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Apply Francis composition weighting method TA1.8

Source: R/SSMethod.TA1.8.R
SSMethod.TA1.8.Rd

Uses method TA1.8 (described in Appendix A of Francis 2011) to do stage-2 weighting of composition data from a Stock Synthesis model. Outputs a multiplier, w (with bootstrap 95% confidence interval), so that N2y = w x N1y, where N1y and N2y are the stage-1 and stage-2 multinomial sample sizes for the data set in year y. Optionally makes a plot of observed (with confidence limits, based on N1y) and expected mean lengths (or ages).

CAUTIONARY/EXPLANATORY NOTE. The large number of options available in SS makes it very difficult to be sure that what this function does is appropriate for all combinations of options. The following notes might help anyone wanting to check or correct the code.

  1. The code first takes the appropriate database (lendbase, sizedbase, agedbase, or condbase) and removes unneeded rows.

  2. The remaining rows of the database are grouped into individual comps (indexed by vector indx) and relevant statistics (e.g., observed and expected mean length or age), and ancillary data, are calculated for each comp (these are stored in pldat - one row per comp). If the data are to be plotted, the comps are grouped, with each group corresponding to a panel in the plot, and groups are indexed by plindx.

  3. A single multiplier is calculated to apply to all the comps.

Usage

SSMethod.TA1.8(
  fit,
  type,
  fleet,
  part = 0:2,
  sexes = 0:3,
  seas = NULL,
  method = NULL,
  plotit = TRUE,
  printit = FALSE,
  datonly = FALSE,
  plotadj = !datonly,
  maxpanel = 1000,
  fleetnames = NULL,
  label.part = TRUE,
  label.sex = TRUE,
  set.pars = TRUE,
  add = FALSE
)

Arguments

fit

Stock Synthesis output as read by r4SS function SS_output

type

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 (the output N multiplier applies to all fleets combined)

part

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

sexes

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

seas

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.S If is.null(seas) it is assumed that there is only one season in the selected data (a warning is output if this is not true) and option 'comb' is used.

method

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

plotit

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

printit

if TRUE, print results to R console.

datonly

if TRUE, don't show the model expectations

plotadj

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

maxpanel

maximum number of panels within a plot

fleetnames

Optional replacement for fleetnames used in data file.

label.part

Include labels indicating which partitions are included?

label.sex

Include labels indicating which sexes are included?

set.pars

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

add

add to existing plot

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.

See also

Other tuning functions: SSMethod.Cond.TA1.8(), tune_comps()

Author

R.I.C Chris Francis, Andre E. Punt, Ian G. Taylor

Examples

if (FALSE) { # \dontrun{
Nfleet <- length(myreplist[["FleetNames"]])
for (Ifleet in 1:Nfleet) {
  SSMethod.TA1.8(myreplist, "len", fleet = Ifleet, maxpanel = maxpanel)
}
for (Ifleet in 1:Nfleet) {
  SSMethod.TA1.8(myreplist, "age", fleet = Ifleet, maxpanel = maxpanel)
}
for (Ifleet in 1:Nfleet) {
  SSMethod.TA1.8(myreplist, "size", fleet = Ifleet, maxpanel = maxpanel)
}
for (Ifleet in 1:Nfleet) {
  SSMethod.TA1.8(myreplist, "con", fleet = Ifleet, maxpanel = maxpanel)
}
for (Ifleet in 1:Nfleet) {
  SSMethod.Cond.TA1.8(myreplist, fleet = Ifleet, maxpanel = maxpanel)
}
} # }