Package 'ss3diags' reference manual

Title:	Stock Synthesis Model Diagnostics for Intergated Stock Assessments
Description:	Compilation of diagnostic functions for Stock Synthesis models, which developed for the manuscript "Using Model Diagnostics in Integrated Stock Assessments".
Authors:	Henning Winker [aut], Felipe Carvalho [aut], Massimiliano Cardinale [aut], Laurence Kell [aut], Megumi Oshima [aut, cre], Eric Fletcher [aut]
Maintainer:	Megumi Oshima <[email protected]>
License:	EUPL
Version:	2.2.1
Built:	2024-11-20 03:39:14 UTC
Source:	https://github.com/PIFSCstockassessments/ss3diags

Francis Weighting for compositional data

Description

TA1.8 Francis function modified from r4ss::SSMethod.TA1.8 and r4ss::SSMethod.Cond.TA1.8 apply Francis weighting method TA1.8 to length-, age-, generalized size-composition data, or conditional age-at-length data from a Stock Synthesis model. For conditional age-at-length data, the mean age by year is calculated based on recommendations by Punt (2015). The main purpose is to create a dataframe of the annual observed and expected mean length or age for each fleet that is used to calculate residuals for testing model fit. This function is used in SSplotRunstest and SSplotJABBAres.

Usage

SScompsTA1.8(
  ss3rep,
  type = c("len", "age", "size", "con"),
  fleet = NULL,
  seas = NULL,
  plotit = FALSE,
  maxpanel = 1000
)
SScompsTA1.8(
  ss3rep,
  type = c("len", "age", "size", "con"),
  fleet = NULL,
  seas = NULL,
  plotit = FALSE,
  maxpanel = 1000
)

Arguments

`ss3rep`	Stock Synthesis output as read by r4SS function SS_output
`type`	string of either 'len' (for length composition data), 'size' (for generalized size composition data), 'age' (for age composition data), or 'con' (for conditional age at length data)
`fleet`	vector of one or more fleet numbers whose data are to be analysed simultaneously, if NULL, all fleets will be analysed
`seas`	string indicating how to treat data from multiple seasons 'comb' - combine seasonal data for each year and plot against Yr 'sep' - treat season separately, plotting against Yr.S. If is.null(seas), it is assumed that there is only one season and option 'comb' is used.
`plotit`	if TRUE, make an illustrative plot like one or more panels of Fig. 4 in Francis (2011).
`maxpanel`	maximum number of panels within a plot, default 1000

Value

ss_out data.frame of observed, predicted mean length/age and 95% confidence intervals based on stage 1 and stage 2 weighting

runs_dat data.frame of observed and predicted mean length or age for each year/fleet.

Author(s)

Chris Francis, Andre Punt, Ian Taylor (modified by Henning Winker and Meg Oshima)

References

Francis, R.I.C.C. (2011). Data weighting in statistical fisheries stock assessment models. Canadian Journal of Fisheries and Aquatic Sciences 68: 1124-1138.

#' Punt, A.E. (2015). Some insights into data weighting in integrated stock assessments. Fish. Res. <http://dx.doi.org/10.1016/j.fishres.2015.12.006

Joint Distributions for Stock Status Ratios

Description

A function to generate joint distributions for stock status ratios (SSB/SSBref and F/Fref where ref can be MSY, SSB40, F40, etc.) using a Multivariate Log-Normal Distribution. The function produces a Kobe plot, maximum likelihood estimates and the MVLN Monte-Carlo distributions of the Kobe values which can be input into SSplotEnsemble().

Usage

SSdeltaMVLN(
  ss3rep,
  Fref = NULL,
  years = NULL,
  mc = 5000,
  weight = 1,
  run = "MVLN",
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE,
  variance_method = "ww2019",
  bias_correct_mean = FALSE
)
SSdeltaMVLN(
  ss3rep,
  Fref = NULL,
  years = NULL,
  mc = 5000,
  weight = 1,
  run = "MVLN",
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE,
  variance_method = "ww2019",
  bias_correct_mean = FALSE
)

Arguments

`ss3rep`	from r4ss::SS_output
`Fref`	Choice of Fratio c("MSY","Btgt"), correponding to F_MSY and F_Btgt
`years`	single year or vector of years for mvln
`mc`	number of monte-carlo simulations
`weight`	weighting option for model ensembles weight*mc
`run`	qualifier for model run
`plot`	option to show plot
`addprj`	include forecast years
`ymax`	ylim maximum
`xmax`	xlim maximum
`legendcex`	Allows to adjust legend cex
`verbose`	Report progress to R GUI?
`variance_method`	Specify method for approximating the variance and covariance of the multivariate lognormal distribution ww2019 Use the approximation from Walter and Winker 2019 (Default for backwards compatibility). 2T Use the delta-method and a 2nd order Taylor series approximation.
`bias_correct_mean`	Specify if the Stock Synthesis MLE estimates should be bias corrected when used to specify the mean of the multivariate lognormal distribution FALSE Do not apply bias correction (Default for backwards compatibility). TRUE Apply bias correction.

Value

output list of maximum likelihood estimates and the MVLN Monte-Carlo distributions of the Kobe values, and kobe plot

Author(s)

Henning Winker (JRC-EC)

Nicholas Ducharme-Barth (PIFSC)

Joint Distributions for Stock Status Ratios

Description

A function to generate kobe pdfs from a Multivariate Log-Normal Distribution including plotting option. This version is used for older versions of Stock Synthesis. For newer versions (v3.24 and newer), use SSdeltaMVLN().

