I don't know what the current workflow is, but for exploring the fraction of Petrale Sole north of 46 degrees 53.3 minutes, I found it helpful to be able to add a boundary argument to run_sdmtmb(). Perhaps this is unnecessary if you typically run the model once and then separately call calc_index_areas() after the initial estimation. If so, go ahead and delete this PR.
I also added new "North of 46deg 53.3min" and "South of 46deg 53.3min" areas to boundaries_data. If you'd rather not have that file include stuff like this, but think the other commit is useful, please cherry pick as you wish.
These changes allowed me to get everything I wanted in a single call to run_sdmtmb():
run_sdmtmb(
data = data$data_filtered[[1]],
formula = "catch_weight ~ 0 + fyear + pass_scaled",
family = sdmTMB::delta_lognormal(),
anisotropy = TRUE,
n_knots = 500,
boundaries = boundaries_data[c("Coastwide", "North of 46deg 53.3min", "South of 46deg 53.3min")],
spatiotemporal = list("iid", "iid")
)
Related to issue(s)
No issue. Need for petrale calculation discussed by email.
What was changed/addressed
I don't know what the current workflow is, but for exploring the fraction of Petrale Sole north of 46 degrees 53.3 minutes, I found it helpful to be able to add a boundary argument to
run_sdmtmb(). Perhaps this is unnecessary if you typically run the model once and then separately callcalc_index_areas()after the initial estimation. If so, go ahead and delete this PR.I also added new "North of 46deg 53.3min" and "South of 46deg 53.3min" areas to boundaries_data. If you'd rather not have that file include stuff like this, but think the other commit is useful, please cherry pick as you wish.
These changes allowed me to get everything I wanted in a single call to
run_sdmtmb():Related to issue(s)
No issue. Need for petrale calculation discussed by email.