Confirm meaning of NA's

[rBatt]

When the trawl2 object has NA's in it, how should they be interpreted? Currently I am considering them as presences, but of unknown cpue.

[rBatt]

I think my interpretation is right. But trawl2 doesn't exist anymore, using trawlData. Will revisit issue if necessary.

[rBatt]

@JWMorley do you know how an NA wtcpue in SEUS should be interpreted?

[rBatt]

Same question for 0 wtcpue's.

If 0's and NA's for wtcpue indicate that the species was present but of unknown biomass, then at this line abund should just be 1. Otherwise, it should be set to the appropriate piece of logic (e.g., abund:=as.itneger(wtcpue>0)).

As an example, see some of the raw Scotian Shelf data:

raw.shelf[spp=="MERLUCCIUS BILINEARIS"]
      CODE stratum    MISSION SETNO MARKET SAMPWGT  ADJ_TOTWGT    ADJ_TOTNO CALWT REMARKS SIZE_CLASS    SDATE TIME    SLAT   SLONG    ELAT   ELONG AREA DUR
   1:   14         ATC1978279    81     NA   2.000  2.18750000    4.3750000     0                  1 78-07-13  125 4210.00 6630.00      NA      NA  523  30
   2:   14         ATC1978279    82     NA   0.000  0.00000000    1.0937500     0                  1 78-07-13  355 4211.00 6617.00      NA      NA  523  30

That is Silver Hake. In the second row, the sample weight is 0, but there is a non-0 ADJ_TOTNO (adjusted total number [count], I believe). So a 0 wtcpue probably dosen't mean 0 abundance // even with 0 wtcpue, the species might still be present.

Judging by what Jim did for SEUS in Ocean Adapt see here, I'm guessing that at least for SA 0 or NA in the weight still indicates a presence.

[JWMorley]

I believe everything in SEUS has a weight, with a few exceptions. The exceptions were due to them dealing with protected species (turtles), large-unwieldy species (stingray), and I think some species that were being tagged or processed for tissue sampling (horseshoe crab).

As you mentioned in another message, I corrected for these missing weights based on average weights of these species from the survey. The only other option was throwing out select years for those species (b/c they are typically rare species and dropping an individual might throw things off). Jim

@JWMorley do you know how an NA wtcpue in SEUS should be interpreted?

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Reply to this email directly or view it on GitHub: https://github.com/rBatt/trawl/issues/25#issuecomment-191992690

[JWMorley]

I can see three ways a zero biomass might occur: 1) the individual was too small to register a weight on their scales, 2) someone saw the specimen but it got mistakenly pitched overboard before weighing, 3) the specimen got chewed up in the gear/mesh and could still be recognized but wasn't weighed.

In short, I'd count it as a presence. Jim

Same question for 0 wtcpue's.

If 0's and NA's for wtcpue indicate that the species was present but of unknown biomass, then at this line abund should just be 1. Otherwise, it should be set to the appropriate piece of logic (e.g., abund:=as.itneger(wtcpue>0)).

As an example, see some of the raw Scotian Shelf data:

raw.shelf[spp=="MERLUCCIUS BILINEARIS"]
      CODE stratum    MISSION SETNO MARKET SAMPWGT  ADJ_TOTWGT
ADJ_TOTNO CALWT REMARKS SIZE_CLASS    SDATE TIME    SLAT   SLONG
ELAT   ELONG AREA DUR
   1:   14         ATC1978279    81     NA   2.000  2.18750000
4.3750000     0                  1 78-07-13  125 4210.00 6630.00
NA      NA  523  30
   2:   14         ATC1978279    82     NA   0.000  0.00000000
1.0937500     0                  1 78-07-13  355 4211.00 6617.00
NA      NA  523  30

That is Silver Hake. In the second row, the sample weight is 0, but there is a non-0 ADJ_TOTNO (adjusted total number [count], I believe). So a 0 wtcpue probably dosen't mean 0 abundance // even with 0 wtcpue, the species might still be present.

Judging by what Jim did for SEUS in Ocean Adapt see here, I'm guessing that at least for SA 0 or NA in the weight still indicates a presence.

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Reply to this email directly or view it on GitHub: https://github.com/rBatt/trawl/issues/25#issuecomment-192007681