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_targets.R
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##########
##########
# Targets file that has all defined targets to be used in this analysis pipeline
##########
##########
# AUTHOR: Cole B. Brookson
# DATE OF CREATION: 2022-07-31
##########
##########
library(targets)
library(tarchetypes)
library(here)
source(here::here("./R/00_functions_plot_themes.R"))
source(here::here("./R/01_functions_farm_data_cleaning.R"))
source(here::here("./R/02_functions_farm_data_tests.R"))
source(here::here("./R/03_functions_general_data_cleaning.R"))
source(here::here("./R/04_functions_wild_lice_cleaning.R"))
source(here::here("./R/05_functions_wild_lice_regression.R"))
source(here::here("./R/06_functions_wild_lice_scenarios.R"))
source(here::here("./R/07_functions_chalimus_inputation.R"))
source(here::here("./R/08_functions_count_leps.R"))
source(here::here("./R/09_functions_freq_model_fits.R"))
source(here::here("./R/10_functions_freq_model_predictions.R"))
source(here::here("./R/11_functions_predictions_joining.R"))
source(here::here("./R/12_functions_wild_lice_farm_lice_regression.R"))
source(here::here("./R/13_functions_stockrecruit_prep.R"))
source(here::here("./R/14_functions_stockrecruit_models.R"))
source(here::here("./R/15_functions_joining_sr_data.R"))
source(here::here("./R/16_functions_plotting_results.R"))
source(here::here("./R/17_functions_map.R"))
tar_option_set(packages = c("readr", "here", "dplyr", "magrittr", "ggthemes",
"ggplot2", "betareg", "lubridate", "glmmTMB",
"DHARMa", "parallel", "gtable", "grid", "cowplot",
"wesanderson", "patchwork", "stringr", "lme4",
"broom.mixed", "tidyr", "ggrepel", "sp"))
list(
####################
# files
####################
tar_target(raw_data_file_marty,
here::here(
"./data/farm-data/raw/marty-2010-data/marty-data-copied.csv"),
format = "file"),
tar_target(dfo_farm_ref_data,
here::here("./data/farm-data/raw/farm-name-reference.csv"),
format = "file"),
tar_target(raw_data_file_bati,
here::here("./data/farm-data/raw/BATI_farm_louse_data_RAW.csv"),
format = "file"),
tar_target(raw_open_dfo_data,
here::here(
"./data/farm-data/raw/gov-open-data/fish-farm-sea-louse-counts-data.csv"),
format = "file"),
tar_target(scfs_raw_data_file,
here::here(
paste0("./data/wild-lice-data/raw/Sea-lice-database-master/",
"Data/BroughtonSeaLice_fishData.csv")),
format = "file"),
tar_target(raw_nuseds_raw,
here::here(
"./data/sr-data/NuSEDS/NuSEDS_20220902.csv"),
format = "file"),
tar_target(raw_psf_exp,
here::here(
"./data/sr-data/PSF-PSE/dataset1_stream.csv"),
format = "file"),
tar_target(raw_pink_exp,
here::here(
"./data/sr-data/dfo-data/raw/pink/english-report-translated.csv"
), format = "file"),
tar_target(raw_pink_recon,
here::here(
"./data/sr-data/dfo-data/clean/pink-reconstructions.csv"
), format = "file"),
tar_target(raw_pink_helper,
here::here(
"./data/sr-data/dfo-data/raw/pink/helper-data-river-cu-match.csv"
), format = "file"),
tar_target(farm_name_location_helper,
here::here(
"./data/farm-data/raw/farm-name-reference.csv"
), format = "file"),
tar_target(geo_spatial_data,
here::here(
"./data/geo-data/gadm36_CAN_1_sp.rds"
), format = "file"),
####################
# cleaning data
####################
tar_target(clean_open_dfo_data,
clean_dfo_open_data(
get_data_dfo_open(raw_open_dfo_data),
here::here("./data/farm-data/clean/dfo-open-data-clean.csv")
)),
tar_target(marty_data,
clean_data_marty(
raw_data_file_marty,
get_data_dfo_ref(dfo_farm_ref_data),
here::here("./data/farm-data/clean/marty-data-clean.csv")),
format = "rds"),
tar_target(bati_data,
clean_data_bati(
raw_data_file_bati,
here::here("./data/farm-data/raw/farm-name-reference.csv"),
here::here("./data/farm-data/clean/bati-data-clean.csv"))),
tar_target(fill_in_missing_inventories,
fill_in_missing_inventory_data(
clean_open_dfo_data,
get_data_marty_cleaned(
here::here("./data/farm-data/clean/marty-data-clean.csv")),
here::here(
"./data/farm-data/clean/missing-inventory-filled-data.csv")
)),
tar_target(fill_in_late_timeseries_inventories,
match_inventory_data(
bati_data,
clean_open_dfo_data,
here::here("./data/farm-data/clean/wakwa-tsaya-inventory.csv")
)),
tar_target(join_all_farm_data,
join_farm_data(
bati_data,
get_data_marty_cleaned(
