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gavinfay / bsb-ss-2022

Black Sea Bass RTA 2022 Stock Synthesis application
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Recreational Fishery Data Length Comp Sample Sizes #17

Open jmcnamee opened 1 year ago

jmcnamee commented 1 year ago

OK, for the recreational length comp sample sizes its pretty straight forward:

  1. For the Harvest data, go to workspace BSB.Fishery.Data.For.SS. In that workspace, there is an object called rec.ab1.len. The sample sizes can be summed by year, area, and semester from the column SampleSize.
  2. For the release data, same workspace, but go to the object rec.b2.len. The sample sizes can be summed by year, area, and semester from the column SampleSizeScaled or SampleSize (they are the same). I am going to update the workspace in a minute, I think Sam made a modification or two since we last uploaded it. I'll work on the other stuff in the morning.
lidach commented 1 year ago

For some CAL data points, the sample size is 0. Will this be a problem?

gavinfay commented 1 year ago

This shouldn't be possible, but it suggests that the length data are imputed somehow. Easiest thing for us right now is to do a filter on the data frame before writing to the dat file to remove rows where there were actually no samples, but I can check what is being referenced in the composition data. Thank you for flagging this!

On Thu, May 4, 2023 at 2:06 AM Lisa Chong @.***> wrote:

For some CAL data points, the sample size is 0. Will this be a problem?

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lidach commented 1 year ago

I uploaded the sample sizes for the length comps and updated the data file but there were a few issues I encountered:

jmcnamee commented 1 year ago

I will loop back on the other bullets, need to look in to those a bit more, but on your first and last bullets, "LIS" is the CT Long Island Sound trawl survey (a.k.a. fleets 17 and 18), so I think this knocks out two of those questions (bullets 1 and 4).

gavinfay commented 1 year ago

at some point during sample size calculations, the recreational discard length compositions have been removed from the processing output. @lidach any idea what happened here?

Also, I notice that many of the sample sizes for length comps seem unreasonably large (in the 1000s).

gavinfay commented 1 year ago

OK, noticing a few errors in the length comp processing code (I think as a result of joining sample sizes to the comps), @gavinfay fixing these.

gavinfay commented 1 year ago

Still struggling to find Recreational Data sample size (or rather what the column 'SampleSize' represents. For example, the rec.ab1.len$SampleSize are by cm. Are these number of fish sampled for each length (not likely because in some cases they are greater than the N_AB1, which seems infeasible), or are they the number of trips that were sampled that caught fish of these lengths? If it is the latter (number of samples where fish of these lengths were measured), summing over the lengths within a year/season/area will not be the total number of trips sampled, because individual trips could (probably did) measure fish of more than 1 length - ie it is duplicating trips. If it is the former (number of fish measured), then we still don't have the sample size information. @jmcnamee & @lidach can you provide some illumination? Alternatively, is there just an easy way of downloading the sample size information? (ie it doesn't have to be connected to the data, just have the sample sizes by year/season/area)

lidach commented 1 year ago

@gavinfay I'm not sure how far you got but it seemed like I made some summing mistakes for the length comps. And I'm not sure about the rec.ab1.len, can't find any information on the data Github repository

jmcnamee commented 1 year ago

Hi @gavinfay and @lidach . On this topic (rec length sample sizes), I am communicating with Sam and I think the solution is to get the number of intercepts (closest analog to trips), it currently is number of fish sampled. I'll follow up once I get that data.

gavinfay commented 1 year ago

@jmcnamee @lidach Was this ever resolved?

gavinfay commented 1 year ago

Asking because there are a lot of garbage sample size values (mainly for discard) of less than 1. (though in some cases the data look quite good) Additionally, there are a lot of comp data (again the discards) that have no sample size information (and the placeholder N of 25 is being applied). The sample sizes are being calculated from variable called SampleSizeTrip in objects rec.b2.len & rec.ab1.len, but there's no intuitive way I can tell of knowing what that variable is. I am going through these because I today discovered a very large error in the commercial discard length comp calculations and wanting to check everything else.