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commfish / seak_sablefish

NSEI sablefish stock assessment
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query/data issues #2

Open ben-williams opened 6 years ago

ben-williams commented 6 years ago

Survey CPUE (survey_cpue_1988_2016.csv)

Current query lacks: 1) depth - will need to run depth standardized and status quo cpue to provide to managers 2) survey station and actual lat/lon

jysullivan commented 6 years ago

Longline (LL) survey biological data - there were two csvs in Kray's files.

  1. 'srv_bio_data' - very detailed that includes time stamp, setstart/end lat/lon, depth, etc. from 1998 to 2015.
  2. 'srv_bio_data2' - minimal, no time stamp, lat/lon, depth from 1988 to 2016.

Use more detailed query in 2017. Also get station lat/lon along with set start/end lat/lon. @aaronpbaldwin can you please make a comment here about the discussion we had about station definitions on the NSEI LL survey?

Need: 1) An explanation of 'Effort No'

jysullivan commented 6 years ago

fishery biological data (fishery_bio_2000_2016.csv):

ALEX QUERY CRITERIA FOR FISH_BIO_DATA Year BETWEEN 1980 AND 2015 AND species_code = '710' AND g_management_area_code = 'NSEI' AND project_code = '02'

KVK NOTE: when running, always make sure that all data have been read and uploaded into IFDB by the ADU

Need an explanation of 1) G_STAT_AREA_GROUP (e.g. NSEI 22, NSEI 15) 2) SPECIMEN_NO 3) SAMPLE_TYPE_CODE 4) WEIGHT_KILOGRAMS (round? ice/slime? some of these are really heavy, e.g. 17 kg)

jysullivan commented 6 years ago

Lengths - what are the length type code definitions? is there an established conversion between total and fork length?

Weights - when are they dressed, round, ice/slimed? conversion factors?

Maturity code definitions

Age readability codes

Release condition codes

Discard status codes

Depth - I have some of these coming to me as meters and others as fathoms

jysullivan commented 6 years ago

Pot survey data 'potsurvey_bio_2009_2015.csv'

Only have age/sex data for 2009.

Aaron Baldwin 2017-10-24

Up until 2010 we collected biological data on a subset of sablefish. On the marking survey all fish are measured (when possible), even fish not tagged due to injury or mortality. The only real exception are when pots are dumped at rail due to reaching tagging goal. There are always a few that sneak through, either they escape prior to measuring or the recorder misses the length. But procedurally all sablefish brought onboard are measured regardless of being tagged or not.

There are three length entries that measured to the nearest mm instead of cm. Errors?

aaronpbaldwin commented 6 years ago

Yes, we record all lengths to nearest cm but lengths are recorded in mm. For example, a 74 cm fish is recorded as 740 mm. There are still errors (especially with port samplers as we often borrow seasonal techs used to salmon which are measured to the nearest 5 mm).