here::here("./data/farm-data/clean/marty-data-clean.csv")),
fill_in_missing_inventories,
fill_in_late_timeseries_inventories,
here::here("./data/farm-data/clean/all-farms-joined-clean.csv")
)),
tar_target(test_all_farm_data,
check_lep_tot_values(
join_all_farm_data
)),
tar_target(prepare_wild_lice_data,
clean_data_scfs(
get_data_scfs(scfs_raw_data_file),
here::here("./data/wild-lice-data/clean/scfs-data-clean.csv")
)),
####################
# wild lice regressions
####################
tar_target(motile_proportions_logistic_regression,
lep_regression_mot(
prepare_wild_lice_data,
here::here("./outputs/model-outputs/mot-regression/")
)),
tar_target(cope_proportions_logistic_regression,
lep_regression_cope(
prepare_wild_lice_data,
here::here("./outputs/model-outputs/cope-regression/")
)),
tar_target(wild_lice_nonlinear_regression,
nonlinear_regression_scenario(
prepare_wild_lice_data,
here::here("./outputs/model-outputs/nonlinear-regression/")
)),
tar_target(wild_lice_beta_regression,
beta_regression_scenario(
prepare_wild_lice_data,
here::here("./outputs/model-outputs/beta-regression/")
)),
tar_target(counting_unid_lice_scenarios,
count_unidentified_lice(
prepare_wild_lice_data,
motile_proportions_logistic_regression,
cope_proportions_logistic_regression,
wild_lice_nonlinear_regression,
wild_lice_beta_regression,
here::here(
"./data/wild-lice-data/clean/prepared-unid-counted-lice.csv")
)),
####################
# chalimus inputation
####################
tar_target(chalimus_inputation,
inpute_all_chal_data(
counting_unid_lice_scenarios,
here::here(
"./data/wild-lice-data/clean/chalimus-counted-lice.csv")
)),
####################
# lice counting options
####################
tar_target(scenario_1_indiv_counts,
scenario1_indiv(
chalimus_inputation,
here::here(
"./data/prepped-data/scfs-regression-scen1-indiv.csv"
)
)),
tar_target(scenario_1_year_counts,
scenario1_year(
chalimus_inputation,
here::here(
"./data/prepped-data/scfs-regression-scen1-year.csv"
)
)),
tar_target(scenario_2_counts,
scenario2(
chalimus_inputation,
here::here(
"./data/prepped-data/scfs-regression-scen2.csv"
)
)),
tar_target(scenario_3_counts,
scenario3(
chalimus_inputation,
here::here(
"./data/prepped-data/scfs-regression-scen3.csv"
)
)),
tar_target(scenario_4_counts,
scenario4(
chalimus_inputation,
here::here(
"./data/prepped-data/scfs-regression-scen4.csv"
)
)),
####################
# scenario-specific models of lice per fish
####################
tar_target(scenario_1_indiv_model,
execute_scenario_models(
scenario_1_indiv_counts,
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-1-indiv/")
)
)),
tar_target(scenario_1_year_model,
execute_scenario_models(
scenario_1_year_counts,
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-1-year/")
)
)),
tar_target(scenario_2_model,
execute_scenario_models(
scenario_2_counts,
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-2/")
)
)),
tar_target(scenario_3_model,
execute_scenario_models(
scenario_3_counts,
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-3/")
)
)),
tar_target(scenario_4_model,
execute_scenario_models(
scenario_4_counts,
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-4/")
)
)),
tar_target(scenario_1_indiv_prediction,
execute_model_predictions(
scenario_1_indiv_counts,
join_all_farm_data,
scenario_1_indiv_model,
"scen1_indiv",
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-1-indiv/")
)
)),
tar_target(scenario_1_year_prediction,
execute_model_predictions(
scenario_1_year_counts,
join_all_farm_data,
scenario_1_year_model,
"scen1_year",
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-1-year/")
)
)),
tar_target(scenario_2_prediction,
execute_model_predictions(
scenario_2_counts,
join_all_farm_data,
scenario_2_model,
"scen2",
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-2/")
)
)),
tar_target(scenario_3_prediction,
execute_model_predictions(
scenario_3_counts,
join_all_farm_data,
scenario_3_model,
"scen3",
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-3/")
)
)),
tar_target(scenario_4_prediction,
execute_model_predictions(
scenario_4_counts,
join_all_farm_data,
scenario_4_model,
"scen4",
here::here(
paste0("./outputs/model-outputs/lice-per-fish",
"-regression/scenario-4/")
)
)),
tar_target(join_all_scenario_predictions,
