simulations/Makefile

   1
   2 SHELL=bash
   3
   4 Ns=[1000, 5000, 10000]
   5 ms=[100, 200, 400]
   6 seeds=[$(shell seq -s, 1 500)]
   7 explained_variances=[0.1]
   8
   9 all:remembr.RDS remember_irr.RDS
  10 supplement: remember_robustness_misspec.RDS
  11
  12 srun=sbatch --wait --verbose run_job.sbatch
  13
  14
  15 joblists:example_1_jobs example_2_jobs example_3_jobs
  16
  17 # test_true_z_jobs: test_true_z.R simulation_base.R
  18 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["test_true_z.feather"], "y_explained_variancevari":${explained_variances}, "Bzx":${Bzx}}' --outfile test_true_z_jobsb
  19
  20 # test_true_z.feather: test_true_z_jobs
  21 #       rm -f test_true_z.feather
  22 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 test_true_z_jobs
  23 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 test_true_z_jobs
  24
  25
  26 example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py pl_methods.R
  27         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[1]}' --outfile example_1_jobs
  28
  29 example_1.feather: example_1_jobs
  30         rm -f example_1.feather
  31         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_1_jobs
  32         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_1_jobs
  33         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_1_jobs
  34         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_1_jobs
  35         sbatch --wait --verbose --array=4001-$(shell cat example_1_jobs | wc -l)  run_simulation.sbatch 0 example_1_jobs
  36
  37 example_2_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py pl_methods.R
  38         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[1], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y*z*x"]}' --outfile example_2_jobs
  39
  40 example_2.feather: example_2_jobs
  41         rm -f example_2.feather
  42         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_2_jobs
  43         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_2_jobs
  44         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_2_jobs
  45         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_2_jobs
  46         sbatch --wait --verbose --array=4001-$(shell cat example_2_jobs | wc -l)  run_simulation.sbatch 0 example_2_jobs
  47
  48
  49 # example_2_B_jobs: example_2_B.R
  50 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs
  51
  52 # example_2_B.feather: example_2_B_jobs
  53 #       rm -f example_2_B.feather
  54 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs
  55
  56 example_3_jobs: 03_depvar.R simulation_base.R grid_sweep.py pl_methods.R
  57         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 03_depvar.R" --arg_dict '{"N":${Ns},"m":${ms}, "Bxy":[0.7],"Bzy":[-0.7],"seed":${seeds}, "outfile":["example_3.feather"], "y_explained_variance":${explained_variances}}' --outfile example_3_jobs
  58
  59 example_3.feather: example_3_jobs
  60         rm -f example_3.feather
  61         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_3_jobs
  62         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_3_jobs
  63         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_3_jobs
  64         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_3_jobs
  65         sbatch --wait --verbose --array=4001-$(shell cat example_3_jobs | wc -l)  run_simulation.sbatch 0 example_3_jobs
  66
  67 example_4_jobs: 04_depvar_differential.R simulation_base.R grid_sweep.py pl_methods.R
  68         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --outfile example_4_jobs
  69
  70 example_4.feather: example_4_jobs
  71         rm -f example_4.feather
  72         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_4_jobs
  73         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 example_4_jobs
  74         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 example_4_jobs
  75         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 example_4_jobs
  76         sbatch --wait --verbose --array=4001-$(shell cat example_4_jobs | wc -l)  run_simulation.sbatch 0 example_4_jobs
  77
  78
  79
  80 remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feather plot_example.R plot_dv_example.R summarize_estimator.R
  81         rm -f remembr.RDS
  82         ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1"
  83         ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2"
  84         ${srun} Rscript plot_dv_example.R --infile example_3.feather --name "plot.df.example.3"
  85         ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4"
  86
  87
  88 irr_Ns = [1000]
  89 irr_ms = [150,300,600]
  90 irr_seeds=${seeds}
  91 irr_explained_variances=${explained_variances}
  92 irr_coder_accuracy=[0.80]
  93
  94 example_5_jobs: 05_irr_indep.R irr_simulation_base.R grid_sweep.py pl_methods.R measerr_methods.R
