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Directory (or vector of directories) where rebuilder outputfiles are stored.

Vector of filenames containing rebuilder output.Default=c("res.csv").

Titles for plots when using multiple filenames. Default="".

Number of columns to read in output file (fileN). Default=200.

List to get specific plots (currently 1 through 8).Default=list(1:25). If there are multiple files, supply a list of vectors,e.g. list(c(1,5),c(2:5))

List to get specific strategies in the trajectory plots.Default=list(c(1:9)).If there are multiple files, supply a list of vectors,e.g. list(c(1,5),c(2:5))

Location for the legend (for plots with a legend).Default="bottomright".

Maximum year to show in the plots. Set negative to show allyears. Default=-1.

Number of rows, columns for some of the plots.Default=c(2,2).

Number of rows, columns for other plots.Default=c(2,2).

Vector of trajectories to show. Default=c(1,2,3,4).

Vector of individual plots to show. Default=c(1,2,3,4,5,6,7).

Label for biomass type. Default="Spawning biomass".

Units of catch. Default="(mt)".

Units of biomass. Default="(mt)".

Scalar for biomass plot. Default=1.

Optional vector for alternative line colors.Default="default".

Optional vector for alternative legend labels.Default="default".

Option to send figures to pdf file instead of plot window inRgui. Default=FALSE.

Width of the plot window or PDF file (in inches). Default=7.

Height of the plot window or PDF file (in inches). Default=7.

Line width for many of the plot elements. Default=2.

Directory containing Stock Synthesis files(e.g., "C:/Users/James Thorson/Desktop/")

Vector where each element is the standard deviationfor a group of random effects (e.g., a model with a single group of randomeffects will have Input_SD_Group_Vec be a vector of length one)

List (same length asInput_SD_Group_Vec),where eachelement is a vector giving the line number(s) for the random effect standarddeviation parameter or penalty in the CTL file (and where each line willcorrespond to a 7-parameter or 14-parameter line).

List (same length asInput_SD_Group_Vec),where eachelement is a vector giving the parameter number for the random effectcoefficients in that group of random effects. These "parameter numbers"correspond to the number of these parameters in the list of parameters in the".cor" output file.

Vector giving the number in the ".par" vector for eachrandom effect coefficient.

List where each element is a vector, providing a way ofgrouping different random effect groups into a single category. Althoughthis input is still required, it is no has the former input Version has beenhardwired to Version = 1.

Logical flag (TRUE or FALSE) saying whether to start eachround of optimization from a ".par" file (I recommend TRUE)

Logical flag saying whether to display all ss3 runtime outputin the R terminal

Logical flag saying whether to re-do the bias ramp(usingSS_fitbiasramp()) each time Stock Synthesis is run.

Vector giving the line numbers from the CTL filethat contain the information about the bias ramp.

Character vector (same length asInput_SD_Group_Vec),where each element is either "Short_Param", "Long_Penalty", "Long_Penalty".Default is NULL, and if not explicitly specified the program will attempt todetect these automatically based on the length of relevant lines from the CTLfile.

Should R call SS using "system" function instead of "shell".This may be required when running R in Emacs on Windows. Default = FALSE.

SS executable name (excluding extension), either "ss" or "ss3".This string is used for both calling the executable and also finding theoutput files like ss.par. For 3.30, it should always be "ss" since theoutput file names are hardwired in the TPL code.

List created by the functionSSsummarize().

Plot to active plot device?

Print to PNG files?

Which likelihood component to plot. Default is "Length_like".

Title for plot. Should match component.

Optional subset of the models described insummaryoutput. Either "all" or a vector of numbers indicatingcolumns in summary tables.

Optional vector of fleet numbers to include.

Optional character vector of names for each fleet.

Character string used to find parameter over which theprofile was conducted. Ifexact=FALSE, this can be a substring ofone of the SS parameter labels found in the Report.sso file.For instance, the default input 'R0'matches the parameter 'SR_LN(R0)'. Ifexact=TRUE, thenprofile.string needs to be an exact match to the parameter label.

Label for x-axis describing the parameter over whichthe profile was conducted.

Should theprofile.string have to match the parameterlabel exactly, or is a substring OK.

Label for y-axis. Default is "Change in -log-likelihood".

Optional vector of colors for each line.

Optional vector of plot characters for the points.

Line total for the likelihood components.

Line type for the total likelihood.

Line width for the likelihood components.

Line width for the total likelihood.

Character expansion for the points representing the likelihoodcomponents.

Character expansion for the points representing the totallikelihood.

Range for x-axis. Change in likelihood is calculated relative tovalues within this range.

Maximum y-value. Default is 10\plotted.

The style of axis interval calculation to be used for the x-axis(see ?par for more info)

The style of axis interval calculation to be used for the y-axis(see ?par for more info).

Line type (see ?plot for more info).

Include legend?

Location of legend (see ?legend for more info).

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

Point size for PNG file

Character expansion for plot titles

Directory where PNG files will be written. by default it willbe the directory where the model was run.

Add dashed line at ~1.92 to indicate 95% confidence intervalbased on common cutoff of half of chi-squared of p=.95 with 1 degree offreedom:0.5*qchisq(p=cutoff_prob, df=1). The probability valuecan be adjusted using thecutoff_prob below.

Probability associated withadd_cutoff above.

Return updates of function progress to the R GUI? (Doesn't doanything yet.)

Optional character vector, with length equal tothe number of declared fleets, where fleets with the same value areaggregated

choice of "raw" or "raw_times_lambda" (the default)determines whether or not likelihoods plotted are adjusted by lambdas(likelihood weights)

Minimum change in likelihood (over range considered) as afraction of change in total likelihood for a component to be included in thefigure.

Stock Synthesis output as read by r4SS function SS_output

vector of one or more fleet numbers whose data are tobe analysed simultaneously (the output N multiplier appliesto all fleets combined)

vector of one or more partition values; analysis is restrictedto composition data with one of these partition values.Default is to include all partition values (0, 1, 2).

string indicating how to treat data from multiple seasons'comb' - combine seasonal data for each year and plot against Yr'sep' - treat seasons separately, plotting against Yr.SIf is.null(seas) it is assumed that there is only one season inthe selected data (a warning is output if this is not true) andoption 'comb' is used.

if TRUE, make an illustrative plot like one or morepanels of Fig. 4 in Francis (2011).

if TRUE, print results to R console.

if TRUE, don't show the model expectations

if TRUE, plot the confidence intervals associated withthe adjusted sample sizes (TRUE by default unless datonly = TRUE)

maximum number of panels within a plot

Print full diagnostics?

Report the Version B value in addition to the default?

Vector of alternative fleet names to draw from forplot titles and captions. It should have length equal to the numberof fleets in the model, not the number of fleets considered in this function.

add to existing plot

Stock Synthesis output as read by r4SS function SS_output

either 'len' (for length composition data), 'size' (forgeneralized size composition data), 'age' (for age composition data),or 'con' (for conditional age at length data)

vector of one or more fleet numbers whose data are tobe analysed simultaneously (the output N multiplier appliesto all fleets combined)

vector of one or more partition values; analysis is restrictedto composition data with one of these partition values.Default is to include all partition values (0, 1, 2).

vector of one or more values for Sexes; analysis isrestricted to composition data with one of theseSexes values. Ignored if type=='con'.

string indicating how to treat data from multiple seasons'comb' - combine seasonal data for each year and plot against Yr'sep' - treat seasons separately, plotting against Yr.SIf is.null(seas) it is assumed that there is only one season inthe selected data (a warning is output if this is not true) andoption 'comb' is used.

a vector of one or more size-frequency method numbers(ignored unless type = 'size').If !is.null(method), analysis is restricted to size-frequencymethods in this vector. NB comps are separated by method

if TRUE, make an illustrative plot like one or morepanels of Fig. 4 in Francis (2011).

if TRUE, print results to R console.

if TRUE, don't show the model expectations

if TRUE, plot the confidence intervals associated withthe adjusted sample sizes (TRUE by default unless datonly = TRUE)

maximum number of panels within a plot

Vector of alternative fleet names to draw from forplot titles and captions. It should have length equal to the numberof fleets in the model, not the number of fleets considered in this function.

Include labels indicating which partitions are included?

Include labels indicating which sexes are included?

Set the graphical parameters such as mar and mfrow.Can be set to FALSE in order to add plots form multiple calls tothis function as separate panels in one larger figure.

add to existing plot

A list object created bySS_output().

Range of years in which to fill in forecast catches from timeseries

Use average catch over a range of years for forecast(as opposed to using forecast based on control rule)

Range of years to average over

Either single value or vector of annual total forecast catchused to scale values (especially if values are from average catches).For west coast groundfish, total might be ACL for next 2 forecast years

Number of digits to round to in table

TRUE/FALSE switch to choose dead catch instead of retained catch.

Include entries with zero catch (TRUE/FALSE)

Directory where model files are located.

Name of the Stock Synthesis model file (which has the .exe foron Windows) inmydir without the extension (if any), e.g.,"ss" or"ss_win".

Additional command line arguments passed to the executable.The default,"-nohess", runs each jittered model without the hessian.

Number of jitters, or a vector of jitter iterations.Iflength(Njitter) > 1 only the iterations specified will be ran,else1:Njitter will be executed.

Show command line info in R console or keep hidden. The default,TRUE, keeps the executable hidden.

Option to switch between 'shell' and 'system'. The default,FALSE, facilitates using the shell command on Windows.

A logical value specifying if the likelihood values shouldbe printed to the console.

A logical value specifying if output should be printedto the screen.

The value, typically 0.1, used to define a uniformdistribution in cumulative normal space to generate new initial parameter values.The default ofNULL forces the user to specify the jitter_fractionin the starter file, and this value must be greater than zero andwill not be overwritten.

Either zero or one, specifying if the initial values tojitter should be read from the control file or from the par file, respectively.The default isNULL, which will leave the starter file unchanged.