Usage

SSdeltaMVLN_old(
  ss3rep,
  status = c("Bratio", "F"),
  quants = c("SSB", "Recr"),
  Fref = c("MSY", "Ftrg"),
  years = NULL,
  mc = 5000,
  weight = 1,
  run = "MVLN",
  plot = TRUE,
  addtrj = TRUE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)
SSdeltaMVLN_old(
  ss3rep,
  status = c("Bratio", "F"),
  quants = c("SSB", "Recr"),
  Fref = c("MSY", "Ftrg"),
  years = NULL,
  mc = 5000,
  weight = 1,
  run = "MVLN",
  plot = TRUE,
  addtrj = TRUE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)

Arguments

`ss3rep`	from r4ss::SSgetoutput()["replist1"]
`status`	covarying stock status quantaties to extract from Hessian
`quants`	additional stock quantaties to extract from Hessian
`Fref`	Choice of reference point for stock SSB/XFref=c("MSY","Ftrg"),only if F_report_basis: 0 or 3
`years`	single year or vector of years for mvln
`mc`	number of monte-carlo simulations
`weight`	weighting option for model ensembles weight*mc
`run`	qualifier for model run
`plot`	option to show plot
`addtrj`	TRUE/FALSE add trajectory of years. Default is TRUE
`ymax`	ylim maximum
`xmax`	xlim maximum
`legendcex`	Allows to adjust legend cex
`verbose`	Report progress to R GUI?

Value

output list of kobe objects and mle's

Author(s)

Henning Winker (JRC-EC)

MCMC Joint Distributions

Description

A function to generate joint distributions for stock status ratios (SSB/SSBref and F/Fref where ref can be MSY, SSB40, F40, etc.) using MCMC. The function produces a Kobe plot, maximum likelihood estimates and the MVLN Monte-Carlo distributions of the Kobe values which can be input into SSplotEnsemble().

Usage

SSdiagsMCMC(
  mcmc,
  ss3rep,
  Fref = NULL,
  years = NULL,
  run = "MCMC",
  thin = 1,
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)
SSdiagsMCMC(
  mcmc,
  ss3rep,
  Fref = NULL,
  years = NULL,
  run = "MCMC",
  thin = 1,
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)

Arguments

`mcmc`	file path for folder with the derived_posteriors.sso file
`ss3rep`	from r4ss::SS_output
`Fref`	Choice of Fratio c("MSY","Btgt), correponding to F_MSY and F_Btgt
`years`	single year or vector of years for mvln
`run`	qualifier for model run
`thin`	option to use additional thinning
`plot`	option to show plot
`addprj`	include forecast years
`ymax`	ylim maximum
`xmax`	xlim maximum
`legendcex`	Allows to adjust legend cex
`verbose`	Report progress to R GUI?

Value

output list maximum likelihood estimates and the MCMC posterier distributions of the Kobe values and a Kobe plot

Author(s)

Henning Winker (JRC-EC), Massimiliano and Laurence Kell (Sea++)

MCMC Joint Distributions

Description

Usage

SSdiagsMCMC_ancient(
  mcmc,
  ss3rep,
  Fref = NULL,
  years = NULL,
  run = "MCMC",
  thin = 1,
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)
SSdiagsMCMC_ancient(
  mcmc,
  ss3rep,
  Fref = NULL,
  years = NULL,
  run = "MCMC",
  thin = 1,
  plot = TRUE,
  addprj = FALSE,
  ymax = NULL,
  xmax = NULL,
  legendcex = 1,
  verbose = TRUE
)

Arguments

`mcmc`	file path for folder with the derived_posteriors.sso file
`ss3rep`	from r4ss::SS_output
`Fref`	Choice of Fratio c("MSY","Btgt), correponding to F_MSY and F_Btgt
`years`	single year or vector of years for mvln
`run`	qualifier for model run
`thin`	option to use additional thinning
`plot`	option to show plot
`addprj`	include forecast years
`ymax`	ylim maximum
`xmax`	xlim maximum
`legendcex`	Allows to adjust legend cex
`verbose`	Report progress to R GUI?

Value

output list maximum likelihood estimates and the MCMC posterier distributions of the Kobe values and a Kobe plot

Author(s)

Henning Winker (JRC-EC), Massimiliano and Laurence Kell (Sea++)

Mohn's Rho and Forecast Bias

Description

This function produces the statistics from retrospective analysis (Mohn's rho and forecast bias). To visualize the retrospective forecasts from a Stock Synthesis model, use SSplotRetro().

Usage

SShcbias(
  summaryoutput,
  quants = c("SSB", "F"),
  models = "all",
  endyrvec = "default",
  verbose = TRUE
)
SShcbias(
  summaryoutput,
  quants = c("SSB", "F"),
  models = "all",
  endyrvec = "default",
  verbose = TRUE
)

Arguments

`summaryoutput`	List created by r4ss::SSsummarize()
`quants`	SSB or F quantity
`models`	Optional subset of the models described in r4ss function summaryoutput(). Either "all" or a vector of numbers indicating columns in summary tables.
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
`verbose`	Report progress to R GUI?

Author(s)

Henning Winker (JRC-EC) and Laurance Kell (Sea++)

Mean Absolute Scaled Error

Description

MASE for one-step ahead hindcasting cross-validations and computes MASE from prediction residuals of indices. MASE is calculated the average ratio of mean absolute error (MAE) of prediction residuals (MAE.PR) and Naive Predictions (MAE.base) MASE.adj sets the MAE.base to a minimum MAE.base.adj (default=0.1) MASE.adj allow passing (MASE<1) if MAE.PE < 0.1 and thus accurate, when obs show extremely little variation

Usage

SSmase(
  retroSummary,
  quants = c("cpue", "len", "age", "con"),
  Season = "default",
  models = "all",
  endyrvec = "default",
  indexselect = NULL,
  MAE.base.adj = 0.1,
  residuals = FALSE,
  verbose = FALSE,
  indexfleets = 1
)
SSmase(
  retroSummary,
  quants = c("cpue", "len", "age", "con"),
  Season = "default",
  models = "all",
  endyrvec = "default",
  indexselect = NULL,
  MAE.base.adj = 0.1,
  residuals = FALSE,
  verbose = FALSE,
  indexfleets = 1
)

Arguments

`retroSummary`	raw list of retrospective runs created by `r4ss::SSgetoutput()`. Depending on the type of data, the function will call r4ss::SSsummarize or ss3diags:SSretroComps to summarize the list.
`quants`	data type, either "cpue" for index data, "len" for length composition data, or "age" for age composition data. Note, if using "age" or "len", SSretroComps() will be used to extract and summarize the composition data first.
`Season`	option to specify Season as an integer of value 1-4 - Default uses first available, i.e. usual Seas = 1
`models`	Optional subset of the models described in r4ss function summaryoutput(). Either "all" or a vector of numbers indicating columns in summary tables.
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
`indexselect`	Vector of fleet numbers for each model for which to compare
`MAE.base.adj`	minimum MASE demoninator (naive predictions) for MASE.adj (default = 0.1)
`residuals`	If true, includes a dataframe in the output of the prediction residuals and naive prediction residuals. Default is FALSE.
`verbose`	Report progress to R GUI?
`indexfleets`	Single value or vector of length n = number of models in summary object of the fleet number(s) for the index to compare.

