) number or rows of panels in the plot
maximum (or fixed) number or columns of panels in the plot
maximum number of rows for conditional age at length plots
maximum number of columns for conditional age at length plots
number or rows to return to as default for next plots to come or for single plots
number or cols to return to as default for next plots to come or for single plots
Outer margins passed to Andre's multi-panel conditional age-at-length plots.
Number of rows of Andre's conditional age-at-length plots within each page. Default=3.
fix the dimensions at maxrows by maxcols or resize based on number of years of data
fix the dimensions at maxrows by maxcols in aggregate plots or resize based on number of fleets
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.
return updates of function progress to the R GUI?
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.
Add parameter means in addition to medians for MCMC posterior distributions in which the median and mean differ.
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.