Output fromSSsummarize()summarizing results of models to be included

Directory where plots will be created, either relativeto working directory or an absolute path

Year to report output

List the names of the sensitivity runs

Saved file of relative changes

Confidence interval box based on the reference model

Target relative abundance value

Limit relative abundance value

X-axis label

Y-axis label

Which plots to make/save?

vertical breaks that can separate out typesof sensitivities

Horizontal positioning of the sensitivity types labels

Vertical positioning of the sensitivity types labels

Sensitivity types labels

Label for spawning output or spawning biomass. By defaultit will be set to "SO" if any model has spawning output in numbers and "SB"if all models have spawning output in biomass. Subscripts will be addedfor 0 or current year.

Label for yield reference point.By default it will be set to something like "Yield(SPR=0.3)" where the SPRvalue is the SPR target. If the models have different SPR targets, it willbe set to "Yield(tgt SPR)".

Label for F reference point.By default it will be set to something like "F(SPR=0.3)" where the SPRvalue is the SPR target. If the models have different SPR targets, it willbe set to "F(tgt SPR)".

Directory with control file to change.

Control file name. Default="control.ss_new".

Name of new control file to be written.Default="control_modified.ss".

Line numbers of control file to be modified. Either this orthestrings argument are needed. Default=NULL.

Strings (with optional partial matching) indicating whichparameters to be modified. This is an alternative tolinenums.strings correspond to the commented parameter names included incontrol.ss_new, or whatever is written as comment at the endof the 14 number parameter lines. Default=NULL.

Vector of new parameter values. Default=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

If multiple parameter lines match criteria, repeat thenewvals input for each line.

Vector of new lower bounds. Default=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

Vector of new high bounds. Must be the same length as newhisDefault=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

Vector of new prior values.Default=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

Vector of new prior sd values.Default=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

Vector of new prior type.Default=NULL.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remainder parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

Optional vector or single value of TRUE/FALSE for whichparameters are to be estimated. Changes sign of phase to be positive ornegative. DefaultNULL causes no change to phase.

More detailed output to command line. Default=TRUE.

Vector of new phases. Can be a single value, which will berepeated for each parameter, the same length as newvals, where eachvalue corresponds to a single parameter, orNULL, where thephases will not be changed. If one wants to strictly turn parameterson or off and not change the phase in which they are estimated useestimate = TRUE orestimate = FALSE, respectively.The vector can containNA values, which will assign the originalvalue to the given parameter but change the remaining parameters, wherethe vector of values needs to be in the same order as eitherlinenums orstrings.

A list object created bySS_output().

Range of years from which to extract values

Vector of number of digits to round to in table for

• 1 catch

• 2 spawning output

• 3 fraction unfished (column is called "depl")

Directory where everything takes place.

Subdirectory withinmasterdir with existing modelfiles.

Subdirectory withinmasterdir where retrospectiveswill be run. Default is 'retrospectives'.

First part of the pattern of names for the directories inwhich the models will actually be run.

Vector of values to iteratively enter into the starter file forretrospective year. Should be zero or negative values.

Overwrite any input files with matching names in thesubdirectories where models will be run.

Executable file found in directory with model files.On Windows systems, this value will be automatically updated if a singleexecutable exists in the directory of model files. Input exefile=NULL ifthe executable is in your path and doesn't need copying.

Additional commands to use when running SS. Default = "-nox"will reduce the amount of command-line output.

Display runtime information from SS in the R console (vs.saving to a file).

Either "system" or "shell" (choice depends on how you're runningR. Default is "system".

Logical switch determining whether specifications ofblocks is removed from top of control file. Blocks can cause problems forretrospective analyses, but the method for removing them is overlysimplistic and probably won't work in most cases. Default=FALSE.

A list object created bySS_output().

Controls the amount of output to the screen. Default=FALSE.

A vector of 5 values for the starting points in theminimization. Default=NULL.

A method to apply to the 'optim' function. See ?optim foroptions. Default="BFGS". By default, optim is not used, and the optimizationis based on the inputaltmethod.

Make a two-panel plot showing devs as well as transformeduncertainty, or just the second panel in the set? Default=TRUE.

An experimental option to treat the transform the 5quantities to improve minimization. Doesn't work well. Default=FALSE.

Plot to active plot device?

Print to PNG files?

Directory where PNG files will be written. By default it willbe the directory where the model was run.

Include new estimated bias adjustment values on top of valuesused in the model? (TRUE/FALSE)

Optional name of existing control file to modify.Default=NULL.

Optional name of new control file to create from old file withestimated bias adjustment values. Default=NULL.

Optimization tool to use in place of optim, either "nlminb"or "psoptim". If not equal to either of these, then optim is used.

Exclude forecast values in the estimation ofalternative bias adjustment inputs?

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

Resolution of plots printed to files.The default isres = 300.

Character expansion for plot titles.The default iscex.main=1.

A list object created bySS_output().

Directory where PNG files are located.

CSV file with info on PNG files. By default, theplotdir directory will be searched for files with name beginning'plotInfoTable*'

Title for HTML page.

Width of plots (in pixels).

Automatically open index.html in default browser?

Override errors associated with plots from multiple modelruns. Only do this if you know what you're doing.

Add additional notes to home page.

Display more info while running this function?

A list object created bySS_output().

Directory where the text files containing the tables will be written.By default it will be the directory where the model was run.

the largest gradient value for estimated parameter; the default is 1E-3

Directory containing the Stock Synthesis model output.Forward slashes or double backslashes and quotes are necessary.This can also either be an absolute path or relative to the workingdirectory.

Optional directory containing MCMC output. This can either berelative todir, such thatfile.path(dir, dir.mcmc)will end up in the right place, or an absolute path.

Name of the big report file (could be renamed by user).

Name of the composition report file.

Name of the covariance output file.

Name of the forecast file.

Name of the file containing weight at age data.

Name of the file containing warnings.

The maximum number of columns in files being read in. If thisvalue is too big the function runs more slowly, too small and errors willoccur. A warning will be output to the R command line if the value is toosmall. It should be bigger than the maximum age + 10 and the number ofyears + 10. The default value isNULL, which finds the optimum width.

Read the forecast-report file?

Read the Warning.sso file?

Read covar.sso to get variance information and identify badcorrelations?

Read the weight-at-age file?

Check for bad correlations?

The specified threshold for defining high correlations. Aquantity with any correlation above this value is identified.

The specified threshold for defining low correlations. Onlyquantities with all correlations below this value are identified (to findvariables that appear too independent from the model results).

The maximum number of high correlations to print to theR GUI.

The maximum number of low correlations to print to the RGUI.

A logical value specifying if output should be printedto the screen.

Print summary statistics about the output to the R GUI?

Hides some warnings output from the R GUI.

Allow the function to work without a CompReport file.

The largest length bin range allowed for compositiondata to be considered as conditional age-at-length data.

File name of control file including path.

Alternative input of path, where file is assumed to be"control.ss_new". Default=NULL.

SS version number. Currently only "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).

TRUE/FALSE switch for amount of detail produced by function.Default=TRUE.

Should only active parameters (those with positive phase) beoutput? Default=FALSE.

A list object created bySS_output().

Plot sets to be created, see list of plots below. Use tospecify only those plot sets of interest, e.g., c(1,2,5,10). Plots for datanot available in the model run will automatically be skipped, whether calledor not.Current grouping of plots is as follows:

1. Biology

2. Selectivity and retention

3. Timeseries

4. Recruitment deviations

5. Recruitment bias adjustment

6. Spawner-recruit

7. Catch

8. SPR

9. Discards

10. Mean weight

11. Indices

12. Numbers at age

13. Length comp data

14. Age comp data

15. Conditional age-at-length data

16. Length comp fits

17. Age comp fits

18. Conditional age-at-length fits

19. Francis and Punt conditional age-at-length comp fits

20. Mean length-at-age and mean weight-at-age

21. Tags

22. Yield

23. Movement

24. Data range

25. Parameter distributions

26. Diagnostic tables

Deprecated input for backward compatibility, now replaced bypng = TRUE/FALSE.

Send plots to PDF file instead of R GUI?

Send plots to PNG files instead of R GUI?

RunSS_html() on completion? By default has samevalue aspng.

The sub-directory under 'dir' (see below) in which thePNG files will be located. The default sub-directory is "plots".The directory will be created if it doesn\'t exist.If 'printfolder' is set to "", it is ignored and the PNG files will be locatedin the directory specified by 'dir'.

The directory in which a PDF file (if requested) will be createdand within which the printfolder sub-directory (see above) will be createdif png=TRUE. By default it will be the same directory that the report filewas read from by theSS_output function. Alternatives to the defaultcan be either relative (to the working directory) or absolute paths.The function will attempt to create the directory it doesn't exist, but itdoes not do so recursively.

Either the string "all", or a vector of numerical values, likec(1,3), listing fleets or surveys for which plots should be made. Bydefault, plots will be made for all fleets and surveys. Default="all".

Either the string "all", or a vector of numerical values, likec(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 thefunction has not yet been updated for multi-area models). Default="all".

Either the string "default", or a vector of charactersstrings to use for each fleet name. Default="default".

Either the string "default", or a vector of colors to usefor each fleet. Default="default".

Vector of line types used for each fleet in some plots.Default=1.

Vector of point types used for each fleet in some plots.Default=1.

Line width for some plots. Default=1.

Either the string "default", or a vector of colors to usefor each area. Default="default".

Optional vector of names for each area used in titles.Default="default".

Return updates of function progress to the R GUI?Default=TRUE.

Include values in plots showing estimates of uncertainty(requires positive definite hessian in model? Default=TRUE.

Include forecast years in the timeseries plots andplots of time-varying quantities?

Plot the data by itself? This is useful in documentpreparation, but doesn't change across alternative model runs with the samedata, so can be committed to save time once the plots have been created once.Setting datplot=FALSE is equivalent to leaving off plots 15 and 16.Default=TRUE.

Plot the expected numbers at age bubble plots and mean-agetime series? Default=TRUE.

Show sample size plots? Default=TRUE.

Show residuals for composition plots?

