update(SWFSC-sardine.qmd): Update functionality for 0.3.0.0 #53
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alexjensen-NOAA
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kellijohnson-NOAA and
peterkuriyama-NOAA
content/SWFSC-sardine.qmd
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| @@ -105,6 +103,7 @@ fimscatch <- tibble(type = "landings", name = "fleet1", | |||
| age = NA, datestart = paste0(catch$year, "-01-01"), | |||
| dateend = paste0(catch$year, "-12-31"), value = catch$catch, | |||
| unit = "mt", uncertainty = 0.05) | |||
| fimscatch$value <- fimscatch$value | |||
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I am not sure what this line is doing?
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can delete I think
content/SWFSC-sardine.qmd
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| fimswaa <- tibble(type = "weight-at-age", name = wtatage$fleet, | ||
| age = wtatage$age, datestart = paste0(wtatage$year, "-01-01"), | ||
| dateend = paste0(wtatage$year, "-12-31"), | ||
| value = wtatage$value, unit = "kg", uncertainty = NA) |
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Should value be wtatage$value/1000?
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THe units for wtatage$value are already kg, so I don't think it should be divided by 1000
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It depends on what FIMS is expecting to see for WAA units. From the Seaside Chat on Thursday, it sounded as if WAA should be input to FIMS using mt, not kg, which would require the '/1000' adjustment to the conventional input to SS3.
With this adjustment, the summary biomass and numbers at age match for FIMS and SS3 (assuming that FIMS reports numbers at age in terms of fish and SS3 reports numbers of age in terms of thousands of fish).
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I only noticed the need for the WAA adjustment after the initial pull request. I can add in the '/1000' adjustment, remove the redundant line (above), and submit a new pull request, if that's the easiest way to move forward
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No need for a new PR, just make the necessary changes, add the file(s), commit, and push to this branch. Then the PR will be updated.
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Alex - the SS3 convention is that body wt is in kg, catch and population totals are in mt, and numbers are in thousands. |
- Updated SWFSC-sardine.qmd to utilize new wrapper functions - input WAA data into FIMSFrame - Adjust WAA inputs to FIMS by dividing by 1000, convert kg (SS3) to mt (FIMS) - pull correct outputs from FIMS model fitting - Generated new comparison figures with new model run - Adjust reported recruitment from FIMS to match SS3 units (divide by 1000) - uses packagename:: syntax for almost everything but FIMS - converted to base pipe
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What is the feature?
How have you implemented the solution?
Does the PR impact any other area of the project, maybe another repo?