Plots retrospective pattern, including (optional) one-step ahead forecast and computes Mohn's Rho
Usage
SSplotRetro(
summaryoutput,
subplots = c("SSB", "F"),
plot = TRUE,
print = deprecated(),
print_plot = FALSE,
png = deprecated(),
use_png = print_plot,
pdf = deprecated(),
use_pdf = FALSE,
models = "all",
endyrvec = "default",
xlim = NULL,
xmin = NULL,
labels = NULL,
ylim = NULL,
forecast = TRUE,
forecastrho = TRUE,
showrho = TRUE,
col = NULL,
pch = NULL,
lty = 1,
lwd = 2,
tickEndYr = TRUE,
ylimAdj = 1.05,
xaxs = "i",
yaxs = "i",
xylabs = TRUE,
type = "o",
uncertainty = TRUE,
legend = TRUE,
legendlabels = "default",
legendloc = "topright",
legendorder = "default",
legendncol = 1,
legendcex = 1,
legendsp = 0.7,
legendindex = NULL,
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
plotdir = NULL,
filenameprefix = "",
par = list(mar = c(5, 4, 1, 1) + 0.1),
verbose = TRUE,
shadecol = grey(0.4, 0.6),
new = TRUE,
add = FALSE,
mcmcVec = FALSE,
shadecol1 = grey(0.5, 0.4),
indexQlabel = TRUE,
indexQdigits = 4,
shadealpha = 0.3
)Arguments
- summaryoutput
List created by
r4ss::SSsummarize()- subplots
Optional vector of subplots to be created:
"SSB"Spawning Stock Biomass"F"Fishing Mortality
- plot
DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
DEPRECATED, please use
print_plot.- print_plot
Flag to enable plot graphic device to print to PNG or PNG files.
- png
DEPRECATED. Please use
use_png.- use_png
Enables plots to be generated to PNG files. Defaults to print value
DEPRECATED. Please use
use_pdf.- use_pdf
Enables plots to be generated to pdf file.
- models
Optional subset of the models of
summaryoutput(or a similar field with a different name): a list created by the function r4ss::SSsummarize. Either"all"or a vector of numbers indicating columns in summary tables.- endyrvec
Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
- xlim
Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
- xmin
optional minimum year shown in plot (default first yr)
- labels
yaxislabel for biomass (bony fish and sharks)- ylim
option to specify
ylimrange- forecast
Logical. If TRUE, one-step ahead forecasts are shown in plot
- forecastrho
Logical. If TRUE, one-step ahead forecast rho value is denoted in plot
- showrho
Logical flag to include Mohn's rho value. Defaults to TRUE
- col
Optional vector of colors to be used for lines. Input NULL
- pch
Optional vector of plot character values
- lty
Optional vector of line types
- lwd
Optional vector of line widths
- tickEndYr
Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
- ylimAdj
Multiplier for ylim parameter. Allows additional white space.
- xaxs
Choice of xaxs parameter See
?parfor more info.- yaxs
Choice of yaxs parameter. See
?parfor more info.- xylabs
Logical flag: set TRUE or FALSE to include x- and y-axis labels to the plot. Defaults to TRUE
- type
The type of plot to be drawn. For more details, see
plot.- uncertainty
Logical flag to enable plots with uncertainty intervals. Either a single TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F estimated timeseries, or a set of integers corresponding to the choice of models.
- legend
Flag to enable legend to plot. TRUE by default.
- legendlabels
Optional vector of labels to include in 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.- legendorder
Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
- legendncol
Number of columns for the legend.
- legendcex
Allows to adjust legend cex
- legendsp
Space between legend labels
- legendindex
Allows to add legend for selected indices (plots)
- pwidth
Default width of plot printed to plot in units of
punits- pheight
Height of plot printed to plot in units of
punits- punits
Measurement units for
pwidthandpheight. Default is"in"."px"(pixels)"in"(inches)"cm"(centimeters)"mm"(millimeters)
- res
Resolution for plots printed to files.
- ptsize
Point size for plotted text in plots printed in files. See
help("png")for more details- cex.main
Character expansion for plot titles.
- plotdir
Directory where output plot file will be written. By default, it will be the directory where the model was run.
- filenameprefix
Additional text to append to output plot file name. It will be separated from default name by an underscore.
- par
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(). EnteringNULLpasses plot's defaultpar()values (which depends on whether the main title is included or not)- verbose
Flag to print additional diagnostic messages to R console
- shadecol
uncertainty shading of hcxval horizon
- new
Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
- add
suppresses
par()to create multiplot figs- mcmcVec
Logical vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE.
- shadecol1
uncertainty shading of early years not affected by hindcast
- indexQlabel
Logical. If TRUE, add catchability to legend in plot of index fits (currently not used)
- indexQdigits
Number of significant digits for catchability in legend
- shadealpha
set the transparency level (alpha) of the area of uncertainty. Defaults to 0.3 (currently not used)