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remake.yml
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remake.yml
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packages:
- magrittr
- dplyr
- GrasslandAllocatr
- devtools
sources:
- remake/utils/field_data_2010_2011_reshape.R
targets:
all:
depends:
- field_data_by_quadrat_2014
- field_data_transect_2014
- field_data_mu_2014
- casefile_df_2014
- processed_data/casefile_2014.cas
- field_data_mu_2014a
- field_data_quadrat_2015
- field_data_transect_2015
- field_data_mu_2015
- casefile_df_2014_2015
- processed_data/casefile_2014_2015.cas
- field_data_mu_2010_2011
- casefile_df_2010_2011
- processed_data/casefile_2010_2011.cas
- processed_data/grassland_bbn_learned_1.dne
- processed_data/grassland_bbn_learned_2.dne
- processed_data/grassland_bbn_learned_3.dne
- scenario_analysis_prior
- scenario_analysis_snapshot
- scenario_analysis_posterior
- ms/sensitivity_analysis.md
- ms/scenario_analysis.md
field_data_by_quadrat_2014:
command: build_raw_dataset(raw_field_data = "data-raw/field_data_raw_2014.csv",
species_lookup_data = "data-raw/species_lookup_table.csv",
management_lookup_data = "data-raw/field_site_management_2014.csv")
field_data_transect_2014:
command: summarise_by_transect(field_data_by_quadrat_2014)
field_data_mu_2014:
command: summarise_by_mu(field_data_by_transect = field_data_transect_2014, year = 1)
casefile_df_2014:
command: generate_case_file_df(field_data_mu_2014)
processed_data/casefile_2014.cas:
command: write.CaseFile(casefile_df_2014, file = 'processed_data/casefile_2014.cas')
field_data_mu_2014a:
command: summarise_by_mu(field_data_by_transect = field_data_transect_2014, year = 0)
field_data_quadrat_2015:
command: build_raw_dataset(raw_field_data = "data-raw/field_data_raw_2015.csv",
species_lookup_data = "data-raw/species_lookup_table.csv",
management_lookup_data = "data-raw/field_site_management_2015.csv")
field_data_transect_2015:
command: summarise_by_transect(field_data_quadrat_2015)
field_data_mu_2015:
command: summarise_by_mu(field_data_by_transect = field_data_transect_2015, year = 1)
casefile_df_2014_2015:
command: generate_case_file_df(field_data_mu_2014a, field_data_mu_2015)
processed_data/casefile_2014_2015.cas:
command: write.CaseFile(casefile_df_2014_2015, file = 'processed_data/casefile_2014_2015.cas')
field_data_mu_2010_2011:
command: reshape_pauls_data_all_years(file_path = 'data-raw/field_data_by_transect_2010_2011.csv')
casefile_df_2010_2011:
command: generate_case_file_df(field_data_mu_2010_2011)
processed_data/casefile_2010_2011.cas:
command: write.CaseFile(casefile_df_2010_2011, file = 'processed_data/casefile_2010_2011.cas')
# ---------------- Load and Learn Process Model "load_learn_process_model"--------------
processed_data/grassland_bbn_learned_1.dne:
command: learn_grassland_bbn(path = "data/grassland_bbn_no_learning.dne", casefile_path = "processed_data/casefile_2010_2011.cas", save_path = "processed_data/grassland_bbn_learned_1.dne")
processed_data/grassland_bbn_learned_2.dne:
command: learn_grassland_bbn(path = "processed_data/grassland_bbn_learned_1.dne", casefile_path = "processed_data/casefile_2014.cas",save_path = "processed_data/grassland_bbn_learned_2.dne", first_iteration = FALSE)
processed_data/grassland_bbn_learned_3.dne:
command: learn_grassland_bbn(path = "processed_data/grassland_bbn_learned_1.dne", casefile_path = "processed_data/casefile_2014_2015.cas", save_path = "processed_data/grassland_bbn_learned_3.dne")
# --------------- Run Analyses -------------------------------------------------
scenario_analysis_prior:
command: predict_grassland_condition(network_path = "processed_data/grassland_bbn_learned_1.dne",strategies_casefile = "processed_data/management_strategies.cas", sites_casefile = "processed_data/generate-cases.cas")
scenario_analysis_snapshot:
command: predict_grassland_condition(network_path = "processed_data/grassland_bbn_learned_2.dne",strategies_casefile = "processed_data/management_strategies.cas", sites_casefile = "processed_data/generate-cases.cas")
scenario_analysis_posterior:
command: predict_grassland_condition(network_path = "processed_data/grassland_bbn_learned_3.dne",strategies_casefile = "processed_data/management_strategies.cas", sites_casefile = "processed_data/generate-cases.cas")
ms/scenario_analysis.md:
depends:
- scenario_analysis_prior
- scenario_analysis_snapshot
- scenario_analysis_posterior
knitr:
chdir: true
auto_figure_prefix: true
ms/sensitivity_analysis.md:
depends:
- processed_data/grassland_bbn_learned_1.dne
- processed_data/grassland_bbn_learned_2.dne
- processed_data/grassland_bbn_learned_3.dne
knitr:
chdir: true
auto_figure_prefix: true