From acb119418aef75dfa1e882f975ae0638e7736a07 Mon Sep 17 00:00:00 2001 From: Nathan TeBlunthuis Date: Tue, 28 Feb 2023 16:13:36 -0800 Subject: [PATCH] update simulations code --- simulations/01_two_covariates.R | 5 +- simulations/02_indep_differential.R | 6 +- simulations/03_depvar.R | 5 +- simulations/04_depvar_differential.R | 28 +++-- simulations/Makefile | 181 +++++++++++++++++---------- simulations/run_job.sbatch | 5 +- 6 files changed, 140 insertions(+), 90 deletions(-) diff --git a/simulations/01_two_covariates.R b/simulations/01_two_covariates.R index cd688c7..1f317be 100644 --- a/simulations/01_two_covariates.R +++ b/simulations/01_two_covariates.R @@ -79,6 +79,7 @@ parser <- add_argument(parser, "--Bzx", help='Effect of z on x', default=0.3) parser <- add_argument(parser, "--Bzy", help='Effect of z on y', default=-0.3) parser <- add_argument(parser, "--Bxy", help='Effect of x on y', default=0.3) parser <- add_argument(parser, "--Px", help='Base rate of x', default=0.5) +parser <- add_argument(parser, "--confint_method", help='method for approximating confidence intervals', default='quad') args <- parse_args(parser) B0 <- 0 @@ -89,9 +90,9 @@ Bzx <- args$Bzx df <- simulate_data(args$N, args$m, B0, Bxy, Bzy, Bzx, Px, seed=args$seed + 500, y_explained_variance = args$y_explained_variance, prediction_accuracy=args$prediction_accuracy) -result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy, Bzx=Bzx, 'Bzy'=Bzy, 'Px'=Px, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'accuracy_imbalance_difference'=args$accuracy_imbalance_difference, 'outcome_formula'=args$outcome_formula, 'proxy_formula'=args$proxy_formula,truth_formula=args$truth_formula, error='') +result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy, 'Bzx'=Bzx, 'Bzy'=Bzy, 'Px'=Px, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'accuracy_imbalance_difference'=args$accuracy_imbalance_difference, 'outcome_formula'=args$outcome_formula, 'proxy_formula'=args$proxy_formula,truth_formula=args$truth_formula, confint_method=args$confint_method,error='') -outline <- run_simulation(df, result, outcome_formula=as.formula(args$outcome_formula), proxy_formula=as.formula(args$proxy_formula), truth_formula=as.formula(args$truth_formula)) +outline <- run_simulation(df, result, outcome_formula=as.formula(args$outcome_formula), proxy_formula=as.formula(args$proxy_formula), truth_formula=as.formula(args$truth_formula),confint_method=args$confint_method) outfile_lock <- lock(paste0(args$outfile, '_lock'),exclusive=TRUE) if(file.exists(args$outfile)){ diff --git a/simulations/02_indep_differential.R b/simulations/02_indep_differential.R index 4e3a132..9c33be7 100644 --- a/simulations/02_indep_differential.R +++ b/simulations/02_indep_differential.R @@ -141,7 +141,7 @@ parser <- add_argument(parser, "--y_bias", help='coefficient of y on the probabi parser <- add_argument(parser, "--z_bias", help='coefficient of z on the probability a classification is correct', default=0) parser <- add_argument(parser, "--truth_formula", help='formula for the true variable', default="x~z") parser <- add_argument(parser, "--Px", help='base rate of x', default=0.5) - +parser <- add_argument(parser, "--confint_method", help='method for approximating confidence intervals', default='quad') args <- parse_args(parser) B0 <- 0 @@ -159,9 +159,9 @@ if(args$m < args$N){ ## pc.df <- pc(suffStat=list(C=cor(df.pc),n=nrow(df.pc)),indepTest=gaussCItest,labels=names(df.pc),alpha=0.05) ## plot(pc.df) - result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy, 'Bzx'=args$Bzx, 'Bzy'=Bzy, 'Px'=Px, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'accuracy_imbalance_difference'=args$accuracy_imbalance_difference, 'y_bias'=args$y_bias,'outcome_formula'=args$outcome_formula, 'proxy_formula'=args$proxy_formula,truth_formula=args$truth_formula, error='') + result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy, 'Bzx'=args$Bzx, 'Bzy'=Bzy, 'Px'=Px, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'accuracy_imbalance_difference'=args$accuracy_imbalance_difference, 'y_bias'=args$y_bias,'outcome_formula'=args$outcome_formula, 'proxy_formula'=args$proxy_formula,truth_formula=args$truth_formula, confint_method=args$confint_method, error='') - outline <- run_simulation(df, result, outcome_formula=as.formula(args$outcome_formula), proxy_formula=as.formula(args$proxy_formula), truth_formula=as.formula(args$truth_formula)) + outline <- run_simulation(df, result, outcome_formula=as.formula(args$outcome_formula), proxy_formula=as.formula(args$proxy_formula), truth_formula=as.formula(args$truth_formula),confint_method=args$confint_method) outfile_lock <- lock(paste0(args$outfile, '_lock'),exclusive=TRUE) diff --git a/simulations/03_depvar.R b/simulations/03_depvar.R index f0064f2..461c01a 100644 --- a/simulations/03_depvar.R +++ b/simulations/03_depvar.R @@ -79,6 +79,7 @@ parser <- add_argument(parser, "--Bzx", help='coeffficient of z on x', default=- parser <- add_argument(parser, "--B0", help='Base rate of y', default=0.5) parser <- add_argument(parser, "--outcome_formula", help='formula for the outcome variable', default="y~x+z") parser <- add_argument(parser, "--proxy_formula", help='formula for the proxy variable', default="w_pred~y") +parser <- add_argument(parser, "--confint_method", help='method for getting confidence intervals', default="quad") args <- parse_args(parser) @@ -91,9 +92,9 @@ if(args$m < args$N){ df <- simulate_data(args$N, args$m, B0, Bxy, Bzy, Bzx, args$seed, args$prediction_accuracy) # result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'x_bias_y0'=args$x_bias_y0,'x_bias_y1'=args$x_bias_y1,'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula) - result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy, 'Bzx'=Bzx,'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula) + result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy, 'Bzx'=Bzx,'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula, 'confint_method'=args$confint_method) - outline <- run_simulation_depvar(df, result, outcome_formula = as.formula(args$outcome_formula), proxy_formula = as.formula(args$proxy_formula)) + outline <- run_simulation_depvar(df, result, outcome_formula = as.formula(args$outcome_formula), proxy_formula = as.formula(args$proxy_formula), confint_method=args$confint_method) outfile_lock <- lock(paste0(args$outfile, '_lock'),exclusive=TRUE) diff --git a/simulations/04_depvar_differential.R b/simulations/04_depvar_differential.R index b367080..2c43f59 100644 --- a/simulations/04_depvar_differential.R +++ b/simulations/04_depvar_differential.R @@ -31,12 +31,12 @@ source("simulation_base.R") ## one way to do it is by adding correlation to x.obs and y that isn't in w. ## in other words, the model is missing an important feature of x.obs that's related to y. -simulate_data <- function(N, m, B0, Bxy, Bzy, seed, prediction_accuracy=0.73, z_bias=-0.75){ +simulate_data <- function(N, m, B0, Bxy, Bzy, Bxz=0, seed=0, prediction_accuracy=0.73, z_bias=-0.75){ set.seed(seed) # make w and y dependent z <- rnorm(N,sd=0.5) - x <- rbinom(N,1,0.5) + x <- rbinom(N,1,plogis(Bxz*z)) ystar <- Bzy * z + Bxy * x + B0 y <- rbinom(N,1,plogis(ystar)) @@ -70,30 +70,32 @@ parser <- add_argument(parser, "--N", default=1000, help="number of observations parser <- add_argument(parser, "--m", default=500, help="m the number of ground truth observations") parser <- add_argument(parser, "--seed", default=17, help='seed for the rng') parser <- add_argument(parser, "--outfile", help='output file', default='example_4.feather') -parser <- add_argument(parser, "--prediction_accuracy", help='how accurate is the predictive model?', default=0.79) +parser <- add_argument(parser, "--prediction_accuracy", help='how accurate is the predictive model?', default=0.75) ## parser <- add_argument(parser, "--z_bias_y1", help='how is the classifier biased when y = 1?', default=-0.75) ## parser <- add_argument(parser, "--z_bias_y0", help='how is the classifier biased when y = 0 ?', default=0.75) -parser <- add_argument(parser, "--z_bias", help='how is the classifier biased?', default=1.5) -parser <- add_argument(parser, "--Bxy", help='coefficient of x on y', default=0.1) -parser <- add_argument(parser, "--Bzy", help='coeffficient of z on y', default=-0.1) -parser <- add_argument(parser, "--B0", help='coeffficient of z on y', default=-0.1) +parser <- add_argument(parser, "--z_bias", help='how is the classifier biased?', default=-0.5) +parser <- add_argument(parser, "--Bxy", help='coefficient of x on y', default=0.7) +parser <- add_argument(parser, "--Bzy", help='coeffficient of z on y', default=-0.7) +parser <- add_argument(parser, "--Bzx", help='coeffficient of z on y', default=1) +parser <- add_argument(parser, "--B0", help='coeffficient of z on y', default=0) parser <- add_argument(parser, "--outcome_formula", help='formula for the outcome variable', default="y~x+z") parser <- add_argument(parser, "--proxy_formula", help='formula for the proxy variable', default="w_pred~y+z") - +parser <- add_argument(parser, "--confint_method", help='method for approximating confidence intervals', default='quad') args <- parse_args(parser) B0 <- args$B0 Bxy <- args$Bxy Bzy <- args$Bzy - +Bzx <- args$Bzx if(args$m < args$N){ - df <- simulate_data(args$N, args$m, B0, Bxy, Bzy, args$seed, args$prediction_accuracy, args$z_bias) + df <- simulate_data(args$N, args$m, B0, Bxy, Bzx, Bzy, args$seed, args$prediction_accuracy, args$z_bias) -# result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'z_bias_y0'=args$z_bias_y0,'z_bias_y1'=args$z_bias_y1,'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula) - result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'z_bias'=args$z_bias,'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula) +# result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy,'Bzx'=Bzx, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'z_bias_y0'=args$z_bias_y0,'z_bias_y1'=args$z_bias_y1,'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula) + result <- list('N'=args$N,'m'=args$m,'B0'=B0,'Bxy'=Bxy,'Bzy'=Bzy,'Bzx'=Bzx, 'seed'=args$seed, 'y_explained_variance'=args$y_explained_variance, 'prediction_accuracy'=args$prediction_accuracy, 'z_bias'=args$z_bias,'outcome_formula' = args$outcome_formula, 'proxy_formula' = args$proxy_formula, confint_method=args$confint_method) - outline <- run_simulation_depvar(df, result, outcome_formula = as.formula(args$outcome_formula), proxy_formula = as.formula(args$proxy_formula)) + outline <- run_simulation_depvar(df, result, outcome_formula = as.formula(args$outcome_formula), proxy_formula = as.formula(args$proxy_formula),confint_method=args$confint_method) + print(outline$error.cor.z) outfile_lock <- lock(paste0(args$outfile, '_lock'),exclusive=TRUE) diff --git a/simulations/Makefile b/simulations/Makefile index 3e8fdd5..821280b 100644 --- a/simulations/Makefile +++ b/simulations/Makefile @@ -8,7 +8,7 @@ explained_variances=[0.1] all:main supplement main:remembr.RDS -supplement:robustness_1.RDS robustness_1_dv.RDS robustness_2.RDS robustness_2_dv.RDS robustness_3.RDS robustness_3_dv.RDS robustness_4.RDS robustness_4_dv.RDS +supplement:robustness_1.RDS robustness_1_dv.RDS robustness_2.RDS robustness_2_dv.RDS robustness_3.RDS robustness_3_dv.RDS robustness_3_proflik.RDS robustness_3_dv_proflik.RDS robustness_4.RDS robustness_4_dv.RDS srun=sbatch --wait --verbose run_job.sbatch @@ -30,7 +30,7 @@ example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py pl_methods.R example_1.feather: example_1_jobs rm -f example_1.feather sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_1_jobs - sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_1_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_1_jobs sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_1_jobs sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_1_jobs sbatch --wait --verbose --array=4001-$(shell cat example_1_jobs | wc -l) run_simulation.sbatch 0 example_1_jobs @@ -41,10 +41,10 @@ example_2_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py pl_metho example_2.feather: example_2_jobs rm -f example_2.feather sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_2_jobs - sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_2_jobs sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_2_jobs sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_2_jobs - sbatch --wait --verbose --array=4001-$(shell cat example_2_jobs | wc -l) run_simulation.sbatch 0 example_2_jobs + sbatch --wait --verbose --array=4001-$(shell cat example_2_jobs | wc -l) # example_2_B_jobs: example_2_B.R @@ -55,23 +55,24 @@ example_2.feather: example_2_jobs # sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs example_3_jobs: 03_depvar.R simulation_base.R grid_sweep.py pl_methods.R - 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 + 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 example_3.feather: example_3_jobs rm -f example_3.feather sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_3_jobs - sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_3_jobs - sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_3_jobs + sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_3_jobs sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_3_jobs sbatch --wait --verbose --array=4001-$(shell cat example_3_jobs | wc -l) run_simulation.sbatch 0 example_3_jobs example_4_jobs: 04_depvar_differential.R simulation_base.R grid_sweep.py pl_methods.R - sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 04_depvar_differential.R" --arg_dict '{"N":${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 + 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":${seeds}, "outfile":["example_4.feather"], "z_bias":[-0.5], "prediction_accuracy":[0.73]}' --outfile example_4_jobs example_4.feather: example_4_jobs rm -f example_4.feather sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 example_4_jobs sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 example_4_jobs + sbatch --wait --verbose --array=2001-3001 run_simulation.sbatch 0 example_4_jobs sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 example_4_jobs sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 example_4_jobs sbatch --wait --verbose --array=4001-$(shell cat example_4_jobs | wc -l) run_simulation.sbatch 0 example_4_jobs @@ -86,63 +87,73 @@ remembr.RDS:example_1.feather example_2.feather example_3.feather example_4.feat ${srun} Rscript plot_dv_example.R --infile example_4.feather --name "plot.df.example.4" -robustness_1_jobs: 02_indep_differential.R simulation_base.R grid_sweep.py - sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${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 - - - START=0 STEP=1000 ONE=1 -robustness_1.feather: robustness_1_jobs - $(eval END_1!=cat robustness_1_jobs | wc -l) - $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) - rm -f robustness_1.feather - sbatch --wait --verbose --array=1-1000 run_simulation.sbatch 0 robustness_1_jobs - sbatch --wait --verbose --array=1001-2000 run_simulation.sbatch 0 robustness_1_jobs - sbatch --wait --verbose --array=2001-3000 run_simulation.sbatch 0 robustness_1_jobs - sbatch --wait --verbose --array=3001-4000 run_simulation.sbatch 0 robustness_1_jobs - sbatch --wait --verbose --array=4001-$(shell cat robustness_1_jobs | wc -l) run_simulation.sbatch 0 robustness_1_jobs +robustness_Ns=[1000,5000] +robustness_robustness_ms=[100,200] + +#in robustness 1 / example 2 misclassification is correlated with Y. +robustness_1_jobs_p1: 02_indep_differential.R simulation_base.R grid_sweep.py + 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 - $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs;) +robustness_1_jobs_p2: 02_indep_differential.R simulation_base.R grid_sweep.py + sbatch --wait --verbose run_job.sbatch grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":[5000],"m":${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 -robustness_1.RDS: robustness_1.feather +robustness_1.feather: robustness_1_jobs_p1 robustness_1_jobs_p2 + rm -f $@ + $(eval END_1!=cat robustness_1_jobs_p1 | wc -l) + $(eval ITEROBUSTNESS_MS_1!=seq $(START) $(STEP) $(END_1)) + $(eval END_2!=cat robustness_1_jobs_p2 | wc -l) + $(eval ITEROBUSTNESS_MS_2!=seq $(START) $(STEP) $(END_2)) + + $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p1;) + $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_jobs_p2;) + +robustness_1.RDS: robustness_1.feather summarize_estimator.R rm -f robustness_1.RDS ${srun} Rscript plot_example.R --infile $< --name "robustness_1" --remember-file $@ -robustness_1_dv_jobs: simulation_base.R 04_depvar_differential.R grid_sweep.py - ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":${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 +# 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. +robustness_1_dv_jobs_p1: simulation_base.R 04_depvar_differential.R grid_sweep.py + ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[1000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p1 -robustness_1_dv.feather: robustness_1_dv_jobs - rm -f robustness_1_dv.feather - $(eval END_1!=cat robustness_1_dv_jobs | wc -l) - $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) - $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs;) +robustness_1_dv_jobs_p2: simulation_base.R 04_depvar_differential.R grid_sweep.py + ${srun} grid_sweep.py --command 'Rscript 04_depvar_differential.R' --arg_dict '{"N":[5000],"Bzx":[1], "Bxy":[0.7,0],"Bzy":[-0.7,0],"m":${robustness_ms}, "seed":${seeds}, "outfile":["robustness_1_dv.feather"], "proxy_formula":["w_pred~y"],"z_bias":[-0.5]}' --outfile robustness_1_dv_jobs_p2 +robustness_1_dv.feather: robustness_1_dv_jobs_p1 robustness_1_dv_jobs_p2 + rm -f $@ + $(eval END_1!=cat robustness_1_dv_jobs_p1 | wc -l) + $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) + $(eval END_2!=cat robustness_1_dv_jobs_p2 | wc -l) + $(eval ITEMS_2!=seq $(START) $(STEP) $(END_1)) + $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p1;) + $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_1_dv_jobs_p2;) -robustness_1_dv.RDS: robustness_1_dv.feather +robustness_1_dv.RDS: robustness_1_dv.feather summarize_estimator.R rm -f $@ ${srun} Rscript plot_dv_example.R --infile $< --name "robustness_1_dv" --remember-file $@ robustness_2_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_jobs_p4: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_jobs_p3 robustness_2_jobs_p4 + rm $@ $(eval END_1!=cat robustness_2_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_2_jobs_p2 | wc -l) @@ -157,27 +168,28 @@ robustness_2.feather: robustness_2_jobs_p1 robustness_2_jobs_p2 robustness_2_job $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p3;) $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_jobs_p4;) -robustness_2.RDS: plot_example.R robustness_2.feather +robustness_2.RDS: plot_example.R robustness_2.