Upper limit on ymax for polygon/histogram compositionplots. This avoids scaling all plots to have max=1 if there is a vectorwith only a single observed fish in it. Default=0.4.

Specify the F/SPR proxy target. Default=0.4.

Target %unfished to be used in plots showing %unfished. May beomitted by setting to NA.

Threshold depletion to be used in plots showing depletion.May be omitted by setting to NA.

This scalar defines the maximum bubble size for bubbleplots. This option is still available but a better choice is to usebub.scale.pearson and bub.scale.dat, which are allow the same scalingthroughout all plots.

Character expansion (cex) value for a proportion of1.0 in bubble plot of Pearson residuals. Default=1.5.

Character expansion (cex) value for a proportion of 1.0in bubble plot of composition data. Default=3.

This scalar defines the maximum bubble size fornumbers-at-age and numbers-at-length plots.

This scalar defines the maximum bubble size fortagging plots.

This defines the minimum number of years below which blankyears will be added to bubble plots to avoid cropping. Default=8.

Years to plot multi-panel conditional age-at-length fits forall length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking thefit of a dominant year class, critical time period, etc. Default=-1.

The length bin for which multi-panel plots of the fit toconditional age-at-length data will be produced for all years. Useful tosee if growth curves are ok, or to see the information on year classes movethrough the conditional data. Default=-1.

Plot the full set of conditional age-at-length Pearsonresiduals? Turn to FALSE if plots are taking too long and you don't wantthem.

The maximum value to include on plots of input and effectivesample size. Occasionally a calculation of effective N blows up to verylarge numbers, rendering it impossible to observe the relationship for otherdata. Default=5000.

Optional vector of birth years for cohorts for which toadd growth curves to numbers at length bubble plots. Default=c().

Add loess smoother to observed vs. expected index plots andinput vs. effective sample size? Default=TRUE.

Display sample sizes on composition plots? Default=TRUE.

Display effective sample sizes on composition plots?Default=TRUE.

show line for input sample sizes on top of conditionalage-at-length plots (TRUE/FALSE, still in development)

show line for effective sample sizes on top of conditionalage-at-length plots (TRUE/FALSE, still in development)

Display legends in various plots?

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Height of tall plots printed to png files in units ofpunits, where the tall plots are a subset of the plots which typicallywork best in a taller format.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

Resolution of plots printed to files.The default isres = 300.

Logical indicating if a title should be included at the top(not yet implemented for all plots)

Character expansion parameter for plot titles (not yetimplemented for all plots). Default=1.

Vector controlling which lines should be shown onselectivity plots if the model includes retention. Default=1:5.

Number of rows to use for single panel plots. Default=1.

Number of columns to use for single panel plots. Default=1.

Maximum number of rows to for multi-panel plots.

Maximum number of columns for multi-panel plots.

Maximum number of rows for conditional age-at-lengthmulti-panel plots.

Maximum number of rows for conditional age-at-lengthmulti-panel plots.

Number of rows of Andre's conditional age-at-length plotswithin each page.

Number of rows for tagging-related plots.

Number of columns for tagging-related plots.

Number of rows for parameter distribution plots.

Number of columns for parameter distribution plots.

Control whether multi-panel plots all have dimensions equalto maxrows by maxcols, or resized within those limits to fit number ofplots. Default=TRUE.

Open a new window or add to existing plot windows. Default=TRUE.

Size of right-hand margin in data plot (may be toosmall if fleet names are long)

Optional vector of character strings to be added to introHTML page (if created) with notes about the model.

Is catch input in numbers instead of biomass?Default=F.

show catch by fleet as barplot instead of stacked polygons(default=TRUE)

Location for all legends. Default="topleft".

First year to show in time-series and time-varying plots

Last year to show in time-series and time-varying plots. Thiscan either be an alternative to, or redundant with, the forecastplot input.

Which sexes to show in composition plots. Default="all".

Rescale expected and observed proportions in compositionplots by dividing by bin width for models where bins have different widths?Caution!: May not work correctly in all cases.

scale data-only bubbles by sample size, not justproportion within sample? Default=FALSE.

Either NULL to have default labels for timeseries plots ora vector of appropriate length (currently 11) with labels for each figure

Either NULL to have default labels for catch plots ora vector of appropriate length (currently 10) with labels for each figure

The size of the largest bubble in the datasizeplot. Default is 1.0.

Show MLE estimate and asymptotic variance estimate with bluelines in the parameter distribution plots?

Show posterior distribution as bar graph in parameterdistribution plots (requires MCMC results to be available inreplist)?

Show prior distribution as black line in the parameterdistribution plots?

Show initial value as red triangle in the parameterdistribution plots?

Include devs in the parameter distribution plots?

Fit range in parameter distribution plots tightly around MLEand posterior distributions instead of full parameter range?

Additional arguments that will be passed to some subfunctions.

Directory where input files and executable are located.

Source control file. Default = "control.ss_new"

Destination for new control files (must match entry instarter file). Default = "control_modified.ss".

Line number of parameter to be changed. Can be used insteadofstring or left as NULL. Can be a vector if you are profiling multipleparameters at the same time.

String partially matching name of parameter to be changed. Canbe used instead oflinenum or left as NULL. Can be a vector if you areprofiling multiple parameters at the same time.

Vector of values to profile over. If you are profileingover multiple parameters at the same time this should be a data.frame ormatrix with a column for each parameter.

Use PAR file from previous profile step for starting values?

Use global par file ("parfile_original_backup.sso", which isautomatically copied from originalparfile) for all runs insteadof the par file from each successive run

Name of par file to use (for 3.30 models, this needs toremain 'ss.par'). Whenglobalpar=TRUE, the backup copy of thisis used for all runs.

Line number in par file to change (if usepar = TRUE).Can be a vector if you are profiling multiple parameters at the same time.

String in par file preceding line number to change asan alternative to parlinenum (only needed if usepar = TRUE).Can be a vector if you are profiling multiple parameters at the same time.

Copy directories for each run? NOT IMPLEMENTED YET.

Delete exe files in each directory? NOT IMPLEMENTED YET.

Name of executable. Default = "ss".

Additional commands to use when running SS. Default = "-nox"will reduce the amount of command-line output.

Should R call SS using "system" function instead of "shell".This may be required when running R in Emacs. Default = FALSE.

Copy output .SSO files to unique names. Default = TRUE.

Overwrite any existing .SSO files. Default = TRUE. If FALSE,then some runs may be skipped.

Optional vector of run indices to do. This can be used tore-run a subset of the cases in situations where the function wasinterrupted or some runs fail to converge. Must be a subset of 1:n, where nis the length of profilevec.

SS version number. Currently "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).version = NULL is no longer the default or an allowed entry.The default isversion = "3.30".

Check to make sure the starter file is set to includethe prior likelihood contribution in the total likelihood. Default = TRUE.

Read the table of likelihoods from each model as it finishes.Default = TRUE. Changing to FALSE should allow the function to play througheven if something is wrong with reading the table.

Controls amount of info output to command line. Default =TRUE.

A file path to the directory of interest.Typically used withfile, an additional input argument,to specify input and output file paths.The default value isdir = NULL, which leads to usingthe current working directory, and thus, full file paths shouldnot be specified for other arguments as they will be appendedtodir.

A logical that controls if the.ss_new files orthe original input files are read in.The default is to read the original files.

A logical value specifying if output should be printedto the screen.

Filename either with full path or relative to working directory.

A logical value specifying if output should be printedto the screen.

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

SS version number. Currently "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).version = NULL is no longer the default or an allowed entry.The default isversion = "3.30".

Should there be verbose output while running the file?Defaults to FALSE.

Deprecated. Debugging tool (not fully implemented) of echoingblocks of values as it is being read.

LOGICAL. If TRUE, use datlist to derive parameters whichcan not be determined from control file. Defaults to TRUE.

list or character. If list, should be a list produced fromSS_writedat(). If character, should be the file name of an SS data file.

number of seasons in the model. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of spatial areas in the model. Default = 1. This information is notexplicitly available in control file and used only if ifuse_datlist = FALSE.

oldest age in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

Deprecated. Number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of population bins in the model. This information is also notexplicitly available in control file and this information is only required if length basedmaturity vector is directly supplied (Maturity option of 6). and used onlyifuse_datlist = FALSE.

Number of fishing fleets and surveys, for 3.30 models.

Number of fishing fleets, for 3.24 and lower version models.

Flag to indicate if 7 additional ageing error parameters tobe read set 1 (but in fact any non zero numeric in R) or TRUE to enable toread them 0 or FALSE to disable them. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

Number of surveys, for 3.24 and lower version models.

number of tag release group. Default =NA. This informationis not explicitly available control file and used only ifuse_datlist = FALSE. This information is only required if custom tagparameters is enabled (TG_custom=1)

Number of CPUE observations. Used only in control file 3.24syntax ifuse_datlist = FALSE.

Integer vector of fleets using the catch multiplieroption. Defaults to NULL and should be left as such if 1) the catchmultiplier option is not used for any fleet or 2)use_datlist = TRUE anddatlist is specified. Used only in control file 3.30 syntax ifuse_datlist = FALSE.

integer vector of fleets with predator mortality included.Predator mortality fleets are only available in v3.30.18 andhigher. Defaults to NULL and should be left as such if 1) predation mortalityis not used for any fleets; 2)use_datlist = TRUE anddatlist is specified;or 3) if comments in the control file should be used instead to determinethe the predM_fleets. Used only in control file 3.30 syntax ifuse_datlist = FALSE.

The number of catch fleets in the model (fleets of )type 1 or 2; not surveys). Used to set the number of survey parameters.Only used in control file 3.30 reading if tagging data is in the model anduse_datlist = FALSE.

Integer value of the number of parameter lines toread for equilibrium catch. Defaults to NULL, which means the function willattempt to figure out how many lines of equilibrium catch to read from thecontrol file comments. Used only in control file 3.30 syntax ifuse_datlist = FALSE.

Integer value of the number of Dirichlet-Multinomialparameters. Defaults to 0. Used only in control file 3.30 syntax ifuse_datlist = FALSE.