Value

MASE and hcxval statistic

Author(s)

Henning Winker (JRC-EC) and Laurence Kell (Sea++)

Examples

## Not run: 
# calculate MASE for CPUE indices only for fleets 1 and 2
SSmase(retro.sma, quant = "cpue", indexselect = c(1:2))

## End(Not run)

## Not run: 
# calculate MASE for CPUE indices only for fleets 1 and 2
SSmase(retro.sma, quant = "cpue", indexselect = c(1:2))

## End(Not run)

Model ensemble plots

Description

Plots model ensembles and forecasts with uncertainty represented by MVLN or MCMC posteriors

Usage

SSplotEnsemble(
  kb,
  subplots = c("stock", "harvest", "SSB", "F", "Recr", "Catch"),
  models = "all",
  quantiles = list(c(0.025, 0.975)),
  ylabs = NULL,
  endyrvec = "default",
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = FALSE,
  use_pdf = FALSE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = NULL,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "l",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  legendindex = NULL
)
SSplotEnsemble(
  kb,
  subplots = c("stock", "harvest", "SSB", "F", "Recr", "Catch"),
  models = "all",
  quantiles = list(c(0.025, 0.975)),
  ylabs = NULL,
  endyrvec = "default",
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = FALSE,
  use_pdf = FALSE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = NULL,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "l",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  legendindex = NULL
)

Arguments

`kb`	`kb` type output created by `SSdeltaMVLN()`
`subplots`	vector to create subplots with these options: `"stock"` Fish Population `"harvest"` Harvest Rate `"SSB"` Spawning Stock Biomass `"F"` Fishing Mortality `"Recr"` Recruitment `"Catch"` Total Catch
`models`	option to manually subset the models in `kb[["run"]]`
`quantiles`	quantiles for uncertainty in plots. Input as a list, default is the 95TH percentile: `list(c(0.025, 0.975))`
`ylabs`	y-axis labels for quants
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By `"default"` it is set to the ending year specified in each model.
`plot`	DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
`print`	DEPRECATED, please use `print_plot`.
`print_plot`	Flag to enable plot graphic device to print to PNG or PNG files.
`png`	DEPRECATED. Please use `use_png`.
`use_png`	Enables plots to be generated to PNG files. Defaults to print value
`pdf`	DEPRECATED. Please use `use_pdf`.
`use_pdf`	Enables plots to be generated to pdf file.
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
`xlim`	Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space.
`xaxs`	Choice of xaxs parameter See `?par` for more info.
`yaxs`	Choice of yaxs parameter. See `?par` for more info.
`xylabs`	Logical flag: set TRUE or FALSE to include x- and y-axis labels to the plot. Defaults to TRUE
`type`	The type of plot to be drawn. For more details, see `plot`.
`uncertainty`	Logical flag to enable plots with uncertainty intervals. Either a single TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F estimated timeseries, or a set of integers corresponding to the choice of models.
`legend`	Flag to enable legend to plot. TRUE by default.
`legendlabels`	Optional vector of labels to include in legend.
`legendloc`	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See `help("legend")` for more info on the string options.
`legendorder`	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
`legendncol`	Number of columns for the legend.
`legendcex`	Allows to adjust legend cex
`legendsp`	Space between legend labels
`pwidth`	Default width of plot printed to plot in units of `punits`
`pheight`	Height of plot printed to plot in units of `punits`
`punits`	Measurement units for `pwidth` and `pheight`. Default is `"in"`. `"px"` (pixels) `"in"` (inches) `"cm"` (centimeters) `"mm"` (millimeters)
`res`	Resolution for plots printed to files.
`ptsize`	Point size for plotted text in plots printed in files. See `help("png")` for more details
`cex.main`	Character expansion for plot titles.
`plotdir`	Directory where output plot file will be written. By default, it will be the directory where the model was run.
`filenameprefix`	Additional text to append to output plot file name. It will be separated from default name by an underscore.
`par`	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot,which is passed to `par()`. Entering `NULL` passes plot's default `par()` values (which depends on whether the main title is included or not)
`verbose`	Flag to print additional diagnostic messages to R console
`shadealpha`	Transparency adjustment used to make uncertainty regions, default is 0.3
`new`	Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
`add`	suppresses `par()` to create multiplot figs
`mcmcVec`	Logical vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE.
`indexQlabel`	TRUE/FALSE include labels for indices. Default is TRUE (currently not used)
`indexQdigits`	Number of significant digits for catchability in legend. Default is 4
`legendindex`	Allows to add legend for selected indices (plots)

Author(s)

Mostly adopted from r4ss::SSplotComparisons by Taylor et al

Examples

## Not run: 

mvln <- SSdeltaMVLN(simple, run = "Simple")
sspar(mfrow = c(3, 2), plot.cex = 0.7)
SSplotEnsemble(mvln[["kb"]], ylabs = mvln[["labels"]], add = T, verbose = F)

## End(Not run)
## Not run: 

mvln <- SSdeltaMVLN(simple, run = "Simple")
sspar(mfrow = c(3, 2), plot.cex = 0.7)
SSplotEnsemble(mvln[["kb"]], ylabs = mvln[["labels"]], add = T, verbose = F)

