[Schiano-NOAA]

place model approaches into own R files to setup improvement for testing and example datasets

[sbreitbart-NOAA]

Does this mean that, if I want to convert BAM output, I'll use conout_bam()? I recommend continuing to use convert_output() for all models, but putting conout_ss3(), conout_rceattle() and conout_bam() into that function. It'll keep users' workflows the same while continuing to modularize the conversion steps to individual functions (which I agree with!) Ex:

convert_output() <- function(
if BAM conout_bam(...)
if SS3 conout_ss3(...)
)

etc.

[Schiano-NOAA]

@sbreitbart-NOAA no nothing changes for the user. It is just for maintenance and easier testing/updating example data. That's why they aren't exported. There should be an ifelse statement checking for the model then calling each of the sub fuctions.

[sbreitbart-NOAA]

Oh! I see now (there was so much deleted code I didn't see the new additions). You're doing what I was hoping for!

• Could you please add documentation for these new fxns?
• Also, this didn't work for BAM for me:

test <- convert_output(here::here("inst", "extdata", "VermilionSnapper.rdat"))

Error in conout_bam(file = file, out_new = out_new, fleet_names = fleet_names) : 
  object 'model' not found

• Does this work for r4ss-converted ss3 data? I didn't see an option for that filetype.
• Lastly, I see the fxn differentiates between two types based on ".RDS" vs ".rds" extension (wham/fims). Would it be possible for the authors to have data that's not expected by the fxn simply because it was changed to be all upper or lowercase? Wondering if testing by file extension is sufficient for wham vs fims.

[Schiano-NOAA]

Oh! I see now (there was so much deleted code I didn't see the new additions). You're doing what I was hoping for!

• Could you please add documentation for these new fxns?
• Also, this didn't work for BAM for me:

test <- convert_output(here::here("inst", "extdata", "VermilionSnapper.rdat"))

Error in conout_bam(file = file, out_new = out_new, fleet_names = fleet_names) : 
  object 'model' not found

• Does this work for r4ss-converted ss3 data? I didn't see an option for that filetype.
• Lastly, I see the fxn differentiates between two types based on ".RDS" vs ".rds" extension (wham/fims). Would it be possible for the authors to have data that's not expected by the fxn simply because it was changed to be all upper or lowercase? Wondering if testing by file extension is sufficient for wham vs fims.

Yeah I can add some documentation, but will not be exporting it. I will test these all again. I ran the scripts based on the changes so idk how it's not working.

There should be an action for r4ss example data. It's within the conout_ss3 because they are sort of intertwined with the approach in the beginning.

Could you highlight the line for FIMS that looks at an rda? I don't anticipate people loading in data that way because it's an object in their environment like Rceattle, but they could still differentiate it by stating model = "FIMS" or "WHAM" in the arguments.

[Schiano-NOAA]

Nvm on the FIMS highlight. I found it and made an adjustment