Plot spawner-recruit curve based on output from Stock Synthesis model.
SSplotSpawnrecruit(
replist,
subplot = 1:3,
add = FALSE,
plot = TRUE,
print = FALSE,
xlim = NULL,
ylim = NULL,
labels = c("Spawning biomass (mt)", "Recruitment (1,000s)", "Spawning output",
expression(paste("Spawning output (relative to ", italic(B)[0], ")")),
expression(paste("Recruitment (relative to ", italic(R)[0], ")")),
"Log recruitment deviation"),
bioscale = "default",
plotdir = "default",
pwidth = 6.5,
pheight = 6.5,
punits = "in",
res = 300,
ptsize = 10,
verbose = TRUE,
colvec = c("blue", "black", "black", gray(0, 0.7)),
ltyvec = c(1, 2, 1, NA),
ptcol = "default",
legend = TRUE,
legendloc = NULL,
minyr = "default",
textmindev = 0.5,
relative = FALSE,
expected = TRUE,
estimated = TRUE,
bias_adjusted = TRUE,
show_env = TRUE,
virg = TRUE,
init = TRUE,
forecast = FALSE
)A list object created by SS_output().
vector of which subplots to show. 1=plot without labels, 2=plot with year labels.
add to existing plot?
plot to active plot device?
print to PNG files?
optional control of x range
optional control of y range
vector containing x-axis label for models with spawning biomass in metric tons, y-axis label, and alternative x-axis for models with a fecundity relationship making spawning output not equal to spawning biomass.
multiplier on spawning biomass, set to 0.5 for single-sex models
directory where PNG files will be written. by default it will be the directory where the model was run.
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".
Resolution of plots printed to files.
The default is res = 300.
Point size for plotted text in plots printed to files (see
help("png") in R for details).
report progress to R GUI?
vector of length 4 with colors for 3 lines and 1 set of points
(where the 4th value for the points is the color of the circle around the
background color provided by ptcol
vector of length 4 with line types for the 3 lines and 1 set of points, where the points are disconnected (lty=NA) by default
vector or single value for the color of the points, "default"
will by replaced by a vector of colors of length equal to
nrow(replist[["recruit"]])
add a legend to the figure?
location of legend. By default it is chosen as the first value in the set of "topleft", "topright", "bottomright" that results in no overlap with the points in the plot, but the user can override this with their choice of location. See ?legend for more info on the options.
minimum year of recruitment deviation to show in plot
minimum recruitment deviation for label to be added so only extreme devs are labeled (labels are added to first and last years as well). Default=0.7.
scale both axes so that B0 and R0 are at 1 to show spawning output and recruitment relative to the equilibrium
show line for expected recruitment (stock-recruit curve)
show points for estimated recruitment values (including deviations)
show lines for bias adjusted expected recruitment
add line for expected recruitment with environmental variability
add point for equilibrium conditions (x=B0,y=R0)
add point for initial conditions (x=B1,y=R1), only appears if this point differs from virgin values
include forecast years in the curve?