View source: R/SSplotSpawnrecruit.R
SSplotSpawnrecruit | R Documentation |
Plot spawner-recruit curve based on output from Stock Synthesis model.
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()
)
replist |
A list object created by |
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 |
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
|
pheight |
Height of plots printed to png files in units of |
punits |
Units for |
res |
Resolution of plots printed to files.
The default is |
ptsize |
Point size for plotted text in plots printed to files (see
|
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 |
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
|
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 |
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. |
Ian Stewart, Ian Taylor
SS_plots()
, SS_output()
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