simulations/Makefile

   1 .ONESHELL:
   2 SHELL=bash
   3
   4 Ns=[1000, 5000, 10000]
   5 ms=[100, 200, 400]
   6 seeds=[$(shell seq -s, 1 500)]
   7 explained_variances=[0.1]
   8
   9 all:main supplement
  10 main:remembr.RDS
  11 supplement:robustness_1.RDS robustness_1_dv.RDS robustness_2.RDS robustness_2_dv.RDS robustness_3.RDS robustness_3_dv.RDS robustness_3_proflik.RDS robustness_3_dv_proflik.RDS robustness_4.RDS robustness_4_dv.RDS
  12
  13 srun=sbatch --wait --verbose run_job.sbatch
  14
  15
  16 joblists:example_1_jobs example_2_jobs example_3_jobs
  17
  18 # test_true_z_jobs: test_true_z.R simulation_base.R
  19 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["test_true_z.feather"], "y_explained_variancevari":${explained_variances}, "Bzx":${Bzx}}' --outfile test_true_z_jobsb
  20
  21 # test_true_z.feather: test_true_z_jobs
  22 #       rm -f test_true_z.feather
  23 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 test_true_z_jobs
  24 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 test_true_z_jobs
  25
  26
  27 example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py pl_methods.R
  28         ${srun} grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[1]}' --outfile example_1_jobs
  29
  30 example_1.feather: example_1_jobs
  31         rm -f example_1.feather
  32         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_1_jobs
  33         sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_1_jobs
  34         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_1_jobs
  35         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_1_jobs
  36         sbatch --wait --verbose --array=4001-$(shell cat example_1_jobs | wc -l)  run_simulation.sbatch 0 example_1_jobs
  37
  38 example_2_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py pl_methods.R
  39         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
  40
  41 example_2.feather: example_2_jobs
  42         rm -f example_2.feather
  43         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_2_jobs
  44         sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_2_jobs
  45         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_2_jobs
  46         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_2_jobs
  47         sbatch --wait --verbose --array=4001-$(shell cat example_2_jobs | wc -l)
  48
  49
  50 # example_2_B_jobs: example_2_B.R
  51 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs
  52
  53 # example_2_B.feather: example_2_B_jobs
  54 #       rm -f example_2_B.feather
  55 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs
  56
  57 example_3_jobs: 03_depvar.R simulation_base.R grid_sweep.py pl_methods.R
  58         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
  59
  60 example_3.feather: example_3_jobs
  61         rm -f example_3.feather
  62         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_3_jobs
  63         sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_3_jobs
  64          sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_3_jobs
  65         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_3_jobs
  66         sbatch --wait --verbose --array=4001-$(shell cat example_3_jobs | wc -l)  run_simulation.sbatch 0 example_3_jobs
  67
  68 example_4_jobs: 04_depvar_differential.R simulation_base.R grid_sweep.py pl_methods.R
  69         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${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
  70
  71 example_4.feather: example_4_jobs
  72         rm -f example_4.feather
  73         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_4_jobs
  74         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_4_jobs
  75         sbatch --wait --verbose --array=2001-3001 run_simulation.sbatch 0 example_4_jobs
  76         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_4_jobs
  77         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_4_jobs
  78         sbatch --wait --verbose --array=4001-$(shell cat example_4_jobs | wc -l)  run_simulation.sbatch 0 example_4_jobs
  79
  80
  81
  82 remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feather plot_example.R plot_dv_example.R summarize_estimator.R
  83         rm -f remembr.RDS
  84         ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1"
  85         ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2"
  86         ${srun} Rscript plot_dv_example.R --infile example_3.feather --name "plot.df.example.3"
  87         ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4"
  88
  89
  90 START=0
  91 STEP=1000
  92 ONE=1
  93
  94 robustness_Ns=[1000,5000]
  95 robustness_robustness_ms=[100,200]
  96
  97 #in robustness 1 / example 2 misclassification is correlated with Y.
  98 robustness_1_jobs_p1: 02_indep_differential.R simulation_base.R grid_sweep.py
  99         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":[1000],"m":${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
 100
 101 robustness_1_jobs_p2: 02_indep_differential.R simulation_base.R grid_sweep.py
 102         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
 103
 104 robustness_1.feather: robustness_1_jobs_p1 robustness_1_jobs_p2
 105         rm -f $@
 106         $(eval END_1!=cat robustness_1_jobs_p1 | wc -l)
 107         $(eval ITEROBUSTNESS_MS_1!=seq $(START) $(STEP) $(END_1))
 108         $(eval END_2!=cat robustness_1_jobs_p2 | wc -l)
 109         $(eval ITEROBUSTNESS_MS_2!=seq $(START) $(STEP) $(END_2))
 110
 111         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p1;)
 112         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p2;)
 113
 114 robustness_1.RDS: robustness_1.feather summarize_estimator.R
 115         rm -f robustness_1.RDS
 116         ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@
 117
 118 # 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.