## End(Not run)

Hindcasting Cross-Validations of Multiple Models

Description

Plots one-step ahead hindcasting cross-validations and computes MASE from prediction residuals.MASE is calculated as the average ratio of mean absolute error (MAE) of prediction residuals (MAE.PR) and naive predictions (MAE.base). MASE.adj sets the MAE.base to a minimum MAE.base.adj (default=0.1). MASE.adj allow passing (MASE<1) if MAE.PE < 0.1 and thus accurate if obs show very little annual variation

Usage

SSplotHCxval(
  retroSummary,
  subplots = c("cpue", "len", "age"),
  Season = "default",
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  endyrvec = "default",
  xmin = NULL,
  indexselect = NULL,
  MAE.base.adj = 0.1,
  show.mase.adj = TRUE,
  indexUncertainty = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  xlim = "default",
  ylimAdj = 1.15,
  ylim = NULL,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = grey(0.5, 0.4),
  shadecol2 = grey(0.5, 0.4),
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  indexfleets = 1,
  plot = TRUE,
  shadecol1 = grey(0.5, 0.4)
)
SSplotHCxval(
  retroSummary,
  subplots = c("cpue", "len", "age"),
  Season = "default",
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  endyrvec = "default",
  xmin = NULL,
  indexselect = NULL,
  MAE.base.adj = 0.1,
  show.mase.adj = TRUE,
  indexUncertainty = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  xlim = "default",
  ylimAdj = 1.15,
  ylim = NULL,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = grey(0.5, 0.4),
  shadecol2 = grey(0.5, 0.4),
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  indexfleets = 1,
  plot = TRUE,
  shadecol1 = grey(0.5, 0.4)
)

Arguments

`retroSummary`	List created by `r4ss::SSsummarize()` or `SSretroComps()`
`subplots`	optional use of the following: `"cpue"` Index of abundance data `"len"` Length-composition data `"age"` Age-composition data
`Season`	option to specify Season as an integer of value 1-4. Default uses first available, i.e. usual Seas = 1
`print`	DEPRECATED, please use `print_plot`.
`print_plot`	Flag to enable plot graphic device to print to PNG or PNG files.
`png`	DEPRECATED. Please use `use_png`.
`use_png`	Enables plots to be generated to PNG files. Defaults to print value
`pdf`	DEPRECATED. Please use `use_pdf`.
`use_pdf`	Enables plots to be generated to pdf file.
`models`	Optional subset of the models of `summaryoutput` (or a similar field with a different name): a list created by the function r4ss::SSsummarize. Either `"all"` or a vector of numbers indicating columns in summary tables.
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
`xmin`	optional number first year shown in plot (if available)
`indexselect`	Vector of fleet numbers for each model for which to compare
`MAE.base.adj`	minimum `MASE` denominator (naive predictions) for `MASE.adj` (default = 0.1)
`show.mase.adj`	if TRUE, it show `mase.adj` in plot
`indexUncertainty`	Show fixed uncertainty intervals on index (not estimated)
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
`xlim`	Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space.
`ylim`	will over-write `ylimAdj` if specified
`xaxs`	Choice of xaxs parameter See `?par` for more info.
`yaxs`	Choice of yaxs parameter. See `?par` for more info.
`xylabs`	Logical flag: set TRUE or FALSE to include x- and y-axis labels to the plot. Defaults to TRUE
`type`	The type of plot to be drawn. For more details, see `plot`.
`uncertainty`	Logical flag to enable plots with uncertainty intervals. Either a single TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F estimated timeseries, or a set of integers corresponding to the choice of models.
`legend`	Flag to enable legend to plot. TRUE by default.
`legendlabels`	Optional vector of labels to include in legend.
`legendloc`	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See `help("legend")` for more info on the string options.
`legendorder`	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
`legendncol`	Number of columns for the legend.
`legendcex`	Allows to adjust legend cex
`legendsp`	Space between legend labels
`legendindex`	Allows to add legend for selected indices (plots)
`pwidth`	Default width of plot printed to plot in units of `punits`
`pheight`	Height of plot printed to plot in units of `punits`
`punits`	Measurement units for `pwidth` and `pheight`. Default is `"in"`. `"px"` (pixels) `"in"` (inches) `"cm"` (centimeters) `"mm"` (millimeters)
`res`	Resolution for plots printed to files.
`ptsize`	Point size for plotted text in plots printed in files. See `help("png")` for more details
`cex.main`	Character expansion for plot titles.
`plotdir`	Directory where output plot file will be written. By default, it will be the directory where the model was run.
`filenameprefix`	Additional text to append to output plot file name. It will be separated from default name by an underscore.
`par`	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot,which is passed to `par()`. Entering `NULL` passes plot's default `par()` values (which depends on whether the main title is included or not)
`verbose`	Flag to print additional diagnostic messages to R console
`shadecol`	uncertainty shading of hcxval horizon
`shadecol2`	color for uncertainty in early years not affected by hindcast
`shadealpha`	Transparency adjustment used to make default `shadecol`. (currently not used)
`new`	Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
`add`	suppresses `par()` to create multiplot figs
`mcmcVec`	Logical vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE.
`indexQlabel`	Logical flag to add catchability to legend in plot of index fits.
`indexQdigits`	Number of significant digits for catchability in legend
`indexfleets`	Fleet numbers for each model to compare indices of abundance. Can take different forms: integer: (default) create a single comparison plot for the chosen index NULL: create a separate plot for each index as long as the fleet numbering is the same across all models. vector of length equal to number of models: a single fleet number for each model to be compared in a single plot list: list of fleet numbers associated with indices within each model to be compared, where the list elements are each a vector of the same length but the names of the list elements don't matter and can be absent.
`plot`	DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
`shadecol1`	uncertainty shading of early years not affected by hindcast (currently not used)

Author(s)

Henning Winker (JRC-EC) and Laurence Kell (Sea++)

Residual plot

Description

Plots residuals for all indices as boxplot (color coded by fleet) with a loess showing systematic trends over time. This function is from the package JABBA (Just Another Bayesian Biomass Assessment).

