simulations/Makefile

   1 .ONESHELL:
   2 SHELL=bash
   3
   4 Ns=[1000, 5000, 10000]
   5 ms=[100, 200, 400]
   6 seeds=[$(shell seq -s, 1 500)]
   7 explained_variances=[0.1]
   8
   9 all:main supplement
  10 main:remembr.RDS
  11 supplement:robustness_1.RDS robustness_1_dv.RDS robustness_2.RDS robustness_2_dv.RDS robustness_3.RDS robustness_3_dv.RDS robustness_4.RDS robustness_4_dv.RDS
  12
  13 srun=sbatch --wait --verbose run_job.sbatch
  14
  15
  16 joblists:example_1_jobs example_2_jobs example_3_jobs
  17
  18 # test_true_z_jobs: test_true_z.R simulation_base.R
  19 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${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-$(shell cat example_2_jobs | wc -l)  run_simulation.sbatch 0 example_2_jobs
  48
  49
  50 # example_2_B_jobs: example_2_B.R
  51 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${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],"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],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.3], "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=2001-3000  run_simulation.sbatch 0 example_4_jobs
  76         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_4_jobs
  77         sbatch --wait --verbose --array=4001-$(shell cat example_4_jobs | wc -l)  run_simulation.sbatch 0 example_4_jobs
  78
  79
  80
  81 remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feather plot_example.R plot_dv_example.R summarize_estimator.R
  82         rm -f remembr.RDS
  83         ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1"
  84         ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2"
  85         ${srun} Rscript plot_dv_example.R --infile example_3.feather --name "plot.df.example.3"
  86         ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4"
  87
  88
  89 robustness_1_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py
  90         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${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
  91
  92
  93
  94 START=0
  95 STEP=1000
  96 ONE=1
  97
  98 robustness_1.feather: robustness_1_jobs
  99         $(eval END_1!=cat robustness_1_jobs | wc -l)
 100         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 101         rm -f robustness_1.feather
 102         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 robustness_1_jobs
 103         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 robustness_1_jobs
 104         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 robustness_1_jobs
 105         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 robustness_1_jobs
 106         sbatch --wait --verbose --array=4001-$(shell cat robustness_1_jobs | wc -l)  run_simulation.sbatch 0 robustness_1_jobs
 107
 108         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs;)
 109
 110 robustness_1.RDS: robustness_1.feather
 111         rm -f robustness_1.RDS
 112         ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@
 113
 114 robustness_1_dv_jobs: simulation_base.R 04_depvar_differential.R grid_sweep.py
 115         ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[0.5]}' --outfile robustness_1_dv_jobs
 116
 117 robustness_1_dv.feather: robustness_1_dv_jobs
 118         rm -f robustness_1_dv.feather
 119         $(eval END_1!=cat robustness_1_dv_jobs | wc -l)
 120         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 121         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs;)
 122
 123
 124 robustness_1_dv.RDS: robustness_1_dv.feather
 125         rm -f $@
 126         ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --remember-file $@
 127
 128
 129 robustness_2_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 130         rm -f $@
 131         ${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 $@
 132
 133 robustness_2_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 134         rm -f $@
 135         ${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 $@
 136
 137 robustness_2_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 138         rm -f $@
 139         ${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 $@
 140
 141 robustness_2_jobs_p4: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 142         rm -f $@
 143         ${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 $@
 144
 145 robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_jobs_p3 robustness_2_jobs_p4
 146         $(eval END_1!=cat robustness_2_jobs_p1 | wc -l)
 147         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 148         $(eval END_2!=cat robustness_2_jobs_p2 | wc -l)
 149         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 150         $(eval END_3!=cat robustness_2_jobs_p3 | wc -l)
 151         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 152         $(eval END_4!=cat robustness_2_jobs_p4 | wc -l)
 153         $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
 154
 155         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p1;)
 156         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p2;)
 157         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p3;)
 158         $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p4;)
 159
 160 robustness_2.RDS: plot_example.R robustness_2.feather
 161         rm -f $@
 162         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2" --remember-file $@
 163
 164 robustness_2_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 165         rm -f $@
 166         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2_dv.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 $@
 167
 168 robustness_2_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 169         rm -f $@
 170         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2_dv.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 $@
 171
 172 robustness_2_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 173         rm -f $@
 174         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2_dv.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 $@
 175
 176 robustness_2_dv_jobs_p4: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 177         rm -f $@
 178         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_2_dv.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 $@
 179
 180 robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustness_2_dv_jobs_p3 robustness_2_dv_jobs_p4
 181         $(eval END_1!=cat robustness_2_dv_jobs_p1 | wc -l)
 182         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 183         $(eval END_2!=cat robustness_2_dv_jobs_p2 | wc -l)
 184         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 185         $(eval END_3!=cat robustness_2_dv_jobs_p3 | wc -l)
 186         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 187         $(eval END_4!=cat robustness_2_dv_jobs_p4 | wc -l)
 188         $(eval ITEMS_4!=seq $(START) $(STEP) $(END_4))
 189
 190         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p1;)
 191         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p2;)
 192         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p3;)
 193         $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p4;)
 194
 195 robustness_2_dv.RDS: plot_example.R robustness_2_dv.feather
 196         rm -f $@
 197         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2_dv" --remember-file $@
 198
 199
 200 robustness_3_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 201         rm -f $@