 119 robustness_1_dv_jobs_p1: simulation_base.R 04_depvar_differential.R grid_sweep.py
 120         ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[1000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p1
 121
 122 robustness_1_dv_jobs_p2: simulation_base.R 04_depvar_differential.R grid_sweep.py
 123         ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[5000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p2
 124
 125 robustness_1_dv.feather: robustness_1_dv_jobs_p1 robustness_1_dv_jobs_p2
 126         rm -f $@
 127         $(eval END_1!=cat robustness_1_dv_jobs_p1 | wc -l)
 128         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 129         $(eval END_2!=cat robustness_1_dv_jobs_p2 | wc -l)
 130         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_1))
 131         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p1;)
 132         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p2;)
 133
 134 robustness_1_dv.RDS: robustness_1_dv.feather summarize_estimator.R
 135         rm -f $@
 136         ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --remember-file $@
 137
 138
 139 robustness_2_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 140         rm -f $@
 141         ${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 $@
 142
 143 robustness_2_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 144         rm -f $@
 145         ${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 $@
 146
 147 robustness_2_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 148         rm -f $@
 149         ${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 $@
 150
 151 robustness_2_jobs_p4: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 152         rm -f $@
 153         ${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 $@
 154
 155 robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_jobs_p3 robustness_2_jobs_p4
 156         rm $@
 157         $(eval END_1!=cat robustness_2_jobs_p1 | wc -l)
 158         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 159         $(eval END_2!=cat robustness_2_jobs_p2 | wc -l)
 160         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 161         $(eval END_3!=cat robustness_2_jobs_p3 | wc -l)
 162         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 163         $(eval END_4!=cat robustness_2_jobs_p4 | wc -l)
 164         $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
 165
 166         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p1;)
 167         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p2;)
 168         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p3;)
 169         $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p4;)
 170
 171 robustness_2.RDS: plot_example.R robustness_2.feather summarize_estimator.R
 172         rm -f $@
 173         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2" --remember-file $@
 174
 175 robustness_2_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 176         rm -f $@
 177         ${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 $@
 178
 179 robustness_2_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 180         rm -f $@
 181         ${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 $@
 182
 183 robustness_2_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 184         rm -f $@
 185         ${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 $@
 186
 187 robustness_2_dv_jobs_p4: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 188         rm -f $@
 189         ${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 $@
 190
 191 robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustness_2_dv_jobs_p3 robustness_2_dv_jobs_p4
 192         rm -f $@
 193         $(eval END_1!=cat robustness_2_dv_jobs_p1 | wc -l)
 194         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 195         $(eval END_2!=cat robustness_2_dv_jobs_p2 | wc -l)
 196         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 197         $(eval END_3!=cat robustness_2_dv_jobs_p3 | wc -l)
 198         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 199         $(eval END_4!=cat robustness_2_dv_jobs_p4 | wc -l)
 200         $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
 201
 202         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p1;)
 203         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p2;)
 204         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p3;)
 205         $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p4;)
 206
 207 robustness_2_dv.RDS: plot_dv_example.R robustness_2_dv.feather summarize_estimator.R
 208         rm -f $@
 209         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2_dv" --remember-file $@
 210
 211
 212 robustness_3_proflik_jobs: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 213         rm -f $@
 214         ${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 $@
 215
 216 robustness_3_proflik.feather: robustness_3_proflik_jobs
 217         rm -f $@
 218         $(eval END_1!=cat robustness_3_proflik_jobs | wc -l)
 219         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 220         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_proflik_jobs;)
 221
 222 robustness_3_proflik.RDS: plot_example.R robustness_3_proflik.feather summarize_estimator.R
 223         rm -f $@
 224         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_proflik" --remember-file $@
 225
 226
 227 robustness_3_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 228         rm -f $@
 229         ${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 $@
 230
 231 robustness_3_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 232         rm -f $@
 233         ${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 $@
 234
 235 robustness_3_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 236         rm -f $@
 237         ${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 $@
 238
 239 robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_jobs_p3
 240         rm -f $@
 241         $(eval END_1!=cat robustness_3_jobs_p1 | wc -l)
 242         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 243         $(eval END_2!=cat robustness_3_jobs_p2 | wc -l)
 244         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 245         $(eval END_3!=cat robustness_3_jobs_p3 | wc -l)
 246         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 247
 248         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p1;)
 249         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p2;)
 250         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p3;)
 251
 252 robustness_3.RDS: plot_example.R robustness_3.feather summarize_estimator.R
