Check for OR SP samples

[chantelwetzel-noaa]

https://github.com/nwfsc-assess/PacFIN.Utilities/blob/562be10030cc252fc8bbf8ce2b9b7833f6a9e191/R/cleanPacFIN.R#L295

I think this line of code can be removed since "badORnums" is no longer being passed as an input to the function.

[kellijohnson-NOAA]

It was never passed as input, it is a data object that all functions have access to. Though, we could remove it I think because the last time I checked PacFIN had corrected those samples in their data base. I would want to remove the data object as well.

[chantelwetzel-noaa]

Thank you for the clarification. I had thought I remembered this being an input to the function in 2019, but that might not have been correct. I now see that the badORnums are loaded into the workspace. I won't close this issue at this moment so we can use it as a reminder for us to remove this check and objects from the package later.

[andi-stephens-NOAA]

That was for Owen, a one-off.

On Tue, Feb 16, 2021 at 1:22 PM Chantel Wetzel notifications@github.com wrote:

Thank you for the clarification. I had thought I remembered this being an input to the function in 2019, but that might not have been correct. I now see that the badORnums are loaded into the workspace. I won't close this issue at this moment so we can use it as a reminder for us to remove this check and objects from the package later.

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[kellijohnson-NOAA]

These samples were noticed as being incorrectly labeled during the 2019 sablefish assessment. And, I just checked PacFIN and some of these samples still are not listed as SP instead of O. So, we should keep the check.

[kellijohnson-NOAA]

• [ ] check PacFIN database to ensure that these samples have been removed
• [ ] clean up the code to deprecate this function

[kellijohnson-NOAA]

@aliwhitman there are OR sablefish samples that are Special Project samples labeled as Market samples in PacFIN. Some have been changed to SP but not all. How do we go about fixing the remainder? Here is a list of sample numbers, though some have been fixed. 781067 781068 781069 781070 781071 791069 791070 791071 791072 791073 791074 791075 801141 801142 801143 801144 801145 811169 811170 811171 811172 811173 811174 820001 821300 821301 821302 821303 832042 832043 832044 851253 851254 851255 851256 851257 851258 851259 851260 851261 851262 851263 851264 851265 851266 851267 851268 851269 851270 851271 851272 851273 851274 851275 851276 851277 851278 851279 851280 851281 851282 860001 860002 869251 869252 869253 869254 869255 869256 869257 869258 869259 869260 869261 869262 869263 869264 869265 869266 869267 869268 869269 869270 869271 869272 869273 869274 869275 869276 869277
869278 869279 869280 869281 869282 869283 869284 869285 869286 869287 869288 869289 869290 869291 869292 869293 869294 869295 869296 869297
869298 869299 869300 869301 869302 869303 869304 869305 869306 869307
869308 869309 869310 869311 869312 869313 869314 869315 869316 869317
869318 869319 869320 869321 869322 869323 869324 869325 869326 869327 869328 869329 869330 869331 869332 869333 869334 869335 869336 869337
869338 869339 869340 869341 869342 869343 869344 869345 869346 869347
869348 869349 869350 869351 869352 869353 869354 869355 869356 869357
869358

[aliwhitman]

I'm happy to check on this but I am confused - how can they be labeled as both SP and Market samples in PacFIN?

[kellijohnson-NOAA]

They are labeled M but they should be labeled SP.

[aliwhitman]

Still confused - sorry! perhaps the right question is why should they be labeled SP? But I will send the sample numbers to our data shop for them to fix and then resubmit to PacFIN. And I'll give you an ETA when we have them fixed!

[kellijohnson-NOAA]

@aliwhitman check your email for a string with Ted.R.Calavan@state.or.us from March of 2019 as well as the email I just forwarded.

[aliwhitman]

Gotcha. Thank you! Our data shop are on it, they'll provide updates and I know you need those data ASAP, so I'll stay on it.