LOGICAL ifTRUE, which is the default,a column will be included in the output indicating parameter type.UsingTRUE can be useful, but causes problems forSS_writectl,and therefore is not recommended if you intend to write the listback out into a file.Used only in control file 3.24 syntax.

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Defaults to FALSE.

Deprecated. Debugging tool (not fully implemented) of echoingblocks of values as it is being read.

Deprecated. SS version number. Currently only "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).

LOGICAL if TRUE, use datlist to derive parameters whichcan not be determined from control file. Defaults to TRUE

list or character. if list : produced from SS_writedator character : file name of dat file.

number of seasons in the model. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of spatial areas in the model. Default = 1. This information is notexplicitly available in control file and used only if ifuse_datlist = FALSE.

oldest age in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

Deprecated. Number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of population bins in the model. This information is also notexplicitly available in control file and this information is only required if length basedmaturity vector is directly supplied (Maturity option of 6). and used onlyifuse_datlist = FALSE.

number of fisheries in the model. This information is also notexplicitly available in control file

number of survey fleets in the model. This information is also notexplicitly available in control file

Flag to indicate if 7 additional ageing error parameters tobe read set 1 (but in fact any non zero numeric in R) or TRUE to enable toread them 0 or FALSE to disable them. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of tag release group. Default =NA. This informationis not explicitly available control file and used only ifuse_datlist = FALSE. This information is only required if custom tagparameters is enabled (TG_custom=1)

numeric vector of length=Nfleet+Nsurveys containing numberof data points of each CPUE time series

include a column in the output indicating parameter type?(Can be useful, but causes problems for SS_writectl.) Defaults to FALSE.

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Defaults to FALSE.

Deprecated. Debugging tool (not fully implemented) of echoingblocks of values as it is being read.

Deprecated. SS version number. Currently only "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).

LOGICAL. If TRUE, use datlist to derive parameters whichcan not be determined from control file. Defaults to TRUE.

list or character. If list, should be a list produced fromSS_writedat(). If character, should be the file name of an SS data file.

number of seasons in the model. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of spatial areas in the model. Default = 1. This information is notexplicitly available in control file and used only if ifuse_datlist = FALSE.

oldest age in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

Deprecated. Number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of sexes in the model. This information is also notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of population bins in the model. This information is also notexplicitly available in control file and this information is only required if length basedmaturity vector is directly supplied (Maturity option of 6). and used onlyifuse_datlist = FALSE.

number of fishery and survey fleets in the model. This information is also notexplicitly available in control file

The number of catch fleets in the model (fleets of )type 1 or 2; not surveys). Used to set the number of survey parameters.Only used if tagging data is in the model anduse_datlist is FALSE.

Flag to indicate if 7 additional ageing error parameters tobe read set 1 (but in fact any non zero numeric in R) or TRUE to enable toread them 0 or FALSE to disable them. This information is notexplicitly available in control file and used only ifuse_datlist = FALSE.

number of tag release group. Default =NA. This informationis not explicitly available control file and used only ifuse_datlist = FALSE. This information is only required if custom tagparameters is enabled (TG_custom=1)

integer vector of fleets using the catch multiplieroption. Defaults to NULL and should be left as such if 1) the catchmultiplier option is not used for any fleets or 2) use_datlist = TRUE anddatlist is specified.

integer vector of fleets with predator mortality included.Predator mortality fleets are only available in v3.30.18 andhigher. Defaults to NULL and should be left as such if 1) predation mortalityis not used for any fleets; 2) use_datlist = TRUE and datlist is specified;or 3) if comments in the control file should be used instead to determinethe the predM_fleets.

Integer value of the number of parameter lines toread for equilibrium catch. Defaults to NULL, which means the function willattempt to figure out how many lines of equilibrium catch to read from thecontrol file comments.

Integer value of the number of Dirichlet multinomialparameters. Defaults to 0.

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

SS version number.Currently "2.00", "3.00", "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3). Ifversion is NULL, the version (3.24 or 3.30) will be looked for on the firstline of the file.

Should there be verbose output while running the file?Default=TRUE.

Debugging tool (not fully implemented) of echoing blocks ofdata as it is being read.

Which data set to read. Only applies for a data.ss_new filecreated by Stock Synthesis. Allows the choice of either expected values(section=2) or bootstrap data (section=3+). Leaving default of section=NULLwill read input data, (equivalent to section=1).

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Default=TRUE.

Debugging tool (not fully implemented) of echoing blocks ofdata as it is being read.

Which data set to read. Only applies for a data.ss_new filecreated by Stock Synthesis. Allows the choice of either expected values(section=2) or bootstrap data (section=3+). Leaving default of section=NULLwill read input data, (equivalent to section=1). ## needs to be added

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Default=TRUE.

Debugging tool (not fully implemented) of echoing blocks ofdata as it is being read.

Which data set to read. Only applies for a data.ss_new filecreated by Stock Synthesis. Allows the choice of either expected values(section=2) or bootstrap data (section=3+). Leaving default of section=NULLwill read input data, (equivalent to section=1).

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Default=TRUE.

Debugging tool (not fully implemented) of echoing blocks ofdata as it is being read.

Which data set to read. Only applies for a data.ss_new filecreated by Stock Synthesis. Allows the choice of either expected values(section=2) or bootstrap data (section=3+). Leaving default of section=NULLwill read input data, (equivalent to section=1).

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?Default=TRUE.

Debugging tool (not fully implemented) of echoing blocks ofdata as it is being read.

Which data set to read. Only applies for a data.ss_new filecreated by Stock Synthesis. Allows the choice of either expected values(section=2) or bootstrap data (section=3+). Leaving default of section=NULLwill read input data, (equivalent to section=1).

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Number of fleets (not required in 3.30).

Number of areas (not required in 3.30).

number of seasons (not required in 3.30).

SS version number. Currently "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).version = NULL is no longer the default or an allowed entry.The default isversion = "3.30".

Should the function continue even if Forecast = 0 or -1(at which point SS stops reading)?

Should there be verbose output while running the file?

Filename either with full path or relative to working directory.

list or character. If list, should be a list producedfromSS_writedat(). If character, should be the full file location of anSS data file.

list or character. If list, should be a list producedfromSS_writectl(). If character, should be the full file location of anSS control file.

Should there be verbose output while running the file?Default=TRUE.

Filename either with full path or relative to working directory.

list or character. If list, should be a list producedfromSS_writedat(). If character, should be the full file location of anSS data file.

list or character. If list, should be a list producedfromSS_writectl(). If character, should be the full file location of anSS control file.

Should there be verbose output while running the file?Default=TRUE.

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

Should there be verbose output while running the file?

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

A logical value specifying if output should be printedto the screen.

First year of the recdev vector.

Last year of the recdev vector.

Either NULL to read anew or an already read control file.Default=NULL.

Either NULL to generate anew or an already generated vectorof recdevs. Default=NULL.

Should the recdevs be rescaled to have mean = 0 and std.deviation = sigmaR? Default=TRUE.

Vector of years over which rescaling (if chosen) shouldoccur.

Directory where files are located. Default is to use the workingdirectory in use by R. Default="working_directory".

Name of control file to modify. Default="control.ss_new".

Name of new file to output modified control file.Default="control_modified.ss".

Verbose output to R command line? Default=TRUE.

Write new file? Default=TRUE.

Return contents ctl file as an object in the R workspace.Default=FALSE.

Replace the maximum bias adjustment fraction with anynon-NULL value. Default=NULL.

Directory containing the input file. By default the workingdirectory given by getwd() is used. Default="working_directory".

Directory into which the output file will be written.Default="working_directory".

File name of input data file to be split.Default="Data.SS_New".

File name of output data file. Default="BootData".

Append bootstrap number to the file name chosen inoutpattern? Default=F.

Provide richer command line info of function progress?Default=TRUE.

Replace blank lines with "#". Helps with running on linux.Default=TRUE.

Grab the maximum likelihood values from the second block inData.SS_New (instead of bootstrap values or copies of inputs)? Default=TRUE.

Grab the copy of the input values values from the first blockin Data.SS_New (instead of MLE or bootstrap values)? Default=F.

Notes to the top of the new file (comment indicator "#C" willbe added). Default="".

A list object created bySS_output().

Either the string 'all', or a vector of fleet numbers

Which type of tuning: 'none', 'Francis', 'MI', or 'DM'.The first option,none, will only return information about theFrancis and MI weights that are suggested.

Number of digits to round numbers to.

Write suggested tunings to a file saved to the disk calledsuggested_tunings.ss. This file name is currently hard coded and willbe saved indir.

The number of times to retune models. Defaults to 0,where only the tunings should be calculated and the model is not rerun. Notethat for DM, it will be assumed that 0 means not to run the model andspecifying 1 or greater will only run the model once (because DM is not aniterative retuning method).

Should the model be run before calculating the tunings?Defaults toFALSE. This run is not counted as an iteration forniters_tuning and will not be used ifoption = "DM".

The path to the model directory.

The name of the stock synthesis executable. This model isassumed to be either in the same folder as the model files (specified indir), or in the PATH ifexe_in_path = TRUE. This will not be used ifinit_run = FALSE andniters_tuning = 0.

logical. If TRUE, will look for exe in the PATH. If FALSE,will look for exe in the model folders. Default = FALSE.

Additional commands to use when running SS. Default = "-nox"will reduce the amount of command-line output. A commonly used option is"-nohess" to skip calculating the hessian (and asymptotic uncertainty).

Allow tuning values for Francis or MI > 1? Defaults toFALSE, which caps tuning values at 1.

A logical value specifying if output should be printedto the screen.

Additional arguments to pass torun_SS_models.

Directory with control file to change.

Control file name. Default="control.ss_new".

Name of new control file to be written.Default="control_modified.ss".

Keyword to use as reference for start of section onvariance adjustments

Optional table of new variance adjustment values

Optional vector of new variance adjustment values for a particular row

Which of the 6 rows to replace with 'newrow' if present?

