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timjmiller / wham

State-space, age-structured fish stock assessment model
https://timjmiller.github.io/wham
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data$n_fleets in set_catch is hard wired to 1 fleet #70

Closed chengmatt closed 1 year ago

chengmatt commented 1 year ago

Hi Tim,

Line 52 in the set_catch function hard wires the number of fleets to 1. When I feed my data into prepare_wham_input, it outputs an object that has $n_fleet = 1, and agg_catch_sigma is only 1 column instead of multiple columns/fleets.

When I feed it into WHAM, the model runs fine (although it runs into convergence issues), but when I go to plot it, it results in the following error: Error in (log(catch) - pred_log_catch[1:length(years), ])/sigma : non-conformable arrays

timjmiller commented 1 year ago

The $n_fleet issue should not be resolved on devel branch. Is the plotting issue caused by this error or a separate issue? If everything works with the updated install then please close the issue. Sorry it took so long to get around to this.

chengmatt commented 1 year ago

Hi Tim,

No problem - thanks for fixing this! WHAM ends up running fine, and the plot fxn works as well. I had initially closed the issue because it ended up running fine, but dropped some of the catch data (resulted in some bias).