]> code.communitydata.science - ml_measurement_error_public.git/blobdiff - simulations/Makefile
Added, but didn't test the remaining robustness checks.
[ml_measurement_error_public.git] / simulations / Makefile
index 44910cbc0a9475e66cd1a7e99fb4da52cea1dd0a..feeeaa54dbc1f311152a9f44c026e3fca49c54d7 100644 (file)
@@ -1,20 +1,21 @@
 
 SHELL=bash
 
-Ns=[1000, 2000, 4000]
-ms=[200, 400, 800]
-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 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
@@ -22,45 +23,61 @@ 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},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y*z*x"]}' --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.R simulation_base.R
-       grid_sweep.py --command "Rscript 03_depvar.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 --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "y_explained_variance":${explained_variances}}' --outfile example_4_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-$(shell cat example_4_jobs | wc -l)  run_simulation.sbatch 0 example_4_jobs
+       sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_4_jobs
+       sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_4_jobs
+       sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_4_jobs
+       sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_4_jobs
+       sbatch --wait --verbose --array=4001-$(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 example_4.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"
@@ -68,31 +85,269 @@ remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feat
        ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4"
 
 
-irr_Ns = ${Ns}
-irr_ms = ${ms}
+irr_Ns = [1000]
+irr_ms = [150,300,600]
 irr_seeds=${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 --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}}' --outfile example_5_jobs
+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-$(shell cat example_5_jobs | wc -l)  run_simulation.sbatch 0 example_5_jobs
+       sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_5_jobs
+       sbatch --wait --verbose --array=1001-$(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 --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}}' --outfile example_6_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-$(shell cat example_6_jobs | wc -l)  run_simulation.sbatch 0 example_6_jobs
+# example_6.feather:example_6_jobs
+#      rm -f example_6.feather
+#      sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_6_jobs
+#      sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 1000 example_6_jobs
+#      sbatch --wait --verbose --array=2001-$(shell cat example_6_jobs | wc -l)  run_simulation.sbatch 2000 example_6_jobs
 
