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build_commands.sh
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# Main analysis
Rscript -e "rmarkdown::render('0_Load_and_clean.Rmd', output_dir = 'knit_out')" &&
Rscript -e "rmarkdown::render('1_Exploratory_analysis.Rmd', output_dir = 'knit_out')" &&
Rscript -e "rmarkdown::render('2_Baseline_imputation.Rmd', output_dir = 'knit_out')" &&
time Rscript -e "rmarkdown::render('3a_Outcome_model_fit.Rmd', output_dir = 'knit_out')" &&
time Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out')" &&
time Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out')" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out')" &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out')" &&
Rscript -e "rmarkdown::render('5_Table_2_outcomes.Rmd', output_dir = 'knit_out')" &&
Rscript -e "rmarkdown::render('6_Table_1.Rmd', output_dir = 'knit_out')"
# Sensitivity analysis: SAP model with priors
time Rscript -e "rmarkdown::render('3a_2_Outcome_model_fit_with_priors.Rmd', output_dir = 'knit_out/main_fit_with_priors', params = list(fit_name = 'main_fit_with_priors'))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/main_fit_with_priors', params = list(fit_name = 'main_fit_with_priors'))" &&
Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/main_fit_with_priors', params = list(fit_name = 'main_fit_with_priors'))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/main_fit_with_priors', params = list(fit_name = 'main_fit_with_priors'))" &&
rm output/28-35/main_fit_with_priors/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/main_fit_with_priors', params = list(fit_name = 'main_fit_with_priors'))"
# Sensitivity analysis: Original outcome definition
Rscript -e "rmarkdown::render('0_Load_and_clean.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
Rscript -e "rmarkdown::render('1_Exploratory_analysis.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
Rscript -e "rmarkdown::render('2_Baseline_imputation.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
time Rscript -e "rmarkdown::render('3a_Outcome_model_fit.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
time Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))" &&
rm output/28-30/main_fit/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/28-30', params = list(outcome_min = 28, outcome_max = 30))"
# Sensitivity analysis: Extended outcome definition
Rscript -e "rmarkdown::render('0_Load_and_clean.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
Rscript -e "rmarkdown::render('1_Exploratory_analysis.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
Rscript -e "rmarkdown::render('2_Baseline_imputation.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
## UP TO HERE
time Rscript -e "rmarkdown::render('3a_Outcome_model_fit.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
time Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
rm output/28-40/main_fit/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/28-40', params = list(outcome_min = 28, outcome_max = 40))" &&
# Sensitivity analysis: SAP model with extra covariates
Rscript -e "rmarkdown::render('3a_3_Outcome_model_fit_sap_extras.Rmd', output_dir = 'knit_out/main_fit_sap_extras', params = list(fit_name = 'main_fit_sap_extras'))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/main_fit_sap_extras', params = list(fit_name = 'main_fit_sap_extras'))" &&
Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/main_fit_sap_extras', params = list(fit_name = 'main_fit_sap_extras'))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/main_fit_sap_extras', params = list(fit_name = 'main_fit_sap_extras'))" &&
rm output/28-35/main_fit_sap_extras/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/main_fit_sap_extras', params = list(fit_name = 'main_fit_sap_extras'))" &&
# No-interaction fit
Rscript -e "rmarkdown::render('3a_5_Outcome_model_fit_no_interactions.Rmd', output_dir = 'knit_out/main_fit_no_interactions', params = list(fit_name = 'main_fit_no_interactions'))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/main_fit_no_interactions', params = list(fit_name = 'main_fit_no_interactions'))" &&
Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/main_fit_no_interactions', params = list(fit_name = 'main_fit_no_interactions'))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/main_fit_no_interactions', params = list(fit_name = 'main_fit_no_interactions'))" &&
rm output/28-35/main_fit_no_interactions/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/main_fit_no_interactions', params = list(fit_name = 'main_fit_no_interactions'))"
# Vanderbilt only fit
Rscript -e "rmarkdown::render('3a_7_Outcome_model_fit_Vanderbilt_only.Rmd', output_dir = 'knit_out/main_fit_Vanderbilt_only', params = list(fit_name = 'main_fit_Vanderbilt_only'))" &&
Rscript -e "rmarkdown::render('3b_7_Outcome_model_check_Vanderbilt_only.Rmd', output_dir = 'knit_out/main_fit_Vanderbilt_only', params = list(fit_name = 'main_fit_Vanderbilt_only'))" &&
Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/main_fit_Vanderbilt_only', params = list(fit_name = 'main_fit_Vanderbilt_only'))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/main_fit_Vanderbilt_only', params = list(fit_name = 'main_fit_Vanderbilt_only'))" &&
rm output/28-35/main_fit_Vanderbilt_only/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/main_fit_Vanderbilt_only', params = list(fit_name = 'main_fit_Vanderbilt_only'))"
# # # # # # #
Rscript -e "rmarkdown::render('7_Misc_manuscript_numbers.Rmd', output_dir = 'knit_out')"
Rscript -e "rmarkdown::render('8_Comparing_model_fits.Rmd', output_dir = 'knit_out')"
# # # # # # # # # # EXTRA SENSITIVITY ANALYSES: ONLY IF TIME ALLOWS # # # # # # # # # # # # # # # #
# W/ alternative spline parametrization (w/ linear term)
Rscript -e "rmarkdown::render('3a_6_Outcome_model_fit_alternative_splines.Rmd', output_dir = 'knit_out/main_fit_alternative_splines', params = list(fit_name = 'main_fit_alternative_splines'))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/main_fit_alternative_splines', params = list(fit_name = 'main_fit_alternative_splines'))" &&
Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/main_fit_alternative_splines', params = list(fit_name = 'main_fit_alternative_splines'))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/main_fit_alternative_splines', params = list(fit_name = 'main_fit_alternative_splines'))" &&
rm output/28-35/main_fit_alternative_splines/subgroup_effects/*po* &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/main_fit_alternative_splines', params = list(fit_name = 'main_fit_alternative_splines'))"
# Sensitivity analysis: SAP model w/ no splines (linear terms only)
# Rscript -e "rmarkdown::render('3a_3_Outcome_model_fit_linear.Rmd', output_dir = 'knit_out/main_fit_linear')"
# Day ~14 outcome (?)
# Sensitivity analysis: D14 outcome definition
Rscript -e "rmarkdown::render('0_Load_and_clean.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
Rscript -e "rmarkdown::render('1_Exploratory_analysis.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
Rscript -e "rmarkdown::render('2_Baseline_imputation.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
time Rscript -e "rmarkdown::render('3a_Outcome_model_fit.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
Rscript -e "rmarkdown::render('3b_Outcome_model_check.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
time Rscript -e "rmarkdown::render('4a_Subgroup_effects_paired_tables.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
time Rscript -e "rmarkdown::render('4b_Subgroup_effect_estimates.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))" &&
time Rscript -e "rmarkdown::render('4c_Conditional_effects.Rmd', output_dir = 'knit_out/13-16', params = list(outcome_min = 13, outcome_max = 16))"