36 lines
1.9 KiB
Bash
Executable File
36 lines
1.9 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Run the current learning project workflow end to end.
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#
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# This is intentionally simpler than a targets pipeline.
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# It gives us one command that runs the simulation smoke check and renders the
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# Quarto notebooks while the project is still small.
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set -euo pipefail
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# Make the script work even if it is called from another directory.
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script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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cd "$script_dir"
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mkdir -p "outputs/reports"
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Rscript "scripts/01_simulate_icu_data.R"
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quarto render "notebooks/01_target_trial_basics.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/02_explore_simulated_data.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/03_why_naive_analysis_is_biased.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/04_inverse_probability_weighting.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/05_treatment_assignment_windows.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/06_censoring_and_ipcw.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/07_full_emulation_pipeline.qmd" --output-dir "../outputs/reports"
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quarto render "notebooks/01_target_trial_basics.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/02_explore_simulated_data.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/03_why_naive_analysis_is_biased.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/04_inverse_probability_weighting.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/05_treatment_assignment_windows.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/06_censoring_and_ipcw.qmd" --to docx --output-dir "../outputs/reports"
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quarto render "notebooks/07_full_emulation_pipeline.qmd" --to docx --output-dir "../outputs/reports"
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printf '\nWorkflow complete. Reports are in outputs/reports/.\n'
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