execute_predictions_plot(
scenario_1_indiv_prediction,
scenario_1_year_prediction,
scenario_2_prediction,
scenario_3_prediction,
scenario_4_prediction,
here::here(
paste0("./data/wild-lice-data/clean/",
"all-scenario-yearly-lice-per-fish-estimates.csv")
),
here::here(
"./figs/yearly-lice-per-fish/"
)
)),
####################
# wild lice vs. farm lice regressions & results plots
####################
tar_target(model_all_farm_combos_and_scenarios,
execute_wild_farm_regressions(
join_all_farm_data,
join_all_scenario_predictions,
here::here(
"./outputs/model-outputs/wild-farm-regressions/"
),
here::here(
"./figs/wild-farm-regressions/"
),
here::here(
"./data/prepped-data/predicted-lice-abundance.csv"
)
)),
####################
# prepare nuseds data
####################
tar_target(exploitation_rate_data_prep,
execute_sr_data_prep(
raw_nuseds_raw,
raw_pink_exp,
raw_pink_recon,
raw_pink_helper,
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
)
)),
# scenario 1 - indiv
tar_target(sr_3_pairs_scen1_indiv,
execute_sr_database(
exploitation_rate_data_prep,
3,
join_all_scenario_predictions,
"scen1_indiv",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
tar_target(sr_20_pairs_scen1_indiv,
execute_sr_database(
exploitation_rate_data_prep,
20,
join_all_scenario_predictions,
"scen1_indiv",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
# scenario 1 - year
tar_target(sr_3_pairs_scen1_year,
execute_sr_database(
exploitation_rate_data_prep,
3,
join_all_scenario_predictions,
"scen1_year",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
tar_target(sr_20_pairs_scen1_year,
execute_sr_database(
exploitation_rate_data_prep,
20,
join_all_scenario_predictions,
"scen1_year",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
# scenario 2
tar_target(sr_3_pairs_scen2,
execute_sr_database(
exploitation_rate_data_prep,
3,
join_all_scenario_predictions,
"scen2",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
tar_target(sr_20_pairs_scen2,
execute_sr_database(
exploitation_rate_data_prep,
20,
join_all_scenario_predictions,
"scen2",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
# scenario 3
tar_target(sr_3_pairs_scen3,
execute_sr_database(
exploitation_rate_data_prep,
3,
join_all_scenario_predictions,
"scen3",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
tar_target(sr_20_pairs_scen3,
execute_sr_database(
exploitation_rate_data_prep,
20,
join_all_scenario_predictions,
"scen3",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
# scenario 4
tar_target(sr_3_pairs_scen4,
execute_sr_database(
exploitation_rate_data_prep,
3,
join_all_scenario_predictions,
"scen4",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
tar_target(sr_20_pairs_scen4,
execute_sr_database(
exploitation_rate_data_prep,
20,
join_all_scenario_predictions,
"scen4",
here::here(
"./data/prepped-data/stock-recruit-data-frames/"
),
here::here(
"./figs/stock-recruit-data/"
)
)),
####################
# fit stock recruit models
####################
# scenario 1 - indiv - 3 pairs
tar_target(prep_bootstrap_data_scen1indiv_3pairs,
prep_bootstrap_data(
sr_3_pairs_scen1_indiv,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/three-pairs/"
))
)),
tar_target(sr_c_estimate_scen1indiv_3pairs,
perform_bootstrapping(
sr_3_pairs_scen1_indiv,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/three-pairs/"
))
)),
tar_target(sr_percent_mort_scen1indiv_3pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen1indiv_3pairs,
sr_c_estimate_scen1indiv_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/three-pairs/"
))
)),
tar_target(sr_future_mort_scen1indiv_3pairs,
predict_future_mortality(
prep_bootstrap_data_scen1indiv_3pairs,
sr_percent_mort_scen1indiv_3pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/three-pairs/"
))
)),
# scenario 1 - year - 3 pairs
tar_target(prep_bootstrap_data_scen1year_3pairs,
prep_bootstrap_data(
sr_3_pairs_scen1_year,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/three-pairs/"
))
)),
tar_target(sr_c_estimate_scen1year_3pairs,
perform_bootstrapping(
sr_3_pairs_scen1_year,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/three-pairs/"
))
)),
tar_target(sr_percent_mort_scen1year_3pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen1year_3pairs,