Usage

SSplotJABBAres(
  ss3rep,
  subplots = c("cpue", "len", "age", "size", "con")[1],
  seas = NULL,
  plot = TRUE,
  print = lifecycle::deprecated(),
  print_plot = FALSE,
  png = lifecycle::deprecated(),
  use_png = print_plot,
  pdf = lifecycle::deprecated(),
  use_pdf = FALSE,
  indexselect = NULL,
  miny = 3,
  col = NULL,
  pch = 21,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  xlim = "default",
  ylim = "default",
  ylimAdj = 1.1,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  legend = TRUE,
  legendlabels = "default",
  legendloc = "bottomleft",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  boxcol = grey(0.8, 0.5),
  new = TRUE,
  add = FALSE
)
SSplotJABBAres(
  ss3rep,
  subplots = c("cpue", "len", "age", "size", "con")[1],
  seas = NULL,
  plot = TRUE,
  print = lifecycle::deprecated(),
  print_plot = FALSE,
  png = lifecycle::deprecated(),
  use_png = print_plot,
  pdf = lifecycle::deprecated(),
  use_pdf = FALSE,
  indexselect = NULL,
  miny = 3,
  col = NULL,
  pch = 21,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  xlim = "default",
  ylim = "default",
  ylimAdj = 1.1,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  legend = TRUE,
  legendlabels = "default",
  legendloc = "bottomleft",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  boxcol = grey(0.8, 0.5),
  new = TRUE,
  add = FALSE
)

Arguments

`ss3rep`	Stock Synthesis output as read by `r4ss::SS_output()`
`subplots`	string of type of data to plot: `"cpue"` Index of abundance data `"len"` Length-composition data `"age"` Age-composition data `"size"` Generalized size composition data `"con"` Conditional age-at-length data.
`seas`	string indicating how to treat data from multiple seasons: `"comb"` Combine seasonal data for each year and plot against Yr `"sep"` Treat season separately, plotting against `Yr.S`. `NULL` If NULL, it is assumed that there is only one season and option `"comb"` is used.
`plot`	DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
`print`	DEPRECATED, please use `print_plot`.
`print_plot`	Flag to enable plot graphic device to print to PNG or PNG files.
`png`	DEPRECATED. Please use `use_png`.
`use_png`	Enables plots to be generated to PNG files. Defaults to print value
`pdf`	DEPRECATED. Please use `use_pdf`.
`use_pdf`	Enables plots to be generated to pdf file.
`indexselect`	Vector of fleet numbers for each model for which to compare
`miny`	minimum abs values of `ylim`
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
`xlim`	Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
`ylim`	Optional, min and max values for the ylim to override the `"default"` value (-0.7, 0.5)
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space.
`xaxs`	Choice of xaxs parameter See `?par` for more info.
`yaxs`	Choice of yaxs parameter. See `?par` for more info.
`xylabs`	Logical flag. Enables x- and y-axis labels.
`type`	The type of plot to be drawn. For more details, see `plot`.
`legend`	Flag to enable legend to plot. TRUE by default.
`legendlabels`	Optional vector of labels to include in legend.
`legendloc`	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See `help("legend")` for more info on the string options.
`legendorder`	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
`legendncol`	Number of columns for the legend.
`legendcex`	Allows to adjust legend cex
`legendsp`	Space between legend labels
`legendindex`	Allows to add legend for selected indices (plots)
`pwidth`	Default width of plot printed to plot in units of `punits`
`pheight`	Height of plot printed to plot in units of `punits`
`punits`	Measurement units for `pwidth` and `pheight`. Default is `"in"`. `"px"` (pixels) `"in"` (inches) `"cm"` (centimeters) `"mm"` (millimeters)
`res`	Resolution for plots printed to files.
`ptsize`	Point size for plotted text in plots printed in files. See `help("png")` for more details
`cex.main`	Character expansion for plot titles.
`plotdir`	Directory where output plot file will be written. By default, it will be the directory where the model was run.
`filenameprefix`	Additional text to append to output plot file name. It will be separated from default name by an underscore.
`par`	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot,which is passed to `par()`. Entering `NULL` passes plot's default `par()` values (which depends on whether the main title is included or not)
`verbose`	Flag to print additional diagnostic messages to R console
`boxcol`	color boxes
`new`	Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
`add`	suppresses `par()` to create multiplot figs

Author(s)

Henning Winker (JRC-EC)

KOBE phase plot

Description

Generates a Kobe plot or phase plot illustrating the stock status uncertainty over SSB/SSBmsy and F/Fmsy

Usage

SSplotKobe(
  kb,
  joint = TRUE,
  year = NULL,
  posterior = c("points", "kernel"),
  xlab = expression(SSB/SSB[MSY]),
  ylab = expression(F/F[MSY]),
  ylim = NULL,
  xlim = NULL,
  fill = TRUE,
  showMedian = TRUE,
  legend = TRUE,
  legendpos = "right",
  legendcex = 0.7,
  legendruns = TRUE,
  yr.label = TRUE,
  yr.int = 5,
  verbose = TRUE
)
SSplotKobe(
  kb,
  joint = TRUE,
  year = NULL,
  posterior = c("points", "kernel"),
  xlab = expression(SSB/SSB[MSY]),
  ylab = expression(F/F[MSY]),
  ylim = NULL,
  xlim = NULL,
  fill = TRUE,
  showMedian = TRUE,
  legend = TRUE,
  legendpos = "right",
  legendcex = 0.7,
  legendruns = TRUE,
  yr.label = TRUE,
  yr.int = 5,
  verbose = TRUE
)

Arguments

`kb`	output from SSdeltaMVLN()["kb"]
`joint`	option FALSE shows individual runs
`year`	option to choose year for kobe, last year is default
`posterior`	visualization of posterior c("points","kernel")
`xlab`	graphic parameter
`ylab`	graphic parameter
`ylim`	graphic parameter
`xlim`	graphic parameter
`fill`	shows color-coded quadrants
`showMedian`	option for median trajectory. TRUE by default
`legend`	option for legend. TRUE by default.
`legendpos`	legend position
`legendcex`	legend size
`legendruns`	show legend for run labels
`yr.label`	show year along trajectory
`yr.int`	year intervals along trajectory
`verbose`	Output to R console. Default is TRUE

Value

Kobe Quadrant percentages

Compare Multiple SS Model Estimates

Description

A function to plot SSB, B-ratio, F, Recruits, and/or Index of Abundance fits from multiple SS models. This function uses an object of multiple SS models summarized with r4ss::SSsummarize().

