Plot spawner-recruit curve based on output from Stock Synthesis model.
Usage
SSplotSpawnrecruit(
replist,
subplots = 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 = 1,
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,
subplot = lifecycle::deprecated()
)Arguments
- replist
A list object created by
SS_output().- subplots
Vector of which subplots to show. 1=plot without labels, 2=plot with year labels.
- add
add to existing plot?
- plot
Plot to active plot device?
Print to PNG files?
- xlim
optional control of x range
- ylim
optional control of y range
- labels
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.
- bioscale
scaling for spawning biomass. Default = 1. Previously this was set to 0.5 for single-sex models, and 1.0 for all others, but now single-sex models are assumed to use the -1 option for Nsexes in the data file so the scaling is done automatically by SS3.
- plotdir
Directory where PNG files will be written.
- 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, withpheight_tallused for plots that work best with a taller format and a single plot per page.- punits
Units for
pwidthandpheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default ispunits="in".- res
Resolution of plots printed to files. The default is
res = 300.- ptsize
Point size for plotted text in plots printed to files (see
help("png")in R for details).- verbose
A logical value specifying if output should be printed to the screen.
- colvec
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- ltyvec
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
- ptcol
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"]])- legend
Add a legend?
- legendloc
Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See
help("legend")for more info on the string options.- minyr
minimum year of recruitment deviation to show in plot
- textmindev
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.
- relative
scale both axes so that B0 and R0 are at 1 to show spawning output and recruitment relative to the equilibrium
- expected
show line for expected recruitment (stock-recruit curve)
- estimated
show points for estimated recruitment values (including deviations)
- bias_adjusted
show lines for bias adjusted expected recruitment
- show_env
add line for expected recruitment with environmental variability
- virg
add point for equilibrium conditions (x=B0,y=R0)
- init
add point for initial conditions (x=B1,y=R1), only appears if this point differs from virgin values
- forecast
include forecast years in the curve?
- subplot
Deprecated - use subplots.