 202         ${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 $@
 203
 204 robustness_3_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 205         rm -f $@
 206         ${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 $@
 207
 208 robustness_3_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 209         rm -f $@
 210         ${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 $@
 211
 212 robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_jobs_p3
 213         $(eval END_1!=cat robustness_3_jobs_p1 | wc -l)
 214         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 215         $(eval END_2!=cat robustness_3_jobs_p2 | wc -l)
 216         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 217         $(eval END_3!=cat robustness_3_jobs_p3 | wc -l)
 218         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 219
 220         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p1;)
 221         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p2;)
 222         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p3;)
 223
 224 robustness_3.RDS: plot_example.R robustness_3.feather
 225         rm -f $@
 226         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3" --remember-file $@
 227
 228 robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 229         rm -f $@
 230         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3_dv.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 $@
 231
 232
 233
 234 robustness_3_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 235         rm -f $@
 236         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3_dv.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 $@
 237
 238
 239 robustness_3_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py
 240         rm -f $@
 241         ${srun} $< --command 'Rscript 03_depvar.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_3_dv.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 $@
 242
 243 robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustness_3_dv_jobs_p3
 244         $(eval END_1!=cat robustness_3_dv_jobs_p1 | wc -l)
 245         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 246         $(eval END_2!=cat robustness_3_dv_jobs_p2 | wc -l)
 247         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 248         $(eval END_3!=cat robustness_3_dv_jobs_p3 | wc -l)
 249         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 250
 251         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p1;)
 252         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p2;)
 253          $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p3;)
 254
 255
 256 robustness_3_dv.RDS: plot_dv_example.R robustness_3_dv.feather
 257         rm -f $@
 258         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv" --remember-file $@
 259
 260
 261 robustness_4_jobs_p1: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 262         rm -f $@
 263         ${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 $@
 264
 265 robustness_4_jobs_p2: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 266         rm -f $@
 267         ${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 $@
 268
 269 robustness_4_jobs_p3: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 270         rm -f $@
 271         ${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 $@
 272
 273 robustness_4_jobs_p4: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py
 274         rm -f $@
 275         ${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 $@
 276
 277 robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_jobs_p3
 278         $(eval END_1!=cat robustness_4_jobs_p1 | wc -l)
 279         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 280         $(eval END_2!=cat robustness_4_jobs_p2 | wc -l)
 281         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 282         $(eval END_3!=cat robustness_4_jobs_p3 | wc -l)
 283         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 284
 285         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p1;)
 286         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p2;)
 287         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p3;)
 288
 289 robustness_4.RDS: plot_example.R robustness_4.feather
 290         rm -f $@
 291         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
 292
 293
 294 # '{"N":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --outfile example_4_jobs
 295
 296 robustness_4_dv_jobs_p1: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 297         rm -f $@
 298         ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0,0.1]}' --outfile $@
 299
 300 robustness_4_dv_jobs_p2: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 301         rm -f $@
 302         ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0.25,0.4]}' --outfile $@
 303
 304 robustness_4_dv_jobs_p3: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 305         rm -f $@
 306         ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"], "Bzy":[-0.7],"Bxy":[0.7],"outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0.55,0.7]}' --outfile $@
 307
 308 robustness_4_dv_jobs_p4: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py
 309         rm -f $@
 310         ${srun} $< --command 'Rscript 04_depvar_differential.R'  --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["robustness_4_dv.feather"],"Bzy":[-0.7],"Bxy":[0.7], "outcome_formula":["y~x+z"], "prediction_accuracy":[0.85],"z_bias":[0.85,1]}' --outfile $@
 311
 312 robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3
 313         $(eval END_1!=cat robustness_4_dv_jobs_p1 | wc -l)
 314         $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1))
 315         $(eval END_2!=cat robustness_4_dv_p2 | wc -l)
 316         $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2))
 317         $(eval END_3!=cat robustness_4_dv_p3 | wc -l)
 318         $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3))
 319
 320         $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p1;)
 321         $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p2;)
 322         $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p3;)
 323
 324
 325 robustness_4_dv.RDS: plot_dv_example.R robustness_4_dv.feather
 326         rm -f $@
 327         ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@
 328
 329
 330
 331 clean_main:
 332         rm -f remembr.RDS
 333         rm -f example_1_jobs
 334         rm -f example_2_jobs
 335         rm -f example_3_jobs
 336         rm -f example_4_jobs
 337         rm -f example_1.feather
 338         rm -f example_2.feather
 339         rm -f example_3.feather
 340         rm -f example_4.feather
 341
 342
 343 #
 344 clean_all:
 345         rm *.feather
 346         rm -f remembr.RDS
 347         rm -f remembr*.RDS
 348         rm -f robustness*.RDS
 349         rm -f example_*_jobs
 350         rm -f robustness_*_jobs_*
 351 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 352
 353 # example_2_B_mecor_jobs:
 354 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B_mecor.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B_mecor.feather"]}' --outfile example_2_B_mecor_jobs
 355
 356 # example_2_B_mecor.feather:example_2_B_mecor.R example_2_B_mecor_jobs
 357 #       rm -f example_2_B_mecor.feather
 358 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_mecor_jobs
 359 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs
 360
 361
 362
 363 .PHONY: supplement