unsexed fish in sample weight

pfmc-assessments / PacFIN.Utilities

R code to manipulate data from the PacFIN database for assessments

http://pfmc-assessments.github.io/PacFIN.Utilities

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unsexed fish in sample weight #15

Open kellijohnson-NOAA opened 5 years ago

kellijohnson-NOAA commented 5 years ago

Need to get UNK_NUM and UNK_WGT from PacFIN.

Then there is the bigger picture of unsexed fish needing to be partitioned to sex before creating the expansion factors. Which might mean that the Weight from the LW relationship needs to be created before a new sex based on partitioning is assigned. I am not sure, could create a partitioned sex column. Many things need to be thought through before this change is made.

More to come.

kellijohnson-NOAA commented 5 years ago

@John-R-Wallace can you investigate adding UNK_NUM and UNK_WGT to the bds extraction files that you so kindly provide?

kellijohnson-NOAA commented 5 years ago

Partitioning sex prior to creating the expansion factors Right now, the workflow states that partitioning unsexed fish should be done after creating the expansion factors. The following needs to be accomplished:

document that sex partitioning is done inside the creation of the first expansion factor
- [ ] document getExpansion_1
- [ ] document sexratio
- [ ] change the workflow documentation
create code that allows for all combinations of doing what you need to do to unsexed fish is produced
- [ ] drop unsexed fish
- [ ] partition them to males and females using a user-specified percent
- [ ] partition them to males and females using a calculated percent
- [ ] keep them as unsexed and expand them separately because they will be included as separate compositions
- [x] allow lengths and ages to be treated differently (maybe a bit extreme here, but necessary to accommodate sablefish best practices)
- [ ] add an argument to getExpansion_1 that specifies how sexes are partitioned
- [ ] fix UNK_WGT to UNK_WT
get necessary data into the bds extraction data
- [x] UNK_NUM
- [x] UNK_WGT

John-R-Wallace-NOAA commented 5 years ago

The UNK_NUM and UNK_WT were left in the bds_sample_odfw table and not copied to bds_sample like the females and males weights and numbers.

Note also, that the PacFIN table info online:

https://pacfin.psmfc.org/pacfin_pub/table_cols.php

unk_num Total number of sex unknown fish in sample unk_wgt Total weight (pounds) of sex unknown fish in sample

shows the unk_wt name incorrectly as: unk_wgt

I now have these unknown columns in the SQL code.

On 4/4/2019 2:40 PM, Kelli Johnson wrote:

@John-R-Wallace https://github.com/John-R-Wallace can you investigate adding UNK_NUM and UNK_WGT to the bds extraction files that you so kindly provide?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nwfsc-assess/PacFIN.Utilities/issues/15#issuecomment-480073888, or mute the thread https://github.com/notifications/unsubscribe-auth/AGiX2QT9IV2gMPXYd_oyc7oJIVIoe1Oeks5vdnFIgaJpZM4cTQyb.

kellijohnson-NOAA commented 5 years ago

Thank you @John-R-Wallace