update simulation and mle code

[ml_measurement_error_public.git] / simulations / Makefile

diff --git a/simulations/Makefile b/simulations/Makefile
index dec7889db143e7738293e5825094d7ccc9cac2df..44910cbc0a9475e66cd1a7e99fb4da52cea1dd0a 100644 (file)
--- a/simulations/Makefile
+++ b/simulations/Makefile
@@ -1,12 +1,12 @@
 
 SHELL=bash
 
 
 SHELL=bash
 

-Ns=[1000,3600,14400]
-ms=[75,150,300]
+Ns=[1000, 2000, 4000]
+ms=[200, 400, 800]

 seeds=[$(shell seq -s, 1 250)]
 explained_variances=[0.1]
 
 seeds=[$(shell seq -s, 1 250)]
 explained_variances=[0.1]
 

-all:remembr.RDS
+all:remembr.RDS remember_irr.RDS

 
 srun=srun -A comdata -p compute-bigmem --time=6:00:00 --mem 4G -c 1
 
 
 srun=srun -A comdata -p compute-bigmem --time=6:00:00 --mem 4G -c 1
 


@@ -31,7 +31,7 @@ example_1.feather: example_1_jobs
 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_1_jobs
 
 example_2_jobs: 02_indep_differential.R simulation_base.R
 #      sbatch --wait --verbose --array=3001-6001 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
+       grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"],"y_explained_variance":${explained_variances},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y*z*x"]}' --outfile example_2_jobs

 
 example_2.feather: example_2_jobs 
        rm -f example_2.feather
 
 example_2.feather: example_2_jobs 
        rm -f example_2.feather


@@ -45,19 +45,53 @@ example_2.feather: example_2_jobs
 #      rm -f example_2_B.feather
 #      sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 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 --command "Rscript 03_depvar.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_3.feather"], "y_explained_variance":${explained_variances}}' --outfile example_3_jobs

 
 example_3.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
 
 
 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
 

+example_4_jobs: 04_depvar_differential.R simulation_base.R
+       grid_sweep.py --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "y_explained_variance":${explained_variances}}' --outfile example_4_jobs

 
 

-remembr.RDS:example_1.feather example_2.feather example_3.feather plot_example.R plot_dv_example.R
+example_4.feather: example_4_jobs
+       rm -f example_4.feather 
+       sbatch --wait --verbose --array=1-$(shell cat example_4_jobs | wc -l)  run_simulation.sbatch 0 example_4_jobs
+
+
+remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feather plot_example.R plot_dv_example.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"
+
+
+irr_Ns = ${Ns}
+irr_ms = ${ms}
+irr_seeds=${seeds}
+irr_explained_variances=${explained_variances}
+
+example_5_jobs: 05_irr_indep.R irr_simulation_base.R
+       grid_sweep.py --command "Rscript 05_irr_indep.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_5.feather"], "y_explained_variance":${irr_explained_variances}}' --outfile example_5_jobs
+
+example_5.feather:example_5_jobs
+       rm -f example_5.feather
+       sbatch --wait --verbose --array=1-$(shell cat example_5_jobs | wc -l)  run_simulation.sbatch 0 example_5_jobs
+
+
+example_6_jobs: 06_irr_dv.R irr_dv_simulation_base.R
+       grid_sweep.py --command "Rscript 06_irr_dv.R" --arg_dict '{"N":${irr_Ns},"m":${irr_ms}, "seed":${irr_seeds}, "outfile":["example_6.feather"], "y_explained_variance":${irr_explained_variances}}' --outfile example_6_jobs
+
+example_6.feather:example_6_jobs
+       rm -f example_6.feather
+       sbatch --wait --verbose --array=1-$(shell cat example_6_jobs | wc -l)  run_simulation.sbatch 0 example_6_jobs
+
+remember_irr.RDS: example_5.feather example_6.feather plot_irr_example.R plot_irr_dv_example.R
+       rm -f remember_irr.RDS
+       ${srun} Rscript plot_irr_example.R --infile example_5.feather --name "plot.df.example.5"
+       ${srun} Rscript plot_irr_dv_example.R --infile example_6.feather --name "plot.df.example.6"

 
 clean:
        rm *.feather
 
 clean:
        rm *.feather