sr_c_estimate_scen1year_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/three-pairs/"
))
)),
tar_target(sr_future_mort_scen1year_3pairs,
predict_future_mortality(
prep_bootstrap_data_scen1year_3pairs,
sr_percent_mort_scen1year_3pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/three-pairs/"
))
)),
# scenario 1 - indiv - 20 pairs
tar_target(prep_bootstrap_data_scen1indiv_20pairs,
prep_bootstrap_data(
sr_20_pairs_scen1_indiv,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/twenty-pairs/"
))
)),
tar_target(sr_c_estimate_scen1indiv_20pairs,
perform_bootstrapping(
sr_20_pairs_scen1_indiv,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/twenty-pairs/"
))
)),
tar_target(sr_percent_mort_scen1indiv_20pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen1indiv_20pairs,
sr_c_estimate_scen1indiv_20pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/twenty-pairs/"
))
)),
tar_target(sr_future_mort_scen1indiv_20pairs,
predict_future_mortality(
prep_bootstrap_data_scen1indiv_20pairs,
sr_percent_mort_scen1indiv_20pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-indiv/twenty-pairs/"
))
)),
# scenario 1 - year - 20 pairs
tar_target(prep_bootstrap_data_scen1year_20pairs,
prep_bootstrap_data(
sr_20_pairs_scen1_year,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/twenty-pairs/"
))
)),
tar_target(sr_c_estimate_scen1year_20pairs,
perform_bootstrapping(
sr_20_pairs_scen1_year,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/twenty-pairs/"
))
)),
tar_target(sr_percent_mort_scen1year_20pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen1year_20pairs,
sr_c_estimate_scen1year_20pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/twenty-pairs/"
))
)),
tar_target(sr_future_mort_scen1year_20pairs,
predict_future_mortality(
prep_bootstrap_data_scen1year_20pairs,
sr_percent_mort_scen1year_20pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen1-year/twenty-pairs/"
))
)),
# scenario 2 - 3 pairs
tar_target(prep_bootstrap_data_scen2_3pairs,
prep_bootstrap_data(
sr_3_pairs_scen2,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/three-pairs/"
))
)),
tar_target(sr_c_estimate_scen2_3pairs,
perform_bootstrapping(
sr_3_pairs_scen2,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/three-pairs/"
))
)),
tar_target(sr_percent_mort_scen2_3pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen2_3pairs,
sr_c_estimate_scen2_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/three-pairs/"
))
)),
tar_target(sr_future_mort_scen2_3pairs,
predict_future_mortality(
prep_bootstrap_data_scen2_3pairs,
sr_percent_mort_scen2_3pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/three-pairs/"
))
)),
# scenario 2 - 20 pairs
tar_target(prep_bootstrap_data_scen2_20pairs,
prep_bootstrap_data(
sr_20_pairs_scen2,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/twenty-pairs/"
))
)),
tar_target(sr_c_estimate_scen2_20pairs,
perform_bootstrapping(
sr_20_pairs_scen2,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/twenty-pairs/"
))
)),
tar_target(sr_percent_mort_scen2_20pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen2_20pairs,
sr_c_estimate_scen2_20pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/twenty-pairs/"
))
)),
tar_target(sr_future_mort_scen2_20pairs,
predict_future_mortality(
prep_bootstrap_data_scen2_20pairs,
sr_percent_mort_scen2_20pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen2/twenty-pairs/"
))
)),
# scenario 3 - 3 pairs
tar_target(prep_bootstrap_data_scen3_3pairs,
prep_bootstrap_data(
sr_3_pairs_scen3,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/three-pairs/"
))
)),
tar_target(sr_c_estimate_scen3_3pairs,
perform_bootstrapping(
sr_3_pairs_scen3,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/three-pairs/"
))
)),
tar_target(sr_percent_mort_scen3_3pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen3_3pairs,
sr_c_estimate_scen3_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/three-pairs/"
))
)),
tar_target(sr_future_mort_scen3_3pairs,
predict_future_mortality(
prep_bootstrap_data_scen3_3pairs,
sr_percent_mort_scen3_3pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/three-pairs/"
))
)),
# scenario 3 - 20 pairs
tar_target(prep_bootstrap_data_scen3_20pairs,
prep_bootstrap_data(
sr_20_pairs_scen3,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/twenty-pairs/"
