View source: R/SSplotBiology.R
SSplotBiology | R Documentation |
Plot biology related quantities from Stock Synthesis model output, including mean weight, maturity, fecundity, and spawning output.
SSplotBiology(
replist,
plot = TRUE,
print = FALSE,
add = FALSE,
subplots = 1:32,
seas = 1,
morphs = NULL,
forecast = FALSE,
minyr = -Inf,
maxyr = Inf,
colvec = c("red", "blue", "grey20"),
areacols = NULL,
ltyvec = c(1, 2),
shadealpha = 0.1,
imageplot_text = FALSE,
imageplot_text_round = 0,
legendloc = "topleft",
plotdir = "default",
labels = c("Length (cm)", "Age (yr)", "Maturity", "Mean weight (kg) in last year",
"Spawning output", "Length (cm, beginning of the year)", "Natural mortality",
"Female weight (kg)", "Female length (cm)", "Fecundity", "Default fecundity label",
"Year", "Hermaphroditism transition rate", "Fraction females by age in ending year"),
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
mainTitle = TRUE,
verbose = TRUE
)
replist |
A list object created by |
plot |
Plot to active plot device? |
print |
Print to PNG files? |
add |
add to existing plot |
subplots |
vector controlling which subplots to create Numbering of subplots is as follows:
Additional plots not created by default
|
seas |
which season to plot (values other than 1 only work in seasonal models but but maybe not fully implemented) |
morphs |
Which morphs to plot (if more than 1 per sex)? By default this
will be |
forecast |
Include forecast years in plots of time-varying biology? |
minyr |
optional input for minimum year to show in plots |
maxyr |
optional input for maximum year to show in plots |
colvec |
vector of length 3 with colors for various points/lines |
areacols |
Optional vector of colors for each area if model has multiple areas. NULL value will be replaced by a default set of areas. |
ltyvec |
vector of length 2 with lty for females/males in growth plots values can be applied to other plots in the future |
shadealpha |
Transparency parameter used to make default shadecol values (see ?rgb for more info) |
imageplot_text |
Whether to add numerical text to the image plots when using weight at age. Defaults to FALSE. |
imageplot_text_round |
The number of significant digits to which the image plot text is rounded. Defaults to 0, meaning whole numbers. If all your values are small and there's no contrast in the text, you might want to make this 1 or 2. |
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 |
plotdir |
Directory where PNG files will be written. |
labels |
Vector of labels for plots (titles and axis labels). |
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
|
cex.main |
Character expansion for plot titles.
The default is |
mainTitle |
Logical indicating if a title should be included at the top (not yet implemented for all plots). |
verbose |
A logical value specifying if output should be printed to the screen. |
Ian Stewart, Ian Taylor
SS_plots()
, SS_output()
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