SSv3_plots {r4ss}R Documentation

function to plot many quantities related to output from Stock Synthesis

Description

Creates a user-chosen set of plots, including biological quantities, time series, and fits to data. Plots are sent to R GUI, single PDF file, or multiple PNG files.

Usage

SSv3_plots(replist = "ReportObject", plot = 1:24, print = 0, pdf = F,
printfolder = "", dir = "default", fleets = "all", areas = "all",
fleetnames = "default", fleetcols = "default", fleetlty = 1,
fleetpch = 1, lwd = 1, areacols = "default", areanames = "default",
verbose = T, uncertainty = T, forecastplot = F, datplot = F,
Natageplot = T, samplesizeplots = T, compresidplots = T, sprtarg = 0.4,
btarg = 0.4, minbthresh = 0.25, pntscalar = 2.6, minnbubble = 8,
aalyear = -1, aalbin = -1, aalmaxbinrange = 0, aalresids = F,
maxneff = 5000, cohortlines = c(), smooth = T, showsampsize = T,
showeffN = T, showlegend = T, pwidth = 7, pheight = 7, punits = "in",
ptsize = 12, res = 300, cex.main = 1, selexlines = 1:5,
rows = 1, cols = 1, maxrows = 6, maxcols = 6,
maxrows2 = 2, maxcols2 = 4, tagrows = 3, tagcols = 3,
fixdims = T, new = T, catchasnumbers = F, legendloc = "topleft", ...)

Arguments

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

Details

List of plot groups

  1. Biology
  2. Time-varying growth
  3. Time-varying selectivity and retention
  4. Ending selectivity and retention
  5. Basic time series
  6. Recruitment plots
  7. Spawning biomass plots
  8. Depletion plots
  9. Recruitment deviation plots
  10. Discard fractions and mean body weights
  11. Management plots
  12. Stock-recruit curve
  13. CPUE plots
  14. Numbers at age plots
  15. Length-composition data plots
  16. Age-composition data plots
  17. Conditional age-at-length data plots
  18. Fit to length-composition plots
  19. Fit to age-composition plots
  20. Fit to conditional age-at-length data
  21. Fit to length-at-age plots
  22. Production
  23. CPUE data-only plots
  24. Tagging-related plots

Value

Plots returned to R GUI, to single PDF file, or to multiple PNG files depending on the inputs chosen.

Author(s)

Ian Stewart, Ian Taylor, Andre Punt, and other contributors

References

Walters, Hilborn, and Christensen, 2008, Surplus production dynamics in declining and recovering fish populations. Can. J. Fish. Aquat. Sci. 65: 2536-2551

Examples

## Not run: 
SSv3_plots(replist = myreplist)
SSv3_plots(replist = myreplist, pdf=T, pwidth=8, pheight=8, rows=2,
    cols=2)
## End(Not run)

[Package r4ss version 1.04 Index]