Maximum number of columns to search among in 3.24 models(may need to increase from default if you have a huge number of fleets)

Maximum number of rows to search among in 3.30 models(may need to increase from default if you have a huge number of fleets)

Overwrite file if it exists?

SS version number. Currently "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).version = NULL is no longer the default or an allowed entry.The default isversion = "3.30".

TRUE/FALSE switch for amount of detail produced by function.Default=TRUE.

list created bySS_read()

A file path to the directory of interest.Typically used withfile, an additional input argument,to specify input and output file paths.The default value isdir = NULL, which leads to usingthe current working directory, and thus, full file paths shouldnot be specified for other arguments as they will be appendedtodir.

A logical value specifying if the existing file(s)should be overwritten. The default value isoverwrite = FALSE.

A logical value specifying if output should be printedto the screen.

List object created bySS_readdat().

Filename for where to write new control file.

SS version number. Currently "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).version = NULL is no longer the default or an allowed entry.The default isversion = "3.30".

Should existing files be overwritten? Defaults to FALSE.

Should there be verbose output while running the file?Defaults to FALSE.

List object created bySS_readctl().

Filename for where to write new data file.

Should existing files be overwritten? Default=FALSE.

Should there be verbose output while running the file?Defaults to FALSE.

Deprecated. number of season in the model. This information is notexplicitly available in control file

Deprecated. number of spatial areas in the model. This information is also notexplicitly available in control file

Deprecated. Flag to indicate if 7 additional ageing error parameters to be readset 1 (but in fact any non zero numeric in R) or TRUE to enable to read them 0 or FALSE (default)to disable them. This information is not explicitly available in control file, too.

List object created bySS_readctl().

Filename for where to write new data file.

Should existing files be overwritten? Default=FALSE.

Should there be verbose output while running the file?Defaults to FALSE.

List object created bySS_readdat()(or bySS_readdat_3.24() orSS_readdat_3.24())

Filename for where to write new data file.

SS version number. Currently only "3.24" or "3.30" are supported,either as character or numeric values (noting that numeric 3.30 = 3.3).

Should existing files be overwritten? Default=FALSE.

Speed up writing by writing length and age comps without aligningthe columns (by using write.table instead of print.data.frame)

Should there be verbose output while running the file?

List object created bySS_readdat().

Filename for where to write new data file.

Should existing files be overwritten? Default=FALSE.

Speed up writing by writing length and age comps without aligningthe columns (by using write.table instead of print.data.frame)

Should there be verbose output while running the file?

List object created bySS_readdat().

Filename for where to write new data file.

Should existing files be overwritten? Default=FALSE.

Speed up writing by writing length and age comps without aligningthe columns (by using write.table instead of print.data.frame)

Should there be verbose output while running the file?

List object created bySS_readforecast().

Directory for new forecast file. Default=NULL (workingdirectory).

Filename for new forecast file. Default="forecast.ss".

Should the function continue even if Forecast=0(at which point SS stops reading, and remaining elements in list may not beavailable, depending on settings used in SS_readforecast)

Should existing files be overwritten? Default=FALSE.

Should there be verbose output while running the file?Default=TRUE.

List object created bySS_readpar_3.24().

Filename for where to write new parameter file.

Should existing files be overwritten? Default=TRUE.

Should there be verbose output while running the file?

List object created bySS_readpar_3.30().

Filename for where to write new parameter file.

Should existing files be overwritten? Default=TRUE.

Should there be verbose output while running the file?

List object created bySS_readstarter().

Directory for new starter file. Default=NULL (working directory).

Filename for new starter file. Default="starter.ss".

Should existing files be overwritten? Default=FALSE.

Should there be verbose output while running the file?Default=TRUE.

Print warning if overwriting file?

Object created bySS_readwtatage().

A file path to the directory of interest.Typically used withfile, an additional input argument,to specify input and output file paths.The default value isdir = NULL, which leads to usingthe current working directory, and thus, full file paths shouldnot be specified for other arguments as they will be appendedtodir.

Filename for new weight-at-age file, whichwill be appended todir to create a full file path.Default="wtatage.ss".

A logical value specifying if the existing file(s)should be overwritten. The default value isoverwrite = FALSE.

A logical value specifying if output should be printedto the screen.

A logical value specifying if a warning should begenerated if overwritingfile.The default value iswarn = TRUE.

A list object created bySS_output().

The sub-directory under 'dir' (see below) in which thePNG files will be located. The default sub-directory is "plots".The directory will be created if it doesn not exist.If 'printfolder' is set to "", it is ignored and the PNG files willbe located in the directory specified by 'dir'.

The directory in which a PDF file (if requested) will be createdand within which the printfolder sub-directory (see above) will be createdif png=TRUE. By default it will be the same directory that the report filewas read from by theSS_output function. Alternatives to the defaultcan be either relative (to the working directory) or absolute paths.The function will attempt to create the directory it does not exist, but itdoes not do so recursively.

Either the string "default", or a vector of charactersstrings to use for each fleet name. Default="default".

The year to summarize selectivity, the default is the finalmodel yr strings to use for each fleet name. Default="default".

outputs from r4ss::SS_output() or r4ss::SSsummarize()

time steps behind yrs e.g. 0.25 for quarterly

last time step e.g. 2018.75 with a cpue observation

A list object created bySS_output().

Directory where the 'tables' directory will be created.The default is the dir location where the Report.sso file is located.

To calculate confidence intervals, default is set at 0.95

TRUE/FALSE switch to produce only the executive summary tableswill be produced, default is FALSE which will return all executive summarytables, historical catches, and numbers-at-ages

A vector of user-defined names providing a name for each fleet in the model.

Which tables to produce (default is everything). Note: sometables depend on calculations related to previous tables, so will failif requested on their own (e.g. Table 'f' can't be createdwithout also creating Table 'a')

This will allow the user to calculate single sex valuesbased on the new sex specification (-1) in SS for single sex models. Default value is FALSE.TRUE will divide by 2.

Optional input to choose a different ending year for tables(could be useful for catch-only updates)

Vector of adopted ofl values to be printed in the management performancetable. This should be a vector of 10 values.

Vector of adopted abc values to be printed in the management performancetable. This should be a vector of 10 values.

Vector of adopted acl values to be printed in the management performancetable. This should be a vector of 10 values.

Optional input vector for management adopted OFL values for table g. These valueswill be overwrite the OFL values in the projection table, rather than the model estimatedOFL values. Example input: c(1500, 1300)

Optional input vector for management adopted ABC values for table g. These valueswill be overwrite the ABC values in the projection table, rather than the model estimatedABC values. Example input: c(1500, 1300)

Logical. Option to control whether tables are formatted (e.g. commas added, CIs separated with "-"). Theformatting is intended to create tables that can be cut and pasted easily into a word document without additional formattingwork. If the tables are being used by LaTex/Markdown or other documenting software, having formatting turned on preventsthe tables from being formatted further since the objects are no longer numeric.

TRUE/FALSE switch on whether the low and high interval valuesin e_ReferencePoints_ES will be reported with the same number of decimal digitsas the estimate.

Return updates of function progress to the R console?

Directory containing MCMC output.

TRUE/FALSE switch to get more or less information about theprogress of the function.

Write key parameters and certainty nuisance quantities to aCSV file.

Name of file with parameter posteriors (default matches"posteriors.sso" used by SS, but the user could change the name)

Name of file with parameter posteriors (default matches"derived_posteriors.sso" used by SS, but the user could change the name)

First CSV file for key parameters.

Second CSV file for nuisance quantities.

Vector of strings that partially match parameter names towrite to the file csv1. This file intended to feed intomcmc.out().

Vector of strings that partially match derivedquantity names to write to the file csv2. This file intended to feed intomcmc.nuisance().

Optional burn-in value to apply on top of the option in thestarter file.

Optional thinning value to apply on top of the option in thestarter file and in the-mcsave runtime command.

A vector of strings that are appended to the output files fromeach model if models are all in one directory. Default=NULL.

A vector of directories (full path or relative to workingdirectory) in which model output is located. Default=NULL.

Choice to read or not read covar.sso output (saves time andmemory). Default=TRUE.

Choice to read or not read CompReport.sso output (saves timeand memory). Default=TRUE.

Choice to read or not read forecast quantities.Default=FALSE.

Print various messages to the command line as the functionruns? Default=TRUE.

Maximum number of columns in Report.sso (same input as forSS_output()). Default=210.

Save output from each model as a element of a list (i.e.make a list of lists). Default = TRUE.

Add an underscore '_' between any file names and any keysin keyvec. Default=FALSE.

Save each list of parsed output as a .Rdata file (with defaultfilenaming convention based on iteration and date stamp.

a matrix of natural mortality by year and age, starting with age 0

the first year of the natural mortality values (no missing years)

optional file to which the results will be written

if 'outfile' is provided and exists, option to overwrite or not

an indicator of whether the matrix has years in columns or rows

List created bySSsummarize. The expected order for themodels are the full reference model, the retro -1, retro -2, and so forth.

Single year or vector of years representing thefinal year of values to show for each model.

Single year used to calculate the start of the Wood's HoleMohn's Rho value across all years. Defaults to startyr of reference model.

Print messages when running the function?

A list object created bySS_output().

Switch set to either 1 for length at true age or2 for obs. age at true age

Optional input to choose which matrix (slice of the 3D-array)within $AAK or $ALK to plot. By default all slices will be shown.For ageing imprecision this should correspond to the ageing error matrixnumber. Distribution of length at age ($ALK) is ordered by season,sub-season, and then morph. A future version could allow subsetting plotsby these dimensions.

Multiplier for bars showing distribution. Species with many agesbenefit from expanded bars. NULL value causes function to attempt automaticscaling.

Add to existing plot

A character value specifying the color of the grid lines

The color of the filled polygons.

A numeric value specifying the amount to shift the top ofthe polygon up.

A numeric value specifying the amount to shift the bottomof the polygon up.

Plot to active plot device?

Print to PNG files?

