update simulations code

[ml_measurement_error_public.git] / simulations / Makefile

diff --git a/simulations/Makefile b/simulations/Makefile
index dec7889db143e7738293e5825094d7ccc9cac2df..821280b52ddccd919787bc38b2ca385dc5a48917 100644 (file)
--- a/simulations/Makefile
+++ b/simulations/Makefile
@@ -1,20 +1,22 @@
-
+.ONESHELL:

 SHELL=bash
 
 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]
 
 explained_variances=[0.1]
 

-all:remembr.RDS
+all:main supplement
+main:remembr.RDS 
+supplement:robustness_1.RDS robustness_1_dv.RDS robustness_2.RDS robustness_2_dv.RDS robustness_3.RDS robustness_3_dv.RDS robustness_3_proflik.RDS robustness_3_dv_proflik.RDS robustness_4.RDS robustness_4_dv.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
 
 
 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
 
 # test_true_z.feather: test_true_z_jobs 
 #      rm -f test_true_z.feather


@@ -22,51 +24,380 @@ joblists:example_1_jobs example_2_jobs example_3_jobs
 #      sbatch --wait --verbose --array=3001-6001 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 --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
+       ${srun} grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${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
 
 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
 
 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)
+

 
 # example_2_B_jobs: example_2_B.R
 
 # 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_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],"Bzx":[1],"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 
 
 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":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"Bzx":[1], "m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[-0.5], "prediction_accuracy":[0.73]}' --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=2001-3001 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"
        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"

+       ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4"
+
+
+START=0
+STEP=1000
+ONE=1
+
+robustness_Ns=[1000,5000]
+robustness_robustness_ms=[100,200]
+
+#in robustness 1 / example 2 misclassification is correlated with Y.
+robustness_1_jobs_p1: 02_indep_differential.R simulation_base.R grid_sweep.py
+       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":[1000],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3,0],"Bxy":[0.3],"Bzx":[1,0], "outcome_formula":["y~x+z"], "z_bias":[0, 0.5], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~1"]}' --outfile robustness_1_jobs_p1
+
+robustness_1_jobs_p2: 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":[5000],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3,0],"Bxy":[0.3],"Bzx":[1,0], "outcome_formula":["y~x+z"], "z_bias":[0, 0.5], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~1"]}' --outfile robustness_1_jobs_p2
+
+robustness_1.feather: robustness_1_jobs_p1 robustness_1_jobs_p2
+       rm -f $@
+       $(eval END_1!=cat robustness_1_jobs_p1 | wc -l)
+       $(eval ITEROBUSTNESS_MS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_1_jobs_p2 | wc -l)
+       $(eval ITEROBUSTNESS_MS_2!=seq $(START) $(STEP) $(END_2))
+
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p1;)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p2;)
+
+robustness_1.RDS: robustness_1.feather summarize_estimator.R
+       rm -f robustness_1.RDS
+       ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@
+
+# when Bzy is 0 and zbias is not zero, we have the case where P(W|Y,X,Z) has an omitted variable that is conditionanlly independent from Y.  Note that X and Z are independent in this scenario.
+robustness_1_dv_jobs_p1: simulation_base.R 04_depvar_differential.R grid_sweep.py
+       ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[1000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p1
+
+robustness_1_dv_jobs_p2: simulation_base.R 04_depvar_differential.R grid_sweep.py
+       ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[5000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p2
+
+robustness_1_dv.feather: robustness_1_dv_jobs_p1 robustness_1_dv_jobs_p2
+       rm -f $@
+       $(eval END_1!=cat robustness_1_dv_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_1_dv_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_1))
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p1;)
+       $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p2;)
+
+robustness_1_dv.RDS: robustness_1_dv.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --remember-file $@
+
+
+robustness_2_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_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+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} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_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+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} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_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+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} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_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+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.90,0.95]}' --outfile $@
+
+robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_jobs_p3 robustness_2_jobs_p4
+       rm $@
+       $(eval END_1!=cat robustness_2_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_2_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_2_jobs_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+       $(eval END_4!=cat robustness_2_jobs_p4 | wc -l)
+       $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
+
+       $(foreach item,$(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.RDS: plot_example.R robustness_2.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2" --remember-file $@
+
+robustness_2_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_2_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "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} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_2_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "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} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_2_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "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} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_2_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.90,0.95]}' --outfile $@
+
+robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustness_2_dv_jobs_p3 robustness_2_dv_jobs_p4
+       rm -f $@
+       $(eval END_1!=cat robustness_2_dv_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_2_dv_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_2_dv_jobs_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+       $(eval END_4!=cat robustness_2_dv_jobs_p4 | wc -l)
+       $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
+
+       $(foreach item,$(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_2_dv.RDS: plot_dv_example.R robustness_2_dv.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2_dv" --remember-file $@
+
+
+robustness_3_proflik_jobs: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":[1000],"m":[100], "seed":${seeds}, "outfile":["robustness_3_proflik.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"Px":[0.5,0.6,0.7,0.8,0.9,0.95], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85], "confint_method":['spline']}' --outfile $@
+
+robustness_3_proflik.feather: robustness_3_proflik_jobs
+       rm -f $@
+       $(eval END_1!=cat robustness_3_proflik_jobs | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_proflik_jobs;)
+
+robustness_3_proflik.RDS: plot_example.R robustness_3_proflik.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_proflik" --remember-file $@
+
+
+robustness_3_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"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} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"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} $< --command 'Rscript 01_two_covariates.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"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 $@
+
+robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_jobs_p3
+       rm -f $@
+       $(eval END_1!=cat robustness_3_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_3_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_3_jobs_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+
+       $(foreach item,$(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;)