))
)),
tar_target(sr_c_estimate_scen3_20pairs,
perform_bootstrapping(
sr_20_pairs_scen3,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/twenty-pairs/"
))
)),
tar_target(sr_percent_mort_scen3_20pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen3_20pairs,
sr_c_estimate_scen3_20pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/twenty-pairs/"
))
)),
tar_target(sr_future_mort_scen3_20pairs,
predict_future_mortality(
prep_bootstrap_data_scen3_20pairs,
sr_percent_mort_scen3_20pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen3/twenty-pairs/"
))
)),
# scenario 4 - 3 pairs
tar_target(prep_bootstrap_data_scen4_3pairs,
prep_bootstrap_data(
sr_3_pairs_scen4,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/three-pairs/"
))
)),
tar_target(sr_c_estimate_scen4_3pairs,
perform_bootstrapping(
sr_3_pairs_scen4,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/three-pairs/"
))
)),
tar_target(sr_percent_mort_scen4_3pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen4_3pairs,
sr_c_estimate_scen4_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/three-pairs/"
))
)),
tar_target(sr_future_mort_scen4_3pairs,
predict_future_mortality(
prep_bootstrap_data_scen4_3pairs,
sr_percent_mort_scen4_3pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/three-pairs/"
))
)),
# scenario 4 - 20 pairs
tar_target(prep_bootstrap_data_scen4_20pairs,
prep_bootstrap_data(
sr_20_pairs_scen4,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/twenty-pairs/"
))
)),
tar_target(sr_c_estimate_scen4_20pairs,
perform_bootstrapping(
sr_20_pairs_scen4,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/twenty-pairs/"
))
)),
tar_target(sr_percent_mort_scen4_20pairs,
get_percent_mortality_estimates(
prep_bootstrap_data_scen4_20pairs,
sr_c_estimate_scen4_20pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/twenty-pairs/"
))
)),
tar_target(sr_future_mort_scen4_20pairs,
predict_future_mortality(
prep_bootstrap_data_scen4_20pairs,
sr_percent_mort_scen4_20pairs,
join_all_scenario_predictions,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"scen4/twenty-pairs/"
))
)),
####################
# join data
####################
tar_target(join_c_estimates,
collect_estimates(
sr_c_estimate_scen1indiv_20pairs,
sr_c_estimate_scen1indiv_3pairs,
sr_c_estimate_scen1year_20pairs,
sr_c_estimate_scen1year_3pairs,
sr_c_estimate_scen2_20pairs,
sr_c_estimate_scen2_3pairs,
sr_c_estimate_scen3_20pairs,
sr_c_estimate_scen3_3pairs,
sr_c_estimate_scen4_20pairs,
sr_c_estimate_scen4_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"joined-c-estimates.csv"
))
)),
tar_target(join_mortality_estimates,
collect_estimates(
sr_percent_mort_scen1indiv_20pairs,
sr_percent_mort_scen1indiv_3pairs,
sr_percent_mort_scen1year_20pairs,
sr_percent_mort_scen1year_3pairs,
sr_percent_mort_scen2_20pairs,
sr_percent_mort_scen2_3pairs,
sr_percent_mort_scen3_20pairs,
sr_percent_mort_scen3_3pairs,
sr_percent_mort_scen4_20pairs,
sr_percent_mort_scen4_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"joined-mortality-estimates.csv"
))
)),
tar_target(join_future_mortality_estimates,
collect_estimates(
sr_future_mort_scen1indiv_20pairs,
sr_future_mort_scen1indiv_3pairs,
sr_future_mort_scen1year_20pairs,
sr_future_mort_scen1year_3pairs,
sr_future_mort_scen2_20pairs,
sr_future_mort_scen2_3pairs,
sr_future_mort_scen3_20pairs,
sr_future_mort_scen3_3pairs,
sr_future_mort_scen4_20pairs,
sr_future_mort_scen4_3pairs,
here::here(paste0(
"./outputs/model-outputs/stock-recruit-models/",
"joined-future-mortality-estimates.csv"
))
)),
####################
# plot results of stock recruit models
####################
tar_target(results_plot_c,
make_c_plot(
join_c_estimates,
here::here(
"./figs/stock-recruit-results/"
)
)),
tar_target(results_plot_mortality,
make_mortality_plot(
join_future_mortality_estimates,
here::here(
"./figs/stock-recruit-results/"
)
)),
tar_target(results_focal_plot_mortality,
focal_plot(
join_future_mortality_estimates,
here::here(
"./figs/stock-recruit-results/"
)
)),
tar_target(timeseries_plots,
plot_timeseries(
join_all_farm_data,
here::here(
"./figs/timeseries/"
)
)),
tar_target(study_map,
all_make_map_tasks(
geo_spatial_data,
farm_name_location_helper,
join_all_farm_data,
here::here(
"./figs/maps/study-map-area.png"
)
))
)