Vector of labels for plots (titles and axis labels)

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

Point size for PNG file

Character expansion for plot titles

Logical indicating if a title should be included at the top

directory where PNG files will be written. by default it willbe the directory where the model was run.

A list object created bySS_output().

Plot to active plot device?

Print to PNG files?

add to existing plot

vector controlling which subplots to createNumbering of subplots is as follows:

• 1 growth curve only

• 2 growth curve with CV and SD

• 3 growth curve with maturity and weight

• 4 distribution of length at age (still in development)

• 5 length or wtatage matrix

• 6 maturity

• 7 fecundity from model parameters

• 8 fecundity at weight from BIOLOGY section

• 9 fecundity at length from BIOLOGY section

• 10 spawning output at length

• 11 spawning output at age

• 21 Natural mortality (if age-dependent)

• 22 Time-varying growth persp

• 23 Time-varying growth contour

• 24 plot time-series of any time-varying quantities (created if theMGparm_By_Year_after_adjustments table (report:7) is available in theReport.sso file)

• 31 hermaphroditism transition probability

• 32 hermaphroditism cumulative probability

Additional plots not created by default

• 101 diagram with labels showing female growth curve

• 102 diagram with labels showing female growth curve & male offsets

• 103 diagram with labels showing female CV = f(A) (offset type 2)

• 104 diagram with labels showing female CV = f(A) & male offset (type 2)

• 105 diagram with labels showing female CV = f(A) (offset type 3)

• 106 diagram with labels showing female CV = f(A) & male offset (type 3)

which season to plot (values other than 1 only work inseasonal models but but maybe not fully implemented)

Which morphs to plot (if more than 1 per sex)? By default thiswill bereplist[["mainmorphs"]]

Include forecast years in plots of time-varying biology?

optional input for minimum year to show in plots

optional input for maximum year to show in plots

vector of length 3 with colors for various points/lines

vector of length 2 with lty for females/males in growth plotsvalues can be applied to other plots in the future

Transparency parameter used to make default shadecolvalues (see ?rgb for more info)

Whether to add numerical text to the image plotswhen using weight at age. Defaults to FALSE.

The number of significant digits to whichthe image plot text is rounded. Defaults to 0, meaning whole numbers. Ifall your values are small and there's no contrast in the text, you mightwant to make this 1 or 2.

Location of legend (see ?legend for more info)

Directory where PNG files will be written. by default it willbe the directory where the model was run.

Vector of labels for plots (titles and axis labels)

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

Point size for PNG file

Character expansion for plot titles

Logical indicating if a title should be included at the top

Return updates of function progress to the R GUI?

A list object created bySS_output().

Vector controlling which subplots to createNumbering of subplots is as follows,

Basic plots for all models

• 1 landings

• 2 landings stacked

• 3 observed and expected landings (if different)

• 9 harvest rate

Plots for models with discards

• 4 total catch (including discards)

• 5 total catch (including discards) stacked

• 6 discards

• 7 discards stacked plot (depends on multiple fleets)

• 8 discard fraction

• 16 landings + dead discards

Plots for seasonal models

• 10 landings aggregated across seasons

• 11 landings aggregated across seasons stacked

• 12 total catch (if discards present) aggregated across seasons

• 13 total catch (if discards present) aggregated across seasons stacked

• 14 discards aggregated across seasons

• 15 discards aggregated across seasons stacked

Add to existing plot? (not yet implemented)

Optional subset of areas to plot for spatial models

Plot to active plot device?

Print to PNG files?

Type parameter passed to plot function. Default "l" is linesonly. Other options include "o" for overplotting points on lines.

Vector of line type by fleet

Vector of plot character by fleet

Vector of colors by fleet

Optional replacement for fleenames used in data file,should include all fleets (not just those with catch)

Line width

Vector of colors by area. Default uses rich.colors by ArniMagnusson

Names for areas. Default is to use Area1, Area2,...

Optional input for minimum year to show in plots

Optional input for maximum year to show in plots

Include plot of catch aggregated across seasons withineach year

Add points from forecast years

Directory where PNG or PDF files will be written. By defaultit will be the directory where the model was run.

Put legend on plot

Location of legend (see ?legend for more info)

Optional input to change the order of fleets in stacked plots.

x-label for all plots

Vector of labels for plots (titles and axis labels)

Is catch in numbers instead of biomass? Should be setautomatically if set to NULL. If fleets include a mix of biomass andnumbers, then catch plots should be interpreted carefully.

Show catch by fleet as barplot instead of stacked polygons?(default=TRUE)

Add a point on the y-axis for the maximum catch (default=TRUE)

Optional input for ymax value (can be used to add or subtractwhite space at the top of the figure)

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

Character expansion for plot titles

Report progress to R console?

A list object created bySS_output().

Vector controlling which subplots to create

Add to existing plot? (not yet implemented)

Plot to active plot device?

Print to PNG files?

Vector of colors to show for each cohort. Default is rangeof colors shade indicating time period.

What fraction of the cohorts to include in plot. If value< 1 is used, then cohorts are filtered to only include those with thehighest maximum cumulative catch. Value will be overridden bycohortvec.

Optional vector of birth years for cohorts to include inplot. Value overridescohortfrac.

What fraction of the cohorts to label in plot. Bydefault, top 10% of cohorts are labeled. Value will be overridden bycohortlabvec.

Optional vector of birth years for cohorts to label inplot. Value overridescohortlabfrac.

Line width

Directory where PNG or PDF files will be written. By defaultit will be the directory where the model was run.

x-label for all plots

Vector of labels for plots (titles and axis labels)

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

Character expansion for plot titles (no titles in thisfunction yet)

Report progress to R console?

List created bySSsummarize

Vector of subplots to be createdNumbering of subplots is as follows:

• 1 spawning biomass

• 2 spawning biomass with uncertainty intervals

• 3 biomass ratio (hopefully equal to fraction of unfished)

• 4 biomass ratio with uncertainty

• 5 SPR ratio

• 6 SPR ratio with uncertainty

• 7 F value

• 8 F value with uncertainty

• 9 recruits

• 10 recruits with uncertainty

• 11 recruit devs

• 12 recruit devs with uncertainty

• 13 index fits

• 14 index fits on a log scale

• 15 phase plot

• 16 densities

• 17 cumulative densities

Plot to active plot device?

Send plots to PNG files in directory specified byplotdir?

Has same result asprint, included for consistency withSS_plots.

Write output to PDF file? Can't be used in conjunction withpng orprint.

Optional subset of the models described insummaryoutput. Either "all" or a vector of numbers indicatingcolumns in summary tables.

Optional single year or vector of years representing thefinal year of values to show for each model. By default it is set to theending year specified in each model.

Fleet numbers for each model to compareindices of abundance. Can take different forms:

• NULL: (default) create a separate plot for each index as long as the fleetnumbering is the same across all models.

• integer: create a single comparison plot for the chosen index

• vector of length equal to number of models: a single fleet numberfor each model to be compared in a single plot

• list: list of fleet numbers associated with indices within eachmodel to be compared, where the list elements are each a vector of thesame length but the names of the list elements don't matter and can beabsent.

Show uncertainty intervals on index data?Default=FALSE because if models have any extra standard deviations added,these intervals may differ across models.

Add catchability to legend in plot of index fits(TRUE/FALSE)?

Number of significant digits for catchability in legend(ifindexQlabel = TRUE)

Optional replacement for the SE values insummaryoutput[["indices"]] to deal with the issue of differing uncertainty bymodels described above.

TRUE plots the observed index for each model withcolors, or FALSE just plots observed once in black dots.

Vector of labels for plots (titles and axis labels)

Optional vector of colors to be used for lines. Input NULLmakes use ofrich.colors.short function.

Optional vector of colors to be used for shading uncertaintyintervals. The default (NULL) is to use the same colors provided bycol (either the default or a user-chosen input) and make themmore transparent by applying theshadealpha input as an alphatransparency value (using theadjustcolor() function)

Optional vector of plot character values

Optional vector of line types

Optional vector of line widths

Number of years between points shown on top of lines (forlong timeseries, points every year get mashed together)

Number of years to stagger the first point (ifspacepoints > 1) for each line (so that adjacent lines have points indifferent years)

Year value for first point to be added to lines.Points added to plots are those that satisfy(Yr-initpoint)%%spacepoints == (staggerpoints*iline)%%spacepoints

TRUE/FALSE switch to turn on/off extra axis mark at finalyear in timeseries plots.

TRUE/FALSE switch to turn on off shading of years beyondthe maximum ending year of the models

Optional x limits

Multiplier for ylim parameter. Allows additional white spaceto fit legend if necessary. Default=1.05.

Choice of xaxs parameter (see ?par for more info)

Choice of yaxs parameter (see ?par for more info)

Type parameter passed to points (default 'o' overplots points ontop of lines)

Show plots with uncertainty intervals? Either a singleTRUE/FALSE value, or a vector of TRUE/FALSE values for each model,or a set of integers corresponding to the choice of models.

Transparency adjustment used to make default shadecolvalues (implemented asadjustcolor(col=col, alpha.f=shadealpha))

Add a legend?

Optional vector of labels to include in legend. Defaultis 'model1','model2',etc.

Location of legend. Either a string like "topleft" or avector of two numeric values representing the fraction of the maximum inthe x and y dimensions, respectively. Seehelp("legend") for more info onthe string options.

Optional vector of model numbers that can be used to havethe legend display the model names in an order that is different than thatwhich is represented in the summary input object.

Number of columns for the legend.

Target value for SPR-ratio where line is drawn in the SPRplots and phase plot.

Target biomass value at which to show a line (set to 0 toremove)

Minimum biomass threshold at which to show a line (set to0 to remove)

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Resolution of plots printed to files.The default isres = 300.

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

Directory where PNG or PDF files will be written. By defaultit will be the directory where the model was run.

Additional text to append to PNG or PDF file names.It will be separated from default name by an underscore.

