Hi Laura,
It's not totally clear to me what the issue is but here's some more information about what gets plotted.
In the Report.sso there are tables titled LEN_SELEX and AGE_SELEX, which get in the list of stuff produced by the r4ss function SS_output are called $sizeselex and $ageselex (the reasons for the mismatch of "size" vs. "len" are lost to history). Each of these tables shows multiple things as designated by the "Factor" column. The plot below is showing the values associated with the "Lsel" factor in the LEN_SELEX table and there is a similar plot showing the "Asel" factor from AGE_SELEX for models that have age-based selectivity.
In order to convert length-based selectivity to age-based fishing mortality, SS computes the product of the length-based selectivity and the AGE_LENGTH_KEY ($ALK in r4ss) to get a derived age-based selectivity. This is reported in AGE_SELEX as factor "Asel2", but only for the fleets with catch for which mortality needs to be computed. This is shown in the figure below.
In this example, the fishery selectivity was asymptotic in both cases, but it's possible to have a dome-shaped length-based selectivity result in an asymptotic depending on where the selectivity curve is positioned relative to the growth curve. To facilitate this comparison, plots like the one below show selectivity relative to growth.
In this case, the fact that some of the oldest fish are not fully selected leads to the derived age-based selectivity less than 100% for the older fish in that middle plot. If there were a dome-shape in the selectivity that occurred at sizes beyond growth curve, it wouldn't much impact on the derived age-based selectivity which would still appear asymptotic.
To see the combined effect of length-based retention and age-based selectivity, you could look at some of the AGE_SELEX factors at the bottom of the table, including "sel*ret_nums" and "sel*ret*wt". The r4ss function SSplotSelex, which is called by SS_plots to produce the figures above, accepts arguments "sizefactors" and "agefactors" which would allow you to compare retention curves and a variety of other things, but it doesn't seem to work for those factors at the bottom of AGE_SELEX (I'll loook into it when I get the chance).
I hope this helps. It would be easier to diagnose your particular issue if you share some files or figures.
-Ian
