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
)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.
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