Vector of names (or subset of names) of parameters orderived quantities contained insummaryoutput[["pars"]][["Label"]] orsummaryoutput[["quants"]][["Label"]] for which to make density plots

Optional vector of x-axis labels to use in the densityplots (must be equal in length to the printed vector of quantities thatmatch thedensitynames input)

TRUE/FALSE control of automatic rescaling of units intothousands, millions, or billions

Scalar for upper x-limit in density plots (values below1 will cut off the right tail to provide better contrast among narrowerdistributions

Scalar for upper y-limit in density plots (values below1 will cut off top of highest peaks to provide better contrast among broaderdistributions

Multiplier on bandwidth of kernel in density functionused for smoothing MCMC posteriors. See 'adjust' in ?density for details.

Add symbols along lines in density plots. Quantilesarec(0.025,0.1,0.25,0.5,0.75,0.9,0.975).

Shade tails outside of 95% interval darker indensity plots?

Shade middle inside of 95% interval darker indensity plots?

Line width for density plots

Always include 0 in the density plots?

Create new empty plot window

Allows single plot to be added to existing figure. This needs tobe combined with specific 'subplots' input to make sure only one thing getsadded.

list of graphics parameter values passed to theparfunction

Report progress to R GUI?

Vector of TRUE/FALSE values (or single value) indicatingwhether input values are from MCMC or to use normal distribution aroundMLE

Whether to show the equilibrium values forSSB. For some model comparisons, these might not be comparable and thususeful to turn off. Defaults to TRUE.

A list object created bySS_output().

vector controlling which subplots to createNumbering of subplots is as follows, where subplots 21 to 24(aggregated across years) are provided first, and subplots1 to 10 are all repeated for each fleet

• 1 index data by fleet

• 1 multi-panel composition plot

• 2 single panel bubble plot for numbers at length or age

• 3 multi-panel bubble plots for conditional age-at-length

• 4 multi-panel plot of fit to conditional age-at-length for specific years

• 5 Pearson residuals for A-L key

• 6 multi-panel plot of point and line fit to conditionalage-at-length for specific length bins

• 7 sample size plot

• 8 TA1.8 Francis weighting plot

• 9 TA1.8 Francis weighting plot for conditional data

• 10 Andre's mean age and std. dev. in conditional AAL

• 21 composition by fleet aggregating across years

• 22 composition by fleet aggregating across years within each season

• 23 composition by fleet aggregating across seasons within a year

• 24 bubble plot comparison of length or age residuals

indicator of type of plot can be "LEN", "SIZE", "AGE", "cond","GSTAGE", "GSTLEN", "L@A", or "W@A".

if kind = "SIZE" then this switch chooses which of thegeneralized size bin methods will be plotted.

Years to plot multi-panel conditional age-at-length fits forall length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking thefit of a dominant year class, critical time period, etc. Default=-1.

The length bin for which multi-panel plots of the fit toconditional age-at-length data will be produced for all years. Useful tosee if growth curves are ok, or to see the information on year classes movethrough the conditional data. Default=-1.

plot to active plot device?

print to PNG files?

optional vector to subset fleets for which plots will be made

optional vector of fleet names to put in the labels

which sexes to show plots for. Default="all" which will includemales, females, and unsexed. This option is not fully implemented for allplots.

upper limit on ymax for polygon/histogram composition plots

make plots of data without fits?

make sample size plots?

make plots of residuals for fit to composition data?

make bubble plot for numbers at age or size?

Add labels for years to sample size plots?

add sample sizes to plot

add effective sample sizes to plot

separate plots of aggregates across yearsinto different plots for each market category (retained, discarded)?

show line for input sample sizes on top of conditionalage-at-length plots (TRUE/FALSE, still in development)

show line for effective sample sizes on top of conditionalage-at-length plots (TRUE/FALSE, still in development)

number of unique x values before adding buffer. see?bubble3 for more info.

This scalar defines the maximum bubble size for bubbleplots. This option is still available but a better choice is to use cexZ1which allow the same scaling throughout all plots.

scale data-only bubbles by sample size, not justproportion within sample? Default=FALSE.

Character expansion (cex) for point associated with value of 1.

Add legend with example bubble sizes to bubble plots.

Vector of length 3 with colors for females, males, unsexed fish

Color for lines on top of polygons

label style (las) input for x-axis. Default 0 has horizontallabels, input 2 would provide vertical lables.

label style (las) input for y-axis. Default NULL has horizontallabels when all labels have fewer than 6 characters and vertical otherwise.Input 0 would force vertical labels, and 1 would force horizontal.

optional position of bottom axis values

optional position of left size axis values

optional vector of labels for axis1 (either NULL or needs tomatch length of axis1)

Vector of size bin labels corresponding to the generalizedsize frequency method

What color to use for males in bubble plots (default is slightlytransparent blue)

What color to use for females in bubble plots (default is slightlytransparent red)

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

Resolution of plots printed to files.The default isres = 300.

directory where PNG files will be written. by default it willbe the directory where the model was run.

character expansion parameter for plot titles

should lines be added before points (linepos=1) or after(linepos=2)?

show fit to bars instead of points

scale bubbles based on sqrt of size vector. see ?bubble3 formore info.

add loess smoother to observed vs. expected index plots andinput vs. effective sample size?

optional vector of birth years for cohorts for which toadd growth curves to numbers at length bubble plots

vector of labels for plots (titles and axis labels)

show market categories in plot titles?

show sex in plot titles?

maximum (or fixed) number or rows of panels in the plot

maximum (or fixed) number or columns of panels in the plot

maximum number of rows for conditional age at length plots

maximum number of columns for conditional age at lengthplots

number or rows to return to as default for next plots to come orfor single plots

number or cols to return to as default for next plots to come orfor single plots

Outer margins passed to Andre's multi-panel conditionalage-at-length plots.

Number of rows of Andre's conditional age-at-length plotswithin each page. Default=3.

fix the dimensions at maxrows by maxcols or resize based onnumber of years of data

fix the dimensions at maxrows by maxcols in aggregate plotsor resize based on number of fleets

the maximum value to include on plots of input and effectivesample size. Occasionally a calculation of effective N blows up to verylarge numbers, rendering it impossible to observe the relationship for otherdata. Default=5000.

return updates of function progress to the R GUI?

Rescale expected and observed proportions by dividing bybin width for models where bins have different widths? Caution!: May notwork correctly in all cases.

Add parameter means in addition to medians for MCMCposterior distributions in which the median and mean differ.

Logical indicating if a title for the plot should be produced

additional arguments that will be passed tothepar command in themake_multifig() function.

A list object created bySS_output().

plot to active plot device?

print to PNG files?

directory where PNG files will be written. by default it willbe the directory where the model was run.

vector controlling which subplots to createCurrently there are only 2 subplots:

• 1 equal size points showing presence/absence of data type by year/fleet

• 2 points scaled to indicate quantity or precision of data

Either the string "default", or a vector of colors to usefor each fleet. If tagging data is included, an additional color needs to beadded for the tag releases which are not assigned to a fleet.

Either the string "all", or a vector including some subsetof the following: "catch", "cpue", "lendbase", "sizedbase", "agedbase","condbase", "ghostagedbase", "ghostcondbase", "ghostlendbase", "ladbase","wadbase", "mnwgt", "discard", "tagrelease", and "tagdbase1".

Either the string "all", or a vector of numerical values, likec(1,3), listing fleets or surveys to be included in the plot.

A vector of alternative names to use in the plot. Bydefault the parameter names in the data file are used.

TRUE/FALSE indicator for whether to show presence ofcomposition data from ghost fleets (data for which the fit is shown, but isnot included in the likelihood calculations).

width of plot

height of plot

units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

character expansion for plot titles

margins of plot (passed to par() function), which may need tobe increased if fleet names run off right-hand margin

Character expansion for points showing isolated years of data

Line width for lines showing ranges of years of data

The size (cex) of the largest bubble in the datasizeplot. Default is 1.

The transparency of the bubbles in the datasizeplot. Defaults to 1 (no transparency). Useful for models with lots ofoverlapping points.

TRUE/FALSE switch to turn on/off the title on the plot.

report progress to R GUI?

A list object created bySS_output().

Vector of which plots to make (1 = data only, 2 = with fit).Ifplotdat = FALSE then subplot 1 is not created, regardless ofchoice ofsubplots.

Plot to active plot device?

Print to PNG files?

Directory where PNG files will be written. by default it willbe the directory where the model was run.

Optional vector to subset fleets for which plots will be made

Optional replacement for fleenames used in data file

Make data-only plot of discards? This can override the choiceofsubplots.

Vector of labels for plots (titles and axis labels)

Maximum y-value which will always be included in the plot(all data included regardless). Default = 1 so that discard fractions are alwaysplotted on a 0-1 range, but total discard amounts which are greater than this valuewill exceed it.

Optional maximum y-value to include (useful if upper tails ondiscard amounts are very high)

First color to use in plot (for expected values)

Second color to use in plot (for observations and intervals)

Width of plot

Height of plot

Units for PNG file

Resolution of plots printed to files.The default isres = 300.

Point size for PNG file

Character expansion for plot titles

Report progress to R GUI?

A list object created bySS_output().

Y-axis label. Default is "Spawning biomass (mt)" which is replacedby "Spawning output" for models withreplist[["SpawnOutputUnits"]] == "numbers"

Show equilibrium in plot? Applies whether "yrs" is specifiedor not.

Show forecast years in plot? Only applies if yrs = "all".

Which years to include. Default "all" will show startyr to endyr + 1modified by the argumentsforecast.

Plot to active plot device?

Print to PNG files?

Directory where PNG files will be written. By default it willbe the directory where the model was run.

A logical value specifying if output should be printedto the screen.

Show 95% uncertainty intervals around point estimates?These intervals will only appear when uncertainty in the dynamic B0estimates is available via the control file settings for"read specs for more stddev reporting".

Add a legend?

Character vector with labels for the unfishedequilibrium point (ifequilibrium = TRUE) and the two lines showingspawning biomass or output without and with fishing.

Location of legend. Either a string like "topleft" or avector of two numeric values representing the fraction of the maximum inthe x and y dimensions, respectively. Seehelp("legend") for more info onthe string options.

