diff --git a/sandbox/pcod_delta_gamma.R b/sandbox/pcod_delta_gamma.R index 5e00a3a..2221a5d 100644 --- a/sandbox/pcod_delta_gamma.R +++ b/sandbox/pcod_delta_gamma.R @@ -67,7 +67,21 @@ fit_vast <- fit_model( b_i = pcod[, "density"], a_i = pcod[, "effort"], input_grid = input_grid, - working_dir = paste0(here("doc", "appendix-VAST"), "/") + working_dir = paste0(here("doc", "appendix-VAST"), "/"), + run_model = FALSE +) +upperbounds <- fit_vast$Upper +upperbounds["logkappa2"] <- 10 +fit_vast <- fit_model( + settings = settings, + Lat_i = pcod[, "lat"], + Lon_i = pcod[, "lon"], + t_i = pcod[, "year"], + b_i = pcod[, "density"], + a_i = pcod[, "effort"], + input_grid = input_grid, + working_dir = paste0(here("doc", "appendix-VAST"), "/"), + upper = upperbounds ) # saveRDS(fit_vast, file = f) # } else {