Issue with season allocation

[mariazuba]

Hi!

I have a question regarding the function ss3om::readFLSss3(). I am working with an SS3 model with four seasons, where:

• Spawning occurs at the beginning of April (season 2).
• Recruitment is set at the beginning of July (season 3).

However, when reading the model into FLStock using readFLSss3(), it appears that only season 1 is being considered, which results in recruitment being equal to zero (rec = 0).

Upon inspecting the FLStock object, I noticed that the season dimension is set to 1, instead of reflecting the four seasons defined in the SS3 model.

stk
An object of class "FLStock"

Name: ane.27.9aS
Description: 2024, ICES, SS3
Quant: age
Dims: age year unit season area iter
4 36 1 1 1 1

Range: min max pgroup minyear maxyear minfbar maxfbar
0 3 3 1989 2024 0 3

Metrics:
rec: 0 - 0 (1000)
ssb: 11456 - 38736 (t)
catch: 566 - 9528 (t)
fbar: 0.042 - 0.931 (f)

How can I ensure that readFLSss3() correctly reads all seasons from the SS3 model?
Is there a specific option or argument in the function to correctly assign spawning stock biomass (SSB) and recruitment to the appropriate seasons?

I would appreciate any guidance on how to resolve this issue.

María José

[iagomosqueira]

Can you share the input files? What version of SS3 is it?

[mariazuba]

The SS3 input files can be found at the following link:
SS3 Input Files

The SS3 version used is:
SS version: 3.30.22.beta

[iagomosqueira]

I have run it using 3.30.21.1, with the latest version of 'r4ss' and 'ss3om' installed by calling

install.packages(c('ss3om', 'r4ss'), repos=c("https://flr.r-universe.dev"))

The FLStock object has 4 seasons

stk <- readFLSss3('ane27.9aS')

> stk
An object of class "FLStock"

Name: control.SS
Description: ane27.9aS/Report.sso - 3.30
Quant: age
Dims:  age      year    unit    season  area    iter
        4       36      1       4       1       1

Range:  min     max     pgroup  minyear maxyear minfbar maxfbar
        0       3       3       1989    2024    0       3

Metrics:
  rec: 0.0e+00 - 1.2e+07  (1000)
  ssb: 1354 - 38736  (t)
  catch: 3.8 - 3845.0  (t)
  fbar: 0.00057 - 0.78689  (f)
> dim(stk)
[1]  4 36  1  4  1  1
>

What version of ss3om do you have? If it still fails for you, could you please send me the Report.sso file?

[iagomosqueira]

And recruits show up in season 3

> rec(stk)[,1]

An object of class "FLQuant"
, , unit = unique, season = 1, area = unique

   year
age 1989
  0       0

, , unit = unique, season = 2, area = unique

   year
age 1989
  0       0

, , unit = unique, season = 3, area = unique

   year
age 1989
  0 6587650

, , unit = unique, season = 4, area = unique

   year
age 1989
  0 3121930

units:  1000

[mariazuba]

If it worked, thank you very much!