X-Git-Url: https://code.communitydata.science/ml_measurement_error_public.git/blobdiff_plain/46e2d1fe4876a9ed906b723f9e5f74fcc949e339..5c931a7198452ff3ce0ace5b1f68046bfb33d352:/simulations/Makefile diff --git a/simulations/Makefile b/simulations/Makefile index dec7889..b3ab77a 100644 --- a/simulations/Makefile +++ b/simulations/Makefile @@ -1,20 +1,21 @@ SHELL=bash -Ns=[1000,3600,14400] -ms=[75,150,300] -seeds=[$(shell seq -s, 1 250)] +Ns=[1000, 5000, 10000] +ms=[100, 200, 400] +seeds=[$(shell seq -s, 1 500)] explained_variances=[0.1] -all:remembr.RDS +all:remembr.RDS remember_irr.RDS +supplement: remember_robustness_misspec.RDS -srun=srun -A comdata -p compute-bigmem --time=6:00:00 --mem 4G -c 1 +srun=sbatch --wait --verbose run_job.sbatch joblists:example_1_jobs example_2_jobs example_3_jobs # test_true_z_jobs: test_true_z.R simulation_base.R -# grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["test_true_z.feather"], "y_explained_variancevari":${explained_variances}, "Bzx":${Bzx}}' --outfile test_true_z_jobsb +# sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["test_true_z.feather"], "y_explained_variancevari":${explained_variances}, "Bzx":${Bzx}}' --outfile test_true_z_jobsb # test_true_z.feather: test_true_z_jobs # rm -f test_true_z.feather @@ -22,42 +23,127 @@ joblists:example_1_jobs example_2_jobs example_3_jobs # sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 test_true_z_jobs -example_1_jobs: 01_two_covariates.R simulation_base.R - grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[0.1]}' --outfile example_1_jobs +example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py pl_methods.R + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[1]}' --outfile example_1_jobs example_1.feather: example_1_jobs rm -f example_1.feather - sbatch --wait --verbose --array=1-$(shell cat example_1_jobs | wc -l) run_simulation.sbatch 0 example_1_jobs -# sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=4001-$(shell cat example_1_jobs | wc -l) run_simulation.sbatch 0 example_1_jobs -example_2_jobs: 02_indep_differential.R simulation_base.R - grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"],"y_explained_variance":${explained_variances}, "accuracy_imbalance_difference":[0.3], "Bzy":[0.3]}' --outfile example_2_jobs +example_2_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py pl_methods.R + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"],"y_explained_variance":${explained_variances}, "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y*z*x"]}' --outfile example_2_jobs example_2.feather: example_2_jobs rm -f example_2.feather - sbatch --wait --verbose --array=1-$(shell cat example_2_jobs | wc -l) run_simulation.sbatch 0 example_2_jobs -# sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=4001-$(shell cat example_2_jobs | wc -l) run_simulation.sbatch 0 example_2_jobs + # example_2_B_jobs: example_2_B.R -# grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs +# sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs # example_2_B.feather: example_2_B_jobs # rm -f example_2_B.feather # sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs -example_3_jobs: 03_depvar_differential.R simulation_base.R - grid_sweep.py --command "Rscript 03_depvar_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_3.feather"], "y_explained_variance":${explained_variances}}' --outfile example_3_jobs +example_3_jobs: 03_depvar.R simulation_base.R grid_sweep.py pl_methods.R + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 03_depvar.R" --arg_dict '{"N":${Ns},"m":${ms}, "Bxy":[0.7],"Bzy":[-0.7],"seed":${seeds}, "outfile":["example_3.feather"], "y_explained_variance":${explained_variances}}' --outfile example_3_jobs example_3.feather: example_3_jobs rm -f example_3.feather - sbatch --wait --verbose --array=1-$(shell cat example_3_jobs | wc -l) run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=4001-$(shell cat example_3_jobs | wc -l) run_simulation.sbatch 0 example_3_jobs + +example_4_jobs: 04_depvar_differential.R simulation_base.R grid_sweep.py pl_methods.R + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --outfile example_4_jobs + +example_4.feather: example_4_jobs + rm -f example_4.feather + sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_4_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_4_jobs + sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_4_jobs + sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_4_jobs + sbatch --wait --verbose --array=4001-$(shell cat example_4_jobs | wc -l) run_simulation.sbatch 0 example_4_jobs + -remembr.RDS:example_1.feather