diff --git a/R/set_catch.R b/R/set_catch.R index 4a6adc0..1a92b0a 100644 --- a/R/set_catch.R +++ b/R/set_catch.R @@ -62,8 +62,10 @@ set_catch = function(input, catch_info= NULL) { if(!is.null(asap3)) { #data$n_fleets = asap3$n_fleets k <- 1 + cum_n_selblocks <- 0 for(i in 1:length(asap3)) { asap3[[i]]$use_catch_acomp <- rep(1,asap3[[i]]$n_fleets) #default is to use age comp for catch + allselblocks_i <- sort(unique(unlist(asap3[[i]]$sel_block_assign))) for(j in 1:asap3[[i]]$n_fleets) { data$fleet_regions[k] = i #each asap file is a separate region data$agg_catch[,k] = asap3[[i]]$CAA_mats[[j]][,data$n_ages + 1] @@ -85,11 +87,12 @@ set_catch = function(input, catch_info= NULL) { } } data$catch_Neff[,k] = asap3[[i]]$catch_Neff[,j] - temp = asap3[[i]]$sel_block_assign[[j]] - temp = match(temp,sort(unique(temp))) #index unique values - data$selblock_pointer_fleets[,k] = max(data$selblock_pointer_fleets) + temp #max grows each time + temp <- asap3[[i]]$sel_block_assign[[j]] + temp <- match(temp,allselblocks_i) #index unique values + data$selblock_pointer_fleets[,k] = cum_n_selblocks + temp #max grows each time k <- k + 1 } + cum_n_selblocks <- cum_n_selblocks + length(allselblocks_i) } data$agg_catch_sigma[which(data$agg_catch_sigma < 1e-15)] = 100 data$agg_catch_sigma = sqrt(log(data$agg_catch_sigma^2 + 1))