X-Git-Url: https://code.communitydata.science/ml_measurement_error_public.git/blobdiff_plain/588bdd7ed74cf8fe8fd0f15df58a6a40c26ebae5..refs/heads/synced/master:/simulations/Makefile

diff --git a/simulations/Makefile b/simulations/Makefile
index 01c34fc..b3ab77a 100644
--- a/simulations/Makefile
+++ b/simulations/Makefile
@@ -1,56 +1,158 @@
 
 SHELL=bash
 
-Ns=[500,1000,10000,25000]
-ms=[50, 100, 250, 500]
-seeds=[$(shell seq -s, 1 250)]
-all:remembr.RDS
+Ns=[1000, 5000, 10000]
+ms=[100, 200, 400]
+seeds=[$(shell seq -s, 1 500)]
+explained_variances=[0.1]
 
-srun=srun -A comdata -p compute-bigmem --time=10:00:00 --mem 4G -c 1
+all:remembr.RDS remember_irr.RDS
+supplement: remember_robustness_misspec.RDS
 
-example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py
-	grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"]}' --outfile example_1_jobs
+srun=sbatch --wait --verbose run_job.sbatch
 
-example_1.feather: example_1_jobs
+
+joblists:example_1_jobs example_2_jobs example_3_jobs
+
+# test_true_z_jobs: test_true_z.R simulation_base.R
+# 	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":${Bzx}}' --outfile test_true_z_jobsb
+
+# test_true_z.feather: test_true_z_jobs 
+# 	rm -f test_true_z.feather
+# 	sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 test_true_z_jobs
+# 	sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 test_true_z_jobs
+
+
+example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py pl_methods.R
+	sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[1]}' --outfile example_1_jobs
+
+example_1.feather: example_1_jobs 
 	rm -f example_1.feather
-	sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_1_jobs
-	sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_1_jobs
+	sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_1_jobs
+	sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_1_jobs
+	sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_1_jobs
+	sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_1_jobs
+	sbatch --wait --verbose --array=4001-$(shell cat example_1_jobs | wc -l)  run_simulation.sbatch 0 example_1_jobs
 
-example_2_jobs: example_2.R
-	grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"]}' --outfile example_2_jobs
+example_2_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py pl_methods.R
+	sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${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
+example_2.feather: example_2_jobs 
 	rm -f example_2.feather
-	sbatch --wait --verbose --array=1-3000 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
 
-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_2_B_jobs: example_2_B.R
+# 	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_3_jobs: example_3.R
-	grid_sweep.py --command "Rscript example_3.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_3.feather"]}' --outfile example_3_jobs
+# example_2_B.feather: example_2_B_jobs
+# 	rm -f example_2_B.feather
+# 	sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs
+
+example_3_jobs: 03_depvar.R simulation_base.R grid_sweep.py pl_methods.R
+	sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 03_depvar.R" --arg_dict '{"N":${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=1-3000 run_simulation.sbatch 0 example_3_jobs
+	rm -f example_3.feather	
+	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_2_B.feather example_1.feather example_2.feather example_3.feather
+
+
+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_example.R --infile example_2_B.feather --name "plot.df.example.2B"
-	${srun} Rscript plot_example.R --infile example_3.feather --name "plot.df.example.3"
+	${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
+	rm -f remembr.RDS
+	rm -f example_*_jobs
 #	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
@@ -59,3 +161,4 @@ remembr.RDS:example_2_B.feather example_1.feather example_2.feather example_3.fe
 
 
 
+.PHONY: supplement