example_2.feather example_3.feather plot_example.R plot_dv_example.R +remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feather plot_example.R plot_dv_example.R summarize_estimator.R rm -f remembr.RDS ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1" ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2" ${srun} Rscript plot_dv_example.R --infile example_3.feather --name "plot.df.example.3" + ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4" + + +irr_Ns = [1000] +irr_ms = [150,300,600] +irr_seeds=${seeds} +irr_explained_variances=${explained_variances} +irr_coder_accuracy=[0.80] + +example_5_jobs: 05_irr_indep.R irr_simulation_base.R grid_sweep.py pl_methods.R measerr_methods.R + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 05_irr_indep.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_5.feather"], "y_explained_variance":${irr_explained_variances}, "coder_accuracy":${irr_coder_accuracy}}' --outfile example_5_jobs + +example_5.feather:example_5_jobs + rm -f example_5.feather + sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_5_jobs + sbatch --wait --verbose --array=1001-$(shell cat example_5_jobs | wc -l) run_simulation.sbatch 1000 example_5_jobs + # sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 2000 example_5_jobs + # sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 3000 example_5_jobs + # sbatch --wait --verbose --array=2001-$(shell cat example_5_jobs | wc -l) run_simulation.sbatch 4000 example_5_jobs + + + +# example_6_jobs: 06_irr_dv.R irr_dv_simulation_base.R grid_sweep.py pl_methods.R +# sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 06_irr_dv.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_6.feather"], "y_explained_variance":${irr_explained_variances},"coder_accuracy":${irr_coder_accuracy}}' --outfile example_6_jobs + +# example_6.feather:example_6_jobs +# rm -f example_6.feather +# sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_6_jobs +# sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 1000 example_6_jobs +# sbatch --wait --verbose --array=2001-$(shell cat example_6_jobs | wc -l) run_simulation.sbatch 2000 example_6_jobs + + +remember_irr.RDS: example_5.feather plot_irr_example.R plot_irr_dv_example.R summarize_estimator.R + rm -f remember_irr.RDS + sbatch --wait --verbose run_job.sbatch Rscript plot_irr_example.R --infile example_5.feather --name "plot.df.example.5" +# sbatch --wait --verbose run_job.sbatch Rscript plot_irr_dv_example.R --infile example_6.feather --name "plot.df.example.6" + + + +robustness_1_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_1.feather"],"y_explained_variance":${explained_variances}, "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~1"]}' --outfile robustness_1_jobs + + + +robustness_1.feather: robustness_1_jobs + rm -f robustness_1.feather + sbatch --wait --verbose --array=1-$(shell cat robustness_1_jobs | wc -l) run_simulation.sbatch 0 robustness_1_jobs + +robustness_1_dv_jobs: simulation_base.R 04_depvar_differential.R grid_sweep.py + ${srun} bash -c "source ~/.bashrc && grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict \"{'N':${Ns},'m':${ms}, 'seed':${seeds}, 'outfile':['robustness_1_dv.feather'], 'y_explained_variance':${explained_variances}, 'proxy_formula':['w_pred~y']}\" --outfile robustness_1_dv_jobs" + + +robustness_1_dv.feather: robustness_1_dv_jobs + rm -f robustness_1_dv.feather + sbatch --wait --verbose --array=1-$(shell cat example_3_jobs | wc -l) run_simulation.sbatch 0 robustness_1_dv_jobs + + +remember_robustness_misspec.RDS: robustness_1.feather robustness_1_dv.feather + rm -f remember_robustness_misspec.RDS + sbatch --wait --verbose run_job.sbatch Rscript plot_example.R --infile robustness_1.feather --name "plot.df.robustness.1" --remember-file "remember_robustness_misspec.RDS" + sbatch --wait --verbose run_job.sbatch Rscript plot_dv_example.R --infile robustness_1_dv.feather --name "plot.df.robustness.1.dv" --remember-file "remember_robustness_mispec.RDS" + clean: rm *.feather @@ -66,7 +152,7 @@ clean: # sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs # example_2_B_mecor_jobs: -# grid_sweep.py --command "Rscript example_2_B_mecor.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B_mecor.feather"]}' --outfile example_2_B_mecor_jobs +# sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B_mecor.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B_mecor.feather"]}' --outfile example_2_B_mecor_jobs # example_2_B_mecor.feather:example_2_B_mecor.R example_2_B_mecor_jobs # rm -f example_2_B_mecor.feather @@ -75,3 +161,4 @@ clean: +.PHONY: supplement