 
 

-clean:
+robustness_3.RDS: plot_example.R robustness_3.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3" --remember-file $@
+
+robustness_3_dv_proflik_jobs: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":[1000],"m":[100], "seed":${seeds}, "outfile":["robustness_3_dv_proflik.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"B0":[0,0.405,0.846,1.386,2.197,2.944], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"confint_method":['spline']}' --outfile $@
+
+robustness_3_dv_proflik.feather: robustness_3_dv_proflik_jobs
+       rm -f $@
+       $(eval END_1!=cat robustness_3_dv_proflik_jobs | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_proflik_jobs;)
+
+robustness_3_dv_proflik.RDS: plot_dv_example.R robustness_3_dv_proflik.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv_proflik" --remember-file $@
+
+
+ robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"B0":[0,0.405], "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} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1],"B0":[0.847,1.386], "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} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_3_dv.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "B0":[2.197,2.944], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85]}' --outfile $@
+
+robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustness_3_dv_jobs_p3
+       rm -f $@
+       $(eval END_1!=cat robustness_3_dv_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_3_dv_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_3_dv_jobs_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+
+       $(foreach item,$(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_3_dv.RDS: plot_dv_example.R robustness_3_dv.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv" --remember-file $@
+
+
+
+robustness_4_jobs_p1: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85],"y_bias":[-2.944,-2.197]}' --outfile $@
+
+robustness_4_jobs_p2: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85], "y_bias":[-1.386,-0.846]}' --outfile $@
+
+robustness_4_jobs_p3: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 02_indep_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y+x"], "truth_formula":["x~z"], "prediction_accuracy":[0.85],"y_bias":[-0.405,-0.25]}' --outfile $@
+
+robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_jobs_p3
+       rm -f $@
+       $(eval END_1!=cat robustness_4_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_4_jobs_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_4_jobs_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+
+       $(foreach item,$(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.RDS: plot_example.R robustness_4.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
+
+
+# '{"N":${robustness_Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --example_4_jobs
+
+robustness_4_dv_jobs_p1: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7],"Bzx":[1], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0,0.1]}' --outfile $@
+
+robustness_4_dv_jobs_p2: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7],"Bzx":[1], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0.25,0.405]}' --outfile $@
+
+robustness_4_dv_jobs_p3: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7],"Bzx":[1],"outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0.846,1.386]}' --outfile $@
+
+robustness_4_dv_jobs_p4: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
+       rm -f $@
+       ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${robustness_Ns},"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"],"Bzy":[-0.7],"Bxy":[0.7],"Bzx":[1], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[2.197,2.944]}' --outfile $@
+
+robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3 robustness_4_dv_jobs_p4
+       rm -f $@
+       $(eval END_1!=cat robustness_4_dv_jobs_p1 | wc -l)
+       $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
+       $(eval END_2!=cat robustness_4_dv_p2 | wc -l)
+       $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
+       $(eval END_3!=cat robustness_4_dv_p3 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+       $(eval END_3!=cat robustness_4_dv_p4 | wc -l)
+       $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
+
+
+       $(foreach item,$(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;)
+       $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p4;)
+
+
+robustness_4_dv.RDS: plot_dv_example.R robustness_4_dv.feather summarize_estimator.R
+       rm -f $@
+       ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
+
+
+clean_main:
+       rm -f remembr.RDS
+       rm -f example_1_jobs
+       rm -f example_2_jobs
+       rm -f example_3_jobs
+       rm -f example_4_jobs
+       rm -f example_1.feather
+       rm -f example_2.feather
+       rm -f example_3.feather
+       rm -f example_4.feather
+
+
+#      
+clean_all:

        rm *.feather
        rm -f remembr.RDS
        rm *.feather
        rm -f remembr.RDS

+       rm -f remembr*.RDS
+       rm -f robustness*.RDS

        rm -f example_*_jobs
        rm -f example_*_jobs

+       rm -f robustness_*_jobs_*

 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 
 # example_2_B_mecor_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
 
 # example_2_B_mecor.feather:example_2_B_mecor.R example_2_B_mecor_jobs
 #      rm -f example_2_B_mecor.feather


@@ -74,4 +405,4 @@ clean:
 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs
 
 
 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs
 
 

-
+.PHONY: supplement