Usage

SSplotModelcomp(
  summaryoutput,
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  subplots = c("SSB", "Bratio", "Fvalue", "Recruits", "Index", "RecDevs"),
  brp = c("msy", "btargs"),
  fmsy = TRUE,
  ylabs = c("SSB (t)", expression(SSB/SSB[MSY]), "Fishing mortality F",
    "Recruits ('000s)", "Index", "Recruitment Deviations"),
  endyrvec = "default",
  xmin = NULL,
  indexselect = NULL,
  indexUncertainty = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = "default",
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "l",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = NULL,
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  indexfleets = 1
)
SSplotModelcomp(
  summaryoutput,
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  subplots = c("SSB", "Bratio", "Fvalue", "Recruits", "Index", "RecDevs"),
  brp = c("msy", "btargs"),
  fmsy = TRUE,
  ylabs = c("SSB (t)", expression(SSB/SSB[MSY]), "Fishing mortality F",
    "Recruits ('000s)", "Index", "Recruitment Deviations"),
  endyrvec = "default",
  xmin = NULL,
  indexselect = NULL,
  indexUncertainty = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = "default",
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "l",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.9,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = NULL,
  shadealpha = 0.3,
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  indexfleets = 1
)

Arguments

`summaryoutput`	List created by `r4ss::SSsummarize()`
`plot`	DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
`print`	DEPRECATED, please use `print_plot`.
`print_plot`	Flag to enable plot graphic device to print to PNG or PNG files.
`png`	DEPRECATED. Please use `use_png`.
`use_png`	Enables plots to be generated to PNG files. Defaults to print value
`pdf`	DEPRECATED. Please use `use_pdf`.
`use_pdf`	Enables plots to be generated to pdf file.
`models`	Optional subset of the models of `summaryoutput` (or a similar field with a different name): a list created by the function r4ss::SSsummarize. Either `"all"` or a vector of numbers indicating columns in summary tables.
`subplots`	option to "SSB","Bratio","Fvalue","Recruits","Index" `"SSB"` Spawning Stock Biomass `"Bratio"` Stock Biomass relative to biomass reference point `"Fvalue"` Fishing Mortality `"Recruits"` Age-0 Recruits `"Index"` Index of abundance `"RecDev"` Recruitment Deviations
`brp`	option to set reference point `c("msy","btargs")`
`fmsy`	to specify `Fvalue` as `F/Fmsy` if so in starter file setting
`ylabs`	yaxis labels for quants final year of values to show for each model. By default it is set to the
`endyrvec`	Optional single year or vector of years representing the final year of values to show for each model. By `"default"` it is set to the ending year specified in each model.
`xmin`	NULL optional number first year shown in plot (if available)
`indexselect`	Vector of fleet numbers for each model for which to compare
`indexUncertainty`	Show fixed uncertainty intervals on index (not estimated)
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
`xlim`	Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space.
`xaxs`	Choice of xaxs parameter See `?par` for more info.
`yaxs`	Choice of yaxs parameter. See `?par` for more info.
`xylabs`	Logical flag: set TRUE or FALSE to include x- and y-axis labels to the plot. Defaults to TRUE
`type`	The type of plot to be drawn. For more details, see `plot`.
`uncertainty`	Logical flag to enable plots with uncertainty intervals. Either a single TRUE/FALSE value, or a vector of TRUE/FALSE values around SSB or F estimated timeseries, or a set of integers corresponding to the choice of models.
`legend`	Flag to enable legend to plot. TRUE by default.
`legendlabels`	Optional vector of labels to include in legend.
`legendloc`	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See `help("legend")` for more info on the string options.
`legendorder`	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
`legendncol`	Number of columns for the legend.
`legendcex`	Allows to adjust legend cex
`legendsp`	Space between legend labels
`legendindex`	Allows to add legend for selected indices (plots)
`pwidth`	Default width of plot printed to plot in units of `punits`
`pheight`	Height of plot printed to plot in units of `punits`
`punits`	Measurement units for `pwidth` and `pheight`. Default is `"in"`. `"px"` (pixels) `"in"` (inches) `"cm"` (centimeters) `"mm"` (millimeters)
`res`	Resolution for plots printed to files.
`ptsize`	Point size for plotted text in plots printed in files. See `help("png")` for more details
`cex.main`	Character expansion for plot titles.
`plotdir`	Directory where output plot file will be written. By default, it will be the directory where the model was run.
`filenameprefix`	Additional text to append to output plot file name. It will be separated from default name by an underscore.
`par`	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot,which is passed to `par()`. Entering `NULL` passes plot's default `par()` values (which depends on whether the main title is included or not)
`verbose`	Flag to print additional diagnostic messages to R console
`shadecol`	uncertainty shading of hcxval horizon
`shadealpha`	Transparency adjustment used to make default shadecol
`new`	Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
`add`	suppresses `par()` to create multiplot figs
`mcmcVec`	Logical vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE.
`indexQlabel`	Logical. If TRUE add catchability to legend in plot of index fits (currently not used)
`indexQdigits`	Number of significant digits for catchability in legend
`indexfleets`	Fleet numbers for each model to compare indices of abundance. Can take different forms: integer (default): create a single comparison plot for the chosen index NULL: create a separate plot for each index as long as the fleet numbering is the same across all models. vector of length equal to number of models: a single fleet number for each model to be compared in a single plot list: list of fleet numbers associated with indices within each model to be compared, where the list elements are each a vector of the same length but the names of the list elements don't matter and can be absent.

