update simulation and mle code

[ml_measurement_error_public.git] / simulations / Makefile

diff --git a/simulations/Makefile b/simulations/Makefile
index d278c8c2aeb8f0bfc2e7482bdb9b538491a1fd16..44910cbc0a9475e66cd1a7e99fb4da52cea1dd0a 100644 (file)
--- a/simulations/Makefile
+++ b/simulations/Makefile
@@ -1,12 +1,12 @@
 
 SHELL=bash
 
 
 SHELL=bash
 

-Ns=[1000, 2000, 4000, 8000]
-ms=[100, 200, 400, 800]
-seeds=[$(shell seq -s, 1 100)]
+Ns=[1000, 2000, 4000]
+ms=[200, 400, 800]
+seeds=[$(shell seq -s, 1 250)]

 explained_variances=[0.1]
 
 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},  "Bzy":[-0.3],"Bxy":[0.3],"Bzx":[0.3], "outcome_formula":["y~x+z"], "proxy_formula":["w_pred~y*z*x"], "truth_formula":["x~z"]}' --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


@@ -59,6 +59,7 @@ 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
 
        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"
 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"


@@ -66,6 +67,32 @@ remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feat
        ${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"
 
        ${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
        rm -f remembr.RDS
 clean:
        rm *.feather
        rm -f remembr.RDS