 253         rm -f $@
 254         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3" --remember-file $@
 255
 256 robustness_3_dv_proflik_jobs: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 257         rm -f $@
 258         ${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 $@
 259
 260 robustness_3_dv_proflik.feather: robustness_3_dv_proflik_jobs
 261         rm -f $@
 262         $(eval END_1!=cat robustness_3_dv_proflik_jobs | wc -l)
 263         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 264         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_proflik_jobs;)
 265
 266 robustness_3_dv_proflik.RDS: plot_dv_example.R robustness_3_dv_proflik.feather summarize_estimator.R
 267         rm -f $@
 268         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv_proflik" --remember-file $@
 269
 270
 271  robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 272         rm -f $@
 273         ${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 $@
 274
 275
 276
 277 robustness_3_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 278         rm -f $@
 279         ${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 $@
 280
 281
 282 robustness_3_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 283         rm -f $@
 284         ${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 $@
 285
 286 robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustness_3_dv_jobs_p3
 287         rm -f $@
 288         $(eval END_1!=cat robustness_3_dv_jobs_p1 | wc -l)
 289         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 290         $(eval END_2!=cat robustness_3_dv_jobs_p2 | wc -l)
 291         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 292         $(eval END_3!=cat robustness_3_dv_jobs_p3 | wc -l)
 293         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 294
 295         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p1;)
 296         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p2;)
 297          $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p3;)
 298
 299
 300 robustness_3_dv.RDS: plot_dv_example.R robustness_3_dv.feather summarize_estimator.R
 301         rm -f $@
 302         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv" --remember-file $@
 303
 304
 305
 306 robustness_4_jobs_p1: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 307         rm -f $@
 308         ${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 $@
 309
 310 robustness_4_jobs_p2: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 311         rm -f $@
 312         ${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 $@
 313
 314 robustness_4_jobs_p3: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 315         rm -f $@
 316         ${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 $@
 317
 318 robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_jobs_p3
 319         rm -f $@
 320         $(eval END_1!=cat robustness_4_jobs_p1 | wc -l)
 321         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 322         $(eval END_2!=cat robustness_4_jobs_p2 | wc -l)
 323         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 324         $(eval END_3!=cat robustness_4_jobs_p3 | wc -l)
 325         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 326
 327         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p1;)
 328         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p2;)
 329         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p3;)
 330
 331 robustness_4.RDS: plot_example.R robustness_4.feather summarize_estimator.R
 332         rm -f $@
 333         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
 334
 335
 336 # '{"N":${robustness_Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --example_4_jobs
 337
 338 robustness_4_dv_jobs_p1: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 339         rm -f $@
 340         ${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 $@
 341
 342 robustness_4_dv_jobs_p2: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 343         rm -f $@
 344         ${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 $@
 345
 346 robustness_4_dv_jobs_p3: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 347         rm -f $@
 348         ${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 $@
 349
 350 robustness_4_dv_jobs_p4: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 351         rm -f $@
 352         ${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 $@
 353
 354 robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3 robustness_4_dv_jobs_p4
 355         rm -f $@
 356         $(eval END_1!=cat robustness_4_dv_jobs_p1 | wc -l)
 357         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 358         $(eval END_2!=cat robustness_4_dv_p2 | wc -l)
 359         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 360         $(eval END_3!=cat robustness_4_dv_p3 | wc -l)
 361         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 362         $(eval END_3!=cat robustness_4_dv_p4 | wc -l)
 363         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 364
 365
 366         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p1;)
 367         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p2;)
 368         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p3;)
 369         $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p4;)
 370
 371
 372 robustness_4_dv.RDS: plot_dv_example.R robustness_4_dv.feather summarize_estimator.R
 373         rm -f $@
 374         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
 375
 376
 377 clean_main:
 378         rm -f remembr.RDS
 379         rm -f example_1_jobs
 380         rm -f example_2_jobs
 381         rm -f example_3_jobs
 382         rm -f example_4_jobs
 383         rm -f example_1.feather
 384         rm -f example_2.feather
 385         rm -f example_3.feather
 386         rm -f example_4.feather
 387
 388
 389 #
 390 clean_all:
 391         rm *.feather
 392         rm -f remembr.RDS
 393         rm -f remembr*.RDS
 394         rm -f robustness*.RDS
 395         rm -f example_*_jobs
 396         rm -f robustness_*_jobs_*
 397 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 398
 399 # example_2_B_mecor_jobs:
 400 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B_mecor.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B_mecor.feather"]}' --outfile example_2_B_mecor_jobs
 401
 402 # example_2_B_mecor.feather:example_2_B_mecor.R example_2_B_mecor_jobs
 403 #       rm -f example_2_B_mecor.feather
 404 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_mecor_jobs
 405 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs
 406
 407
 408 .PHONY: supplement