Author(s)

Mostly adopted from r4ss::SSplotComparisons by Taylor et al

Retrospective-Forecast with One-Step Ahead Hindcasting

Description

Plots retrospective pattern, including (optional) one-step ahead forecast and computes Mohn's Rho

Usage

SSplotRetro(
  summaryoutput,
  subplots = c("SSB", "F"),
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  endyrvec = "default",
  xlim = NULL,
  xmin = NULL,
  labels = NULL,
  ylim = NULL,
  forecast = TRUE,
  forecastrho = TRUE,
  showrho = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.7,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = grey(0.4, 0.6),
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  shadecol1 = grey(0.5, 0.4),
  indexQlabel = TRUE,
  indexQdigits = 4,
  shadealpha = 0.3
)
SSplotRetro(
  summaryoutput,
  subplots = c("SSB", "F"),
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  models = "all",
  endyrvec = "default",
  xlim = NULL,
  xmin = NULL,
  labels = NULL,
  ylim = NULL,
  forecast = TRUE,
  forecastrho = TRUE,
  showrho = TRUE,
  col = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  tickEndYr = TRUE,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = "default",
  legendloc = "topright",
  legendorder = "default",
  legendncol = 1,
  legendcex = 1,
  legendsp = 0.7,
  legendindex = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  shadecol = grey(0.4, 0.6),
  new = TRUE,
  add = FALSE,
  mcmcVec = FALSE,
  shadecol1 = grey(0.5, 0.4),
  indexQlabel = TRUE,
  indexQdigits = 4,
  shadealpha = 0.3
)

Arguments

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

Author(s)

Henning Winker (JRC-EC) and Laurance Kell (Sea++)

Residual Diagnostics

Description

Function for residual diagnostics. Plots residuals and 3x sigma limits for indices or mean age or length and outputs a runs test table. Note, if you do not want to plot the residuals, use SSrunstest().

Usage

SSplotRunstest(
  ss3rep,
  mixing = "less",
  subplots = c("cpue", "len", "age", "size", "con")[1],
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  indexselect = NULL,
  miny = 1,
  col = NULL,
  pch = 21,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = "default",
  ylim = "default",
  ylimAdj = 1.4,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  legend = TRUE,
  legendloc = "top",
  legendcex = 1,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  new = TRUE,
  add = FALSE
)
SSplotRunstest(
  ss3rep,
  mixing = "less",
  subplots = c("cpue", "len", "age", "size", "con")[1],
  plot = TRUE,
  print = deprecated(),
  print_plot = FALSE,
  png = deprecated(),
  use_png = print_plot,
  pdf = deprecated(),
  use_pdf = FALSE,
  indexselect = NULL,
  miny = 1,
  col = NULL,
  pch = 21,
  lty = 1,
  lwd = 2,
  tickEndYr = FALSE,
  xlim = "default",
  ylim = "default",
  ylimAdj = 1.4,
  xaxs = "i",
  yaxs = "i",
  xylabs = TRUE,
  type = "o",
  legend = TRUE,
  legendloc = "top",
  legendcex = 1,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = NULL,
  filenameprefix = "",
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  new = TRUE,
  add = FALSE
)

Arguments

`ss3rep`	Stock Synthesis output as read by `r4ss::SS_output()`
`mixing`	`c("less","greater","two.sided")`. Default less is checking for positive autocorrelation only
`subplots`	optional flag for: `"cpue"` Index of abundance data `"len"` Length composition data `"size"` Generalized size composition data `"age"` Age composition data `"con"` Conditional age-at-length data
`plot`	DEPRECATED. By default, TRUE, Plots (and subplots) are drawn to the plot device. The option to explicitly disable this option (FALSE), is not implemented. This option flag will be defunct in a future version
`print`	DEPRECATED, please use `print_plot`.
`print_plot`	Flag to enable plot graphic device to print to PNG or PNG files.
`png`	DEPRECATED. Please use `use_png`.
`use_png`	Enables plots to be generated to PNG files. Defaults to print value
`pdf`	DEPRECATED. Please use `use_pdf`.
`use_pdf`	Enables plots to be generated to pdf file.
`indexselect`	Vector of fleet numbers for each model for which to compare
`miny`	the absolute value of the min and max value for `ylim`. Default is 1
`col`	Optional vector of colors to be used for lines. Input NULL
`pch`	Optional vector of plot character values
`lty`	Optional vector of line types
`lwd`	Optional vector of line widths
`tickEndYr`	Logical flag: set TRUE or FALSE to switch to turn on/off extra axis mark at final year in timeseries plots.
`xlim`	Optional, years to use for x-axis. Default value NULL (or "default"), uses all years available.
`ylim`	Optional, values for y-axis range to display on plot. The default: `"default"`, will range from -1 to 1.
`ylimAdj`	Multiplier for ylim parameter. Allows additional white space.
`xaxs`	Choice of xaxs parameter See `?par` for more info.
`yaxs`	Choice of yaxs parameter. See `?par` for more info.
`xylabs`	Logical flag: set TRUE or FALSE to include x- and y-axis labels to the plot. Defaults to TRUE
`type`	The type of plot to be drawn. For more details, see `plot`.
`legend`	Flag to enable legend to plot. TRUE by default.
`legendloc`	Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See `help("legend")` for more info on the string options.
`legendcex`	Allows to adjust legend cex
`pwidth`	Default width of plot printed to plot in units of `punits`
`pheight`	Height of plot printed to plot in units of `punits`
`punits`	Measurement units for `pwidth` and `pheight`. Default is `"in"`. `"px"` (pixels) `"in"` (inches) `"cm"` (centimeters) `"mm"` (millimeters)
`res`	Resolution for plots printed to files.
`ptsize`	Point size for plotted text in plots printed in files. See `help("png")` for more details
`cex.main`	Character expansion for plot titles.
`plotdir`	Directory where output plot file will be written. By default, it will be the directory where the model was run.
`filenameprefix`	Additional text to append to output plot file name. It will be separated from default name by an underscore.
`par`	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot,which is passed to `par()`. Entering `NULL` passes plot's default `par()` values (which depends on whether the main title is included or not)
`verbose`	Flag to print additional diagnostic messages to R console
`new`	Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
`add`	suppresses `par()` to create multiplot figs