-remember_irr.RDS: example_5.feather example_6.feather plot_irr_example.R plot_irr_dv_example.R
+
+remember_irr.RDS: example_5.feather plot_irr_example.R plot_irr_dv_example.R summarize_estimator.R
        rm -f remember_irr.RDS
-       ${srun} Rscript plot_irr_example.R --infile example_5.feather --name "plot.df.example.5"
-       ${srun} Rscript plot_irr_dv_example.R --infile example_6.feather --name "plot.df.example.6"
+       sbatch --wait --verbose run_job.sbatch Rscript plot_irr_example.R --infile example_5.feather --name "plot.df.example.5"
+#      sbatch --wait --verbose run_job.sbatch Rscript plot_irr_dv_example.R --infile example_6.feather --name "plot.df.example.6"
+
+
+robustness_1_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py
+       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_1.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~1"]}' --outfile robustness_1_jobs
+
+
+robustness_1.feather: robustness_1_jobs
+       rm -f robustness_1.feather
+       sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 robustness_1_jobs
+       sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 robustness_1_jobs
+       sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 robustness_1_jobs
+       sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 robustness_1_jobs
+       sbatch --wait --verbose --array=4001-$(shell cat robustness_1_jobs | wc -l)  run_simulation.sbatch 0 robustness_1_jobs
+
+robustness_1.RDS: robustness_1.feather
+       rm -f robustness_1.RDS
+       ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@
+
+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
+
+
+robustness_1_dv.RDS: robustness_1_dv.feather
+       rm -f $@
+       ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --outfile $@
+
+
+robustness_2_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.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~z"], "prediction_accuracy":[0.60,0.65]}' --outfile $@
+
+robustness_2_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.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~z"], "prediction_accuracy":[0.70,0.75]}' --outfile $@
+
+robustness_2_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.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~z"], "prediction_accuracy":[0.80,0.85]}' --outfile $@
+
+robustness_2_jobs_p4: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.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~z"], "prediction_accuracy":[0.90,0.95]}' --outfile $@
+
+START=0
+END_1=$(shell cat robustness_2_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_2_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_2_jobs_p3 | wc -l)
+END_4=$(shell cat robustness_2_jobs_p4 | wc -l)
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+ITEMS_4=$(shell seq $(START) $(STEP) $(END_4))
+
+robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_jobs_p3 robustness_2_jobs_p4
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p3;)
+       $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p4;)
+
+
+robustness_2_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.60,0.65]}' --outfile $@
+
+robustness_2_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.70,0.75]}' --outfile $@
+
+robustness_2_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.80,0.85]}' --outfile $@
+
+robustness_2_dv_jobs_p4: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.90,0.95]}' --outfile $@
+
+START=0
+END_1=$(shell cat robustness_2_dv_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_2_dv_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_2_dv_jobs_p3 | wc -l)
+END_4=$(shell cat robustness_2_dv_jobs_p4 | wc -l)
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+ITEMS_4=$(shell seq $(START) $(STEP) $(END_4))
+
+robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustness_2_dv_jobs_p3 robustness_2_dv_jobs_p4
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p3;)
+       $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p4;)
+
+
+
+robustness_3_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"Px":[0.5,0.6], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+robustness_3_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"Px":[0.7,0.8], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+robustness_3_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"Px":[0.9,0.95], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+START=0
+END_1=$(shell cat robustness_3_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_3_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_3_jobs_p3 | wc -l)
+
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+
+robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_jobs_p3
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p3;)
+
+
+robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"B0":[0.5,0.6], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+robustness_3_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"B0":[0.7,0.8], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+robustness_3_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "B0":[0.9,0.95], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+START=0
+END_1=$(shell cat robustness_3_dv_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_3_dv_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_3_dv_jobs_p3 | wc -l)
+
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+
+robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustness_3_dv_jobs_p3
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p3;)
+
+
+
+robustness_4_jobs_p1: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.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~z"], "prediction_accuracy":[0.85],y_bias=[-1,-0.85]}' --outfile $@
+
+robustness_4_jobs_p2: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.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~z"], "prediction_accuracy":[0.85], y_bias=[-0.70,-0.55]}' --outfile $@
+
+robustness_4_jobs_p3: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.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~z"], "prediction_accuracy":[0.85],y_bias=[-0.4,-0.25]}' --outfile $@
+
+robustness_4_jobs_p4: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.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~z"], "prediction_accuracy":[0.85],y_bias=[-0.1,0]}' --outfile $@
+
+START=0
+END_1=$(shell cat robustness_4_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_4_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_4_jobs_p3 | wc -l)
+END_4=$(shell cat robustness_4_jobs_p3 | wc -l)
+
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+ITEMS_4=$(shell seq $(START) $(STEP) $(END_4))
+
+robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_jobs_p3
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p3;)
+
+
+robustness_4_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"B0":[0.5] "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],z_bias=[0,0.1]}' --outfile $@
+
+robustness_4_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3],"B0":[0.5] "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],z_bias=[0.25,0.4]}' --outfile $@
+
+robustness_4_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "B0":[0.5], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],z_bias=[0.55,0.7]}' --outfile $@
+robustness_4_dv_jobs_p4: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "B0":[0.5], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],z_bias=[0.85,1]}' --outfile $@
+
+
+START=0
+END_1=$(shell cat robustness_4_dv_jobs_p1 | wc -l)
+END_2=$(shell cat robustness_4_dv_jobs_p2 | wc -l)
+END_3=$(shell cat robustness_4_dv_jobs_p3 | wc -l)
+
+STEP=1000
+ONE=1
+ITEMS_1=$(shell seq $(START) $(STEP) $(END_1))
+ITEMS_2=$(shell seq $(START) $(STEP) $(END_2))
+ITEMS_3=$(shell seq $(START) $(STEP) $(END_3))
+
+robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p1)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p2;)
+       $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p3;)
 
+#      
 clean:
        rm *.feather
        rm -f remembr.RDS
@@ -100,7 +355,7 @@ 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
@@ -109,3 +364,4 @@ clean:
 
 
 
+.PHONY: supplement

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