  95         sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 05_irr_indep.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_5.feather"], "y_explained_variance":${irr_explained_variances}, "coder_accuracy":${irr_coder_accuracy}}' --outfile example_5_jobs
  96
  97 example_5.feather:example_5_jobs
  98         rm -f example_5.feather
  99         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_5_jobs
 100         sbatch --wait --verbose --array=1001-$(shell cat example_5_jobs | wc -l)  run_simulation.sbatch 1000 example_5_jobs
 101         # sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 2000 example_5_jobs
 102         # sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 3000 example_5_jobs
 103         # sbatch --wait --verbose --array=2001-$(shell cat example_5_jobs | wc -l)  run_simulation.sbatch 4000 example_5_jobs
 104
 105
 106
 107 # example_6_jobs: 06_irr_dv.R irr_dv_simulation_base.R grid_sweep.py pl_methods.R
 108 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 06_irr_dv.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_6.feather"], "y_explained_variance":${irr_explained_variances},"coder_accuracy":${irr_coder_accuracy}}' --outfile example_6_jobs
 109
 110 # example_6.feather:example_6_jobs
 111 #       rm -f example_6.feather
 112 #       sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 example_6_jobs
 113 #       sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 1000 example_6_jobs
 114 #       sbatch --wait --verbose --array=2001-$(shell cat example_6_jobs | wc -l)  run_simulation.sbatch 2000 example_6_jobs
 115
 116
 117 remember_irr.RDS: example_5.feather plot_irr_example.R plot_irr_dv_example.R summarize_estimator.R
 118         rm -f remember_irr.RDS
 119         sbatch --wait --verbose run_job.sbatch Rscript plot_irr_example.R --infile example_5.feather --name "plot.df.example.5"
 120 #       sbatch --wait --verbose run_job.sbatch Rscript plot_irr_dv_example.R --infile example_6.feather --name "plot.df.example.6"
 121
 122
 123 robustness_1_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py
 124         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
 125
 126
 127 robustness_1.feather: robustness_1_jobs
 128         rm -f robustness_1.feather
 129         sbatch --wait --verbose --array=1-1000  run_simulation.sbatch 0 robustness_1_jobs
 130         sbatch --wait --verbose --array=1001-2000  run_simulation.sbatch 0 robustness_1_jobs
 131         sbatch --wait --verbose --array=2001-3000  run_simulation.sbatch 0 robustness_1_jobs
 132         sbatch --wait --verbose --array=3001-4000  run_simulation.sbatch 0 robustness_1_jobs
 133         sbatch --wait --verbose --array=4001-$(shell cat robustness_1_jobs | wc -l)  run_simulation.sbatch 0 robustness_1_jobs
 134
 135 robustness_1.RDS: robustness_1.feather
 136         rm -f robustness_1.RDS
 137         ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@
 138
 139 robustness_1_dv_jobs: simulation_base.R 04_depvar_differential.R grid_sweep.py
 140         ${srun} bash -c "source ~/.bashrc && grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict \"{'N':${Ns},'m':${ms}, 'seed':${seeds}, 'outfile':['robustness_1_dv.feather'], 'y_explained_variance':${explained_variances}, 'proxy_formula':['w_pred~y']}\" --outfile robustness_1_dv_jobs"
 141
 142
 143 robustness_1_dv.feather: robustness_1_dv_jobs
 144         rm -f robustness_1_dv.feather
 145         sbatch --wait --verbose --array=1-$(shell cat example_3_jobs | wc -l)  run_simulation.sbatch 0 robustness_1_dv_jobs
 146
 147
 148 robustness_1_dv.RDS: robustness_1_dv.feather
 149         rm -f $@
 150         ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --outfile $@
 151
 152
 153 robustness_2_jobs: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py
 154         rm -f $@
 155         ${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":[0.6,0.73,0.8,0.85,0.9,0.95]}' --outfile $@
 156
 157
 158
 159 START=1
 160 END=$(shell cat robustness_2_jobs | wc -l)
 161 STEP=1000
 162 ITEMS=$(shell seq $(START) $(STEP) $(END))
 163
 164 robustness_2.feather: robustness_2_jobs
 165         $(foreach item,$(ITEMS),sbatch --wait --verbose --array=$(shell expr $(item))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 $<)
 166
 167 #
 168 clean:
 169         rm *.feather
 170         rm -f remembr.RDS
 171         rm -f example_*_jobs
 172 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 173
 174 # example_2_B_mecor_jobs:
 175 #       sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript example_2_B_mecor.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B_mecor.feather"]}' --outfile example_2_B_mecor_jobs
 176
 177 # example_2_B_mecor.feather:example_2_B_mecor.R example_2_B_mecor_jobs
 178 #       rm -f example_2_B_mecor.feather
 179 #       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_mecor_jobs
 180 #       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs
 181
 182
 183
 184 .PHONY: supplement