Optional vector of colors to be used for the two lines(single value will apply to both lines).

Optional vector of line types to be used for the two lines(single value will apply to both lines).

Optional vector of line widths to be used for the two lines(single value will apply to both lines).

add to existing plot

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Resolution of plots printed to files.The default isres = 300.

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

Logical indicating if a title should be included at the top(not yet implemented for all plots)

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 topar().

A list object created bySS_output().

vector controlling which subplots to createNumbering of subplots is as follows, where subplot 9 (comparison of all indices) isprovided first:

• 1 index data by fleet

• 2 index data with fit by fleet

• 3 observed vs expected index values with smoother

• 4 index data by fleet on a log scale (lognormal error only)

• 5 index data with fit by fleet on a log scale (lognormal error only)

• 6 log(observed) vs log(expected) with smoother (lognormal error only)

• 7 time series of time-varying catchability (only if actually time-varying)

• 8 catchability vs. vulnerable biomass (if catchability is not constant)

• 9 comparison of all indices

• 10 index residuals based on total uncertainty

• 11 index residuals based on input uncertainty (not currently provided)

• 12 index deviations (independent of index uncertainty)

plot to active plot device?

print to PNG files?

optional vector to subset fleets for which plots will be made

optional replacement for fleenames used in data file

add smoothed line to plots of observed vs. expected samplesizes

add to existing plot (not yet implemented)

make plot of data only?

vector of labels for plots (titles and axis labels)

vector of colors for all fleets (including thosewith no index data)

vector of colors for points in each season for time series plot.Default is red for single season models and a rainbow using therich.colors.short function for multiple seasons.

vector of colors for points in each season for obs. vs. exp.plot. Default is blue for single season models and a rainbow using therich.colors.short function for multiple seasons.

color of line showing expected index in time series plot.Default is blue.

color of smoother shown in obs. vs. exp. plots. Default is red.

single value or vector of plotting characters (pch parameter)for time-series plots of index fit. Default=21.

single value or vector of plotting characters (pch parameter)for sample size plots of index fit. Default=16.

character expansion factor for points showing observed values.Default=1.

Background color for points with pch=21.

add a legend to seasonal colors (only for seasonal models)

add a legend to seasonal colors (default is "topright")

optional vector of names for each season to replacedefaults if a legend is used

width of plot

height of plot

units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

character expansion for plot titles

switch which allows the plot title to be left off

directory where PNG files will be written. by default it willbe the directory where the model was run.

First year to show in plot (for zooming in on a subset ofvalues)

Last year to show in plot (for zooming in on a subset ofvalues)

Maximum allowed value for ymax (specifiedas ratio of y), which overrides anyvalue of ymax that is greater (default = Inf)

Switch controlling whether to add thickeruncertainty interval lines indicating the input uncertainty relative tothe total uncertainty which may result from estimating a parameter forextra standard deviations. This is only added for the plots with indexfit included (the data-only plots only show the input uncertainty).

report progress to R GUI?

Extra arguments to pass to calls toplot

A data frame containing either derived_posteriors.sso or a goodsubset of it. This can be an element of the list created by the theSSgetMCMC() function.

TRUE/FALSE option to add results to an existing plot.

Number of sexes in the model (should match model values but isonly used in the title).

Optional adjustment to the x values to avoid overlap ofintervals when overplotting on an existing plot.

Optional input to make the title better. Default will besomething like "Fleet 1", using the numbering from the model.

Color for points and lines.

A list object created bySS_output().

Vector of which plots to make (1 = data only, 2 = with fit).Ifplotdat = FALSE then subplot 1 is not created, regardless ofchoice ofsubplots.

Optional input to override default ymax value.

plot to active plot device?

print to PNG files?

optional vector to subset fleets for which plots will be made

optional replacement for fleenames used in data file

Make data-only plot of discards? This can override the choiceofsubplots.

vector of labels for plots (titles and axis labels)

first color to use in plot (for expected values)

second color to use in plot (for observations and intervals)

width of plot

height of plot

units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

character expansion for plot titles

directory where PNG files will be written. by default it willbe the directory where the model was run.

report progress to R GUI?

A list object created bySS_output().

range of longitude values in the map

range of latitude values in the map

a list of data frames, each with two columns representingthe longitude and latitude values of the colored polygons. The order ofelements in the list should match the numbering of areas in the SS model.

vector of colors for each polygon (ifreplist isprovided)

color of landmasses in the map

data frame of latitude and longitude values which will beconnected by the arrows representing movement rates. The order should matchthe order of areas inpolygonlist and in the SS model. Not necessaryif no arrows are shown on the map.

age for which movement rates will be represented

season for which movement rates will be represented

scaling factor for arrows in the plot. The largest rate ofmovement shown will be scaled to have a line width equal to this value.

add a legend to show the movement rate associated with thewidest arrows

optional title to be added above map

optional vector of names to be shown on map at coordinatesmatching xytable values

character expansion to apply to text shown by areanames (if used)

A list object created bySS_output().

plot to active plot device?

print to PNG files?

which subplots to create.

where to put the plots (uses model directory by default)

vector of colors for each movement rate in the plot

optional input for y range of the plot. By default plot rangesfrom 0 to 10% above highest movement rate (not including fish staying in anarea).

add a legend designating which color goes with which pair ofareas?

location passed to legend function (if used)

choice of season for which movement rates are shown

Minimum age of movement (in future will come from Report file)

width of plot

height of plot

units for PNG file

Resolution of plots printed to files.The default isres = 300.

point size for PNG file

Character expansion parameter for plot titles

Print information on function progress.

A list object created bySS_output().

vector controlling which subplots to createNumbering of subplots is as follows,

• 1: Expected numbers at age

• 2: Mean age in the population

• 3: Fraction female in numbers at age

• 4: Equilibrium age distribution

• 5: Ageing imprecision: SD of observed age (plot using image() formerlyincluded in this group but now replaced by better distribution plots)

• 6: Expected numbers at length

• 7: Mean length in the population

• 8: Fraction female in numbers at length

• 9: no plot yet

• 10: Distribution of observed age at true age by ageing error type

plot to active plot device?

print to PNG files?

Units for numbers. Default (based on typical Stock Synthesissetup) is thousands (numbers.unit=1000).

optional subset of areas to plot for spatial models

names for areas. Default is to use Area1, Area2,...

vector of colors by area

maximum bubble size for bubble plots; each plot scaledindependently based on this maximum size and the values plotted. Often someplots look better with one value and others with a larger or smaller value.Default=2.6

background color for bubbles(no control over black border at this time)

Add legend with example bubble sizes?

indicator of whether to make plots using numbers at age justfrom the beginning ("B") or middle of the year ("M") (new option startingwith SSv3.11)

add lines for mean age or length on top of bubble plots

add to existing plot? (not yet implemented)

vector of labels for plots (titles and axis labels)

Default width of plots printed to files in units ofpunits. The default ispwidth=6.5.

Height of plots printed to png files in units ofpunits.Default is designed to allow two plots per page, withpheight_tall usedfor plots that work best with a taller format and a single plot per page.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).The default ispunits="in".

Resolution of plots printed to files.The default isres = 300.

Point size for plotted text in plots printed to files (seehelp("png") in R for details).

character expansion for plot titles

directory where PNG files will be written. by default it willbe the directory where the model was run.

Logical indicating if a title should be included at the top

report progress to R GUI?

A list object created bySS_output().

A path to the folder where the plots will be saved. The defaultisNULL, which leads to the plots being created in the folder thatcontains the results.

Label on horizontal axis.

Label on vertical axis.

Show MLE estimate and asymptotic variance estimate with bluelines?

Show posterior distribution as bar graph if MCMC resultsare available inreplist?

Show prior distribution as black line?

Show initial value as red triangle?

Include devs in the plot?

Show the legend?

Fit range tightly around MLE & posterior distributions,instead of full parameter range?

Parameter input for x-axis. See?par for more info.

Optional x-axis limits to be applied to all plots.Otherwise, limits are based on the model results.

Optional y-axis limits to be applied to all plots.Otherwise, limits are based on the model results.

Controls amount of text output (maybe).

Provide additional messages to help with debugging when thefunction fails.

How many rows in multi-figure plot.

How many columns in multi-figure plot.

Vector of line types used for lines showing MLE and priordistributions and the median of the posterior distribution.

Vector of colors used for lines and polygons showing MLE,initial value, prior, posterior, and median of the posterior.

Add to existing plot?

Plot to active plot device?

Print to PNG files?

Default width of plots printed to files in units ofpunits. Default=7.

Default height width of plots printed to files in units ofpunits. Default=7.

Units forpwidth andpheight. Can be "px"(pixels), "in" (inches), "cm" or "mm". Default="in".

Point size for plotted text in plots printed to files (seehelp("png") in R for details). Default=12.

Resolution of plots printed to files.The default isres = 300.

Subset parameters included in the plot using substring fromparameter names (i.e. "SR" will get "SR_LN(R0)" and "SR_steep" if they are bothestimated quantities in this model).

Should strings input match parameter names exactly? Otherwisesubstrings are allowed.

Optional vector of headers for each panel to replace theparameter names.

List created by the functionSSsummarize().

Plot to active plot device?

Print to PNG files?

Optional subset of the models described insummaryoutput. Either "all" or a vector of numbers indicatingcolumns in summary tables.

Character string used to find parameter over which theprofile was conducted. Ifexact=FALSE, this can be a substring ofone of the SS parameter labels found in the Report.sso file.For instance, the default input 'steep'matches the parameter 'SR_BH_steep'. Ifexact=TRUE, thenprofile.string needs to be an exact match to the parameter label.

Label for x-axis describing the parameter over whichthe profile was conducted.

Should theprofile.string have to match the parameterlabel exactly, or is a substring OK.

Label for y-axis. Default is "Change in -log-likelihood".

Vector of likelihood components that may be included inplot. List is further refined by any components that are not present inmodel or have little change over range of profile (based on limitminfraction). Hopefully this doesn't need to be changed.