/
Makefile
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Makefile
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#######################
# Files and directories
# ---------------------
mmods_viz_tools="src/viz/mmods_viz_tools.R"
mmods_analysis_tools = "src/analysis/mmods_analysis_tools.R"
fig_dir="output/figures"
################
# Data cleaning
# --------------
combine_teamdata_round1:
Rscript src/data/combine_processed_files.R \
"data/processed/round1/submissions" \
"data/processed/round1/team_submissions_only_round1.csv"
combine_teamdata_round2:
Rscript src/data/combine_processed_files.R \
"data/processed/round2/submissions" \
"data/processed/round2/team_submissions_only_round2.csv"
data_round2: add_ranks_round2
Rscript src/data/create_rdata_object.R \
"data/processed/round2/team_submissions_incl_agg_round2.csv" \
"data/processed/round2/mmods1_round_2_results_clean.Rdata"
prepare_county_data:
Rscript src/data/prepare_county_data.R \
"data/processed/county/county_attributes.xlsx" \
"data/processed/county/time_series_covid19_deaths_US.csv" \
"data/processed/county/time_series_covid19_confirmed_US.csv" \
"data/processed/county/processed"
################
# Analysis
# --------------
# Calculate aggregate distribution
# add new 'aggregate' column to cleaned data
add_aggregate_round1: combine_teamdata_round1
Rscript src/analysis/calculate_aggregate.R \
$(mmods_analysis_tools) \
"data/processed/round1/team_submissions_only_round1.csv"\
"data/model_weights.csv"\
"data/processed/round1/team_submissions_incl_agg_round1_allquantiles.csv" \
1
add_ranks_round1: add_aggregate_round1
Rscript src/analysis/calculate_ranks.R \
$(mmods_analysis_tools) \
"data/processed/round1/team_submissions_incl_agg_round1_allquantiles.csv" \
"data/processed/round1/team_submissions_incl_agg_round1.csv"
add_aggregate_round2: combine_teamdata_round2
Rscript src/analysis/calculate_aggregate.R \
$(mmods_analysis_tools) \
"data/processed/round2/team_submissions_only_round2.csv"\
"data/model_weights.csv"\
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv" \
2
add_ranks_round2: add_aggregate_round2
Rscript src/analysis/calculate_ranks.R \
$(mmods_analysis_tools) \
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv"\
"data/processed/round2/team_submissions_incl_agg_round2.csv"
compare_rounds:
Rscript src/analysis/round_comparison.R \
"data/processed/round1/team_submissions_incl_agg_round1.csv"\
"data/processed/round2/team_submissions_incl_agg_round2.csv"\
"data/processed/compare_rounds.Rdata"
compare_agg:
Rscript src/analysis/compare_w_aggregate.R \
"data/processed/round1/team_submissions_incl_agg_round1.csv"\
"data/processed/round2/team_submissions_incl_agg_round2.csv"\
"data/processed/compare_aggregate.Rdata"
###############
# Visualization
# -------------
# Figure 1: aggregate and individual model results for
# each objective and intervention pair
fig1:
Rscript src/viz/figure_1.R \
$(mmods_viz_tools) \
"data/processed/round2/mmods1_round_2_results_clean.Rdata" \
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv" \
"$(fig_dir)"
# Figure 2: days closed R1 vs. R2
fig2:
Rscript src/viz/figure_2.R \
$(mmods_viz_tools) \
"data/processed/compare_rounds.Rdata" \
$(fig_dir)
# Figure 3: comparison with county data
fig3:
Rscript src/viz/figure_3.R \
$(mmods_viz_tools) \
"data/processed/county/processed/county_deaths_cdf_closed_strict.csv" \
"data/processed/county/processed/county_deaths_cdf_closed_partial.csv" \
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv" \
$(fig_dir)
fig4_panels:
Rscript src/viz/multipanel_figure.R \
$(mmods_viz_tools) \
"data/processed/round2/mmods1_round_2_results_clean.Rdata" \
"data/processed/compare_rounds.Rdata" \
"output/figures/Figure4_panels"
## supplemental figures
# projection results
# Figure S2 - S15
sfigs_proj:
Rscript src/viz/plotting_targets_round2_abridged.R \
$(mmods_viz_tools) \
"data/processed/round2/mmods1_round_2_results_clean.Rdata" \
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv" \
"data/processed/round1/team_submissions_incl_agg_round1_allquantiles.csv" \
"data/processed/compare_rounds.Rdata" \
"data/processed/compare_aggregate.Rdata" \
"output/figures/supplemental_figures"
# county data comparison results
# Figure S16 - 17
figs_county:
Rscript src/viz/plotting_targets_county.R \
$(mmods_viz_tools) \
"data/processed/county/processed/county_deaths_cdf_closed_strict.csv" \
"data/processed/county/processed/county_deaths_cdf_closed_partial.csv" \
"data/processed/county/processed/county_cases_cdf_closed_strict.csv" \
"data/processed/county/processed/county_cases_cdf_closed_partial.csv" \
"data/processed/round2/team_submissions_incl_agg_round2_allquantiles.csv" \
"output/figures/supplemental_figures"
# model metadata
# Figure S18-20
figs_checklist:
Rscript src/viz/plotting_targets_county.R \
$(mmods_viz_tools) \
"data/processed/round2/checklist_data.csv" \
"data/processed/round2/checklist_parameter_data.csv"
"output/figures/supplemental_figures"