Value

a dataframe with runs test p-value, if the test has passed or failed, 3x sigma high and low limits, and the type of data used. Rows are for each fleet. Note, runs test passed if p-value > 0.05 (residuals are random) and failed if p-value < 0.5 (residuals are not random)

Author(s)

Henning Winker (JRC-EC) and Laurance Kell (Sea++)

Read SS MCMC

Description

A function to read mcmc file outputs from a Stock Synthesis model

Usage

SSreadMCMC(mcmcdir)
SSreadMCMC(mcmcdir)

Arguments

mcmcdir

file path for folder with the derived_posteriors.sso file

Value

Stock Synthesis mcmc output file

Author(s)

Henning Winker (JRC-EC) & Laurence Kell (Sea++)

Retrieve Composition Data from Multiple SS Models

Description

Wrapper to get observed and expected mean length/age from multiple Stock Synthesis models.

Usage

SSretroComps(retroModels)
SSretroComps(retroModels)

Arguments

retroModels

object list of replists from r4ss::SSgetoutput()

Value

list of observed and expected mean Length/age comps (c.f. ss3rep[["cpue"]])

Author(s)

Henning Winker

Function for calculating RMSE used for `SSplotJABBAres()`

Description

Function for calculating RMSE used for SSplotJABBAres()

Usage

SSrmse(
  ss3rep,
  quants = c("cpue", "len", "age", "con"),
  seas = NULL,
  indexselect = NULL
)
SSrmse(
  ss3rep,
  quants = c("cpue", "len", "age", "con"),
  seas = NULL,
  indexselect = NULL
)

Arguments

`ss3rep`	output from `SS_output()`
`quants`	the dataset to calculate RMSE for. "cpue" for index of abundance, "len" for length comp, "age" for age composition, and "con" for conditional age-at-length.
`seas`	string indicating how to treat data from multiple seasons 'comb' - combine seasonal data for each year and plot against Yr 'sep' - treat season separately, plotting against Yr.S. If is.null(seas), it is assumed that there is only one season and option 'comb' is used.
`indexselect`	Vector of fleet numbers for each model for which to compare

Value

returns a list that includes the RMSE table output (by fleet and combined) and the dataframe of residuals which can be used for creating the SSplotJABBAres() plot

Runs Test for Residuals

Description

This function uses randtests::runs.test to do perform a runs test on residuals to determine if they are randomly distributed. It also calculates the 3 x sigma limits

Usage

ssruns_sig3(x, type = NULL, mixing = "less")
ssruns_sig3(x, type = NULL, mixing = "less")

Arguments

`x`	residuals from CPUE fits
`type`	only `c("resid","observations")`
`mixing`	`c("less","greater","two.sided")`. Default less is checking for positive autocorrelation only

Details

runs test is conducted with library(randtests)

Value

runs p value and 3 x sigma limits

Author(s)

Henning Winker (JRC-EC) and Laurence Kell (Sea++)

Residual Diagnostics Plot

Description

Function for residual diagnostics. Outputs a runs test table that gives runs test p-values, if the runs test passed (p-value > 0.05, residuals are random) or failed (p-value < 0.05, residuals are not random), the 3x sigma limits for indices or mean age or length and the type of input data (cpue, length comp, age comp, size comp, or conditional age-at-length).

Usage

SSrunstest(
  ss3rep,
  mixing = "less",
  quants = c("cpue", "len", "age", "con")[1],
  indexselect = NULL,
  verbose = TRUE
)
SSrunstest(
  ss3rep,
  mixing = "less",
  quants = c("cpue", "len", "age", "con")[1],
  indexselect = NULL,
  verbose = TRUE
)

Arguments

`ss3rep`	Stock Synthesis output as read by `r4ss::SS_output()`
`mixing`	`c("less","greater","two.sided")`. Default less is checking for positive autocorrelation only
`quants`	optional use of `c("cpue","len","age","con")`, default uses `"cpue"`. `"cpue"` Index of abundance data `"len"` Length composition data `"age"` Age composition data `"con"` Conditional age-at-length data
`indexselect`	Vector of fleet numbers for each model for which to compare
`verbose`	Report progress to R GUI?

Value

Author(s)

Henning Winker (JRC-EC) and Laurance Kell (Sea++)

Get Stock Status Settings

Description

A function to get Bratio and F settings

Usage

SSsettingsBratioF(ss3rep, status = c("Bratio", "F"), verbose = TRUE)
SSsettingsBratioF(ss3rep, status = c("Bratio", "F"), verbose = TRUE)

Arguments

`ss3rep`	from r4ss::SSgetoutput()
`status`	covarying stock status quantaties to extract from Hessian
`verbose`	Report progress to R GUI?

Value

output list with Bratio and F settings

Author(s)

Henning Winker (JRC-EC)

Package 'ss3diags'

Help Index

Francis Weighting for compositional data

Description

Usage

Arguments

Value

Author(s)

References

Joint Distributions for Stock Status Ratios

Description

Usage

Arguments

Value

Author(s)

Joint Distributions for Stock Status Ratios

Description

Usage

Arguments

Value

Author(s)

MCMC Joint Distributions

Description

Usage

Arguments

Value

Author(s)

See Also

MCMC Joint Distributions

Description

Usage

Arguments

Value

Author(s)

Mohn's Rho and Forecast Bias

Description

Usage

Arguments

Author(s)

See Also

Mean Absolute Scaled Error

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Model ensemble plots

Description

Usage

Arguments

Author(s)

Examples

Hindcasting Cross-Validations of Multiple Models

Description

Usage

Arguments

Author(s)

Residual plot

Description

Usage

Arguments

Author(s)

KOBE phase plot

Description

Usage

Arguments

Value

Compare Multiple SS Model Estimates

Description

Usage

Arguments

Author(s)

Retrospective-Forecast with One-Step Ahead Hindcasting

Description

Usage

Arguments

Author(s)

Residual Diagnostics

Function for calculating RMSE used for `SSplotJABBAres()`