Plot selectivity, including retention and other quantities, with additional plots for time-varying selectivity.
SSplotSelex(
replist,
infotable = NULL,
fleets = "all",
fleetnames = "default",
sizefactors = c("Lsel"),
agefactors = c("Asel", "Asel2"),
years = "endyr",
minyr = -Inf,
maxyr = Inf,
season = 1,
sexes = "all",
selexlines = 1:6,
subplot = 1:25,
skipAgeSelex10 = TRUE,
plot = TRUE,
print = FALSE,
add = FALSE,
labels = c("Length (cm)", "Age (yr)", "Year", "Selectivity", "Retention",
"Discard mortality"),
col1 = "red",
col2 = "blue",
lwd = 2,
spacepoints = 5,
staggerpoints = 1,
legendloc = "bottomright",
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
mainTitle = TRUE,
showmain = lifecycle::deprecated(),
mar = NULL,
plotdir = "default",
verbose = TRUE
)A list object created by SS_output().
Optional table of information controlling appearance of plot and legend. Is produced as output and can be modified and entered as input.
Optional vector to subset fleets for which to make plots
Optional replacement for fleenames used in data file
Which elements of the factors column of SIZE_SELEX should be included in plot of selectivity across multiple fleets?
Which elements of the factors column of AGE_SELEX should be included in plot of selectivity across multiple fleets?
Which years for selectivity are shown in multi-line plot (default = last year of model).
optional input for minimum year to show in plots
optional input for maximum year to show in plots
Which season (if seasonal model) for selectivity shown in multi-line plot (default = 1).
Optional vector to subset genders for which to make plots (1=females, 2=males)
Vector to select which lines get plotted. values are 1. Selectivity, 2. Retention, 3. Discard mortality, 4. Keep.
Vector controlling which subplots to create. Numbering of subplots is as follows,
Plots with all fleets grouped together
1 selectivity at length in end year for all fleets shown together
2 selectivity at age in end year for all fleets shown together (this includes both age-based selectivity "Asel" and age values derived from length-based, "Asel2". You can choose only one using "agefactors" if needed.)
Plots of time-varying length-based selectivity
3 selectivity at length time-varying surface
4 selectivity at length time-varying contour
5 retention at length time-varying surface
6 retention at length time-varying surface
7 discard mortality time-varying surface
8 discard mortality time-varying contour
Selectivity at length in end year by fleet
9 selectivity, retention, and discard mortality at length in ending year
Plots of time-varying age-based selectivity
11 selectivity at age time-varying surface
12 selectivity at age time-varying contour
Selectivity at age in end year by fleet
13 selectivity at age in ending year if time-varying
14 selectivity at age in ending year if NOT time-varying
15 matrix of selectivity deviations for semi-parametric selectivity
Selectivity for both/either age or length
21 selectivity at age and length contour with overlaid growth curve
22 selectivity with uncertainty if requested at end of control file
Exclude plots for age selectivity type 10 (selectivity = 1.0 for all ages beginning at age 1)?
Plot to active plot device?
Print to PNG files?
Add to existing plot (not yet implemented)
vector of labels for plots (titles and axis labels)
color for female growth curve
color for male growth curve
Line widths for plots
number of years between points shown on top of lines (for long timeseries, points every year get mashed together)
number of years to stagger the first point (if
spacepoints > 1) for each line (so that adjacent lines have points in
different years)
location of legend. See ?legend for more info.
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).
character expansion for plot titles
Logical indicating if a title should be included at the top (not yet implemented for all plots)
Deprecated, use mainTitle instead.
Either NULL to allow the default (which depends on whether the main title is included or not) or a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, which is passed to par().
Directory where PNG files will be written. By default it will be the directory where the model was run.
A logical value specifying if output should be printed to the screen.