Usage
SSv3_plots(replist = "ReportObject", plot = 1:24, print = 0, pdf = F,
printfolder = "", dir = "default", fleets = "all", areas = "all",
fleetnames = "default", fleetcols = "default", fleetlty = 1,
fleetpch = 1, lwd = 1, areacols = "default", areanames = "default",
verbose = T, uncertainty = T, forecastplot = F, datplot = F,
Natageplot = T, samplesizeplots = T, compresidplots = T, sprtarg = 0.4,
btarg = 0.4, minbthresh = 0.25, pntscalar = 2.6, minnbubble = 8,
aalyear = -1, aalbin = -1, aalmaxbinrange = 0, aalresids = F,
maxneff = 5000, cohortlines = c(), smooth = T, showsampsize = T,
showeffN = T, showlegend = T, pwidth = 7, pheight = 7, punits = "in",
ptsize = 12, res = 300, cex.main = 1, selexlines = 1:5,
rows = 1, cols = 1, maxrows = 6, maxcols = 6,
maxrows2 = 2, maxcols2 = 4, tagrows = 3, tagcols = 3,
fixdims = T, new = T, catchasnumbers = F, legendloc = "topleft", ...)
Arguments
replist
The name of the object in the R workspace produced by the SSv3_output function. This is the only required input that will never work with the default value. The name of the object should not be in quotes.
plot
Plot sets to be created, see list of plots below. Use to
specify only those plot sets of interest, e.g., c(1,2,5,10). Plots
for data not available in the model run will automatically be
skipped, whether called or not. Default=1:24.
print
Plot set to be printed to files? PNG files are created
in the specified directory for one or more requested plots. Each
plot has a unique name starting with the number of the set it comes
from and attempting to be mildly descriptive. This a
pdf
Send plots to PDF file instead of R GUI? Input plot
must be used and input print must be 0. Default=0.
printfolder
Name of subfolder to create within the working
directory into which any PNG files specified by print will be
saved. By default the working directory is used with no subfolder. Default="".
dir
The directory in which any PNG files requested by print are created. By default it will be the same directory that the report file was read from by the SSv3_output function. Default="default".
fleets
Either the string "all", or a vector of numerical
values, like c(1,3), listing fleets or surveys for which plots should
be made. By default, plots will be made for all fleets and surveys. Default="all".
areas
Either the string "all", or a vector of numerical
values, like c(1,3), listing areas for which plots should be made in
a multi-area model. By default, plots will be made for all areas
(excepting cases where the function has not yet been update
fleetnames
Either the string "default", or a vector of
characters strings to use for each fleet name. Default="default".
fleetcols
Either the string "default", or a vector of colors
to use for each fleet. Default="default".
fleetlty
Vector of line types used for each fleet in some
plots. Default=1.
fleetpch
Vector of point types used for each fleet in some plots. Default=1.
lwd
Line width for some plots. Default=1.
areacols
Either the string "default", or a vector of colors
to use for each area. Default="default".
areanames
Optional vector of names for each area used in
titles. Default="default".
verbose
Return updates of function progress to the R GUI? Default=T.
uncertainty
Include values in plots showing estimates of
uncertainty (requires positive definite hessian in model and
covar=T in SSv3_output)? Default=T.
forecastplot
Include forecast years in the plots? Obviously
requires forecast options to have been used in the model. Default=T.
datplot
Plot the data by itself? This is useful in document
preparation. Setting datplot=F is equivalent to leaving off plots 15
and 16. Default=F.
Natageplot
Plot the expected numbers at age bubble plots and
mean-age time series? Default=T.
samplesizeplots
Show sample size plots? Default=T.
compresidplots
Show residuals for composition plots?
sprtarg
Specify the F/SPR proxy target. Default=0.4.
btarg
Target depletion to be used in plots showing
depletion. May be omitted by setting to NA. Default=0.4.
minbthresh
Threshold depletion to be used in plots showing
depletion. May be omitted by setting to NA. Default=0.25.
pntscalar
This scalar defines the maximum bubble size for
balloon plots; each plot scaled independently based on this maximum
size and the values plotted. Often some plots look better with one
value and others with a larger or smaller value. Default=2.6
minnbubble
This defines the minimum number of years below
which blank years will be added to bubble plots to avoid cropping.
Default=8.
aalyear
Years to plot multi-panel conditional age-at-length
fits for all length bins; must be in a "c(YYYY,YYYY)" format. Useful
for checking the fit of a dominant year class, critical time period,
etc. Default=-1.
aalbin
The length bin for which multi-panel plots of the fit
to conditional age-at-length data will be produced for all years.
Useful to see if growth curves are ok, or to see the information on
year classes move through the conditional data. Default
aalmaxbinrange
The largest length bin range allowed for composition data to be considered as conditional age-at-length data. Default=0.
aalresids
Plot the full set of conditional age-at-length Pearson residuals? Default=F.
maxneff
The maximum value to include on plots of input and effective sample size. Occasionally a calculation of effective N blows up to very large numbers, rendering it impossible to observe the relationship for other data. Default=5000.
cohortlines
Optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots. Default=c().
smooth
Add loess smoother to observed vs. expected index plots and input vs. effective sample size? Default=T.
showsampsize
Display sample sizes on composition plots? Default=T.
showeffN
Display effective sample sizes on composition plots? Default=T.
showlegend
Display legends in various plots? Default=T.
pwidth
Default width of plots printed to files in units of punits. Default=7.
pheight
Default height width of plots printed to files in units of punits. Default=7.
punits
Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".
ptsize
Point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.
res
Resolution of plots printed to files. Default=300.
cex.main
Character expansion parameter for plot titles (only implemented for composition plots so far). Default=1.
selexlines
Vector controling which lines should be shown on
selectivity plots if the model includes retention. Default=1:5.
rows
Number of rows to use for single panel plots. Default=1.
cols
Number of columns to use for single panel plots. Default=1.
maxrows
Maximum number of rows to for multi-panel plots. Default=6.
maxcols
Maximum number of columns for multi-panel plots. Default=6.
maxrows2
Maximum number of rows for conditional age at length multi-panel plots. Default=2.
maxcols2
Maximum number of rows for conditional age at length multi-panel plots. Default=4.
tagrows
Number of rows for tagging-related plots. Default=3.
tagcols
Number of columns for tagging-related plots. Default=3.
fixdims
Control whether multi-panel plots all have dimensions equal to maxrows by maxcols, or resized within those limits to fit number of plots. Default=T.
new
Open a new window or add to existing plot windows. Default=T.
catchasnumbers
Is catch input in numbers instead of biomass?
Default=F.
legendloc
Location for all legends. Default="topleft".
...
Additional arguments that will be passed to some subfunctions.