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2" --remember-file $@ robustness_2_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_dv_jobs_p4: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustness_2_dv_jobs_p3 robustness_2_dv_jobs_p4 + rm -f $@ $(eval END_1!=cat robustness_2_dv_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_2_dv_jobs_p2 | wc -l) @@ -192,24 +204,40 @@ robustness_2_dv.feather: robustness_2_dv_jobs_p1 robustness_2_dv_jobs_p2 robustn $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p3;) $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_2_dv_jobs_p4;) -robustness_2_dv.RDS: plot_example.R robustness_2_dv.feather +robustness_2_dv.RDS: plot_dv_example.R robustness_2_dv.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_2_dv" --remember-file $@ +robustness_3_proflik_jobs: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py + rm -f $@ + ${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 $@ + +robustness_3_proflik.feather: robustness_3_proflik_jobs + rm -f $@ + $(eval END_1!=cat robustness_3_proflik_jobs | wc -l) + $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) + $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_proflik_jobs;) + +robustness_3_proflik.RDS: plot_example.R robustness_3_proflik.feather summarize_estimator.R + rm -f $@ + ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_proflik" --remember-file $@ + + robustness_3_jobs_p1: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_3_jobs_p2: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_3_jobs_p3: grid_sweep.py 01_two_covariates.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_jobs_p3 + rm -f $@ $(eval END_1!=cat robustness_3_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_3_jobs_p2 | wc -l) @@ -221,26 +249,42 @@ robustness_3.feather: robustness_3_jobs_p1 robustness_3_jobs_p2 robustness_3_job $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p2;) $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_jobs_p3;) -robustness_3.RDS: plot_example.R robustness_3.feather +robustness_3.RDS: plot_example.R robustness_3.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3" --remember-file $@ -robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py +robustness_3_dv_proflik_jobs: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py + rm -f $@ + ${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 $@ + +robustness_3_dv_proflik.feather: robustness_3_dv_proflik_jobs + rm -f $@ + $(eval END_1!=cat robustness_3_dv_proflik_jobs | wc -l) + $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) + $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_proflik_jobs;) + +robustness_3_dv_proflik.RDS: plot_dv_example.R robustness_3_dv_proflik.feather summarize_estimator.R rm -f $@ - ${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 $@ + ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv_proflik" --remember-file $@ + + + robustness_3_dv_jobs_p1: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py + rm -f $@ + ${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 $@ robustness_3_dv_jobs_p2: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_3_dv_jobs_p3: grid_sweep.py 03_depvar.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustness_3_dv_jobs_p3 + rm -f $@ $(eval END_1!=cat robustness_3_dv_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_3_dv_jobs_p2 | wc -l) @@ -253,28 +297,26 @@ robustness_3_dv.feather: robustness_3_dv_jobs_p1 robustness_3_dv_jobs_p2 robustn $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_3_dv_jobs_p3;) -robustness_3_dv.RDS: plot_dv_example.R robustness_3_dv.feather +robustness_3_dv.RDS: plot_dv_example.R robustness_3_dv.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_3_dv" --remember-file $@ + robustness_4_jobs_p1: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_4_jobs_p2: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_4_jobs_p3: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ - -robustness_4_jobs_p4: grid_sweep.py 02_indep_differential.R simulation_base.R grid_sweep.py - rm -f $@ - ${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 $@ + ${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 $@ robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_jobs_p3 + rm -f $@ $(eval END_1!=cat robustness_4_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_4_jobs_p2 | wc -l) @@ -286,48 +328,52 @@ robustness_4.feather: robustness_4_jobs_p1 robustness_4_jobs_p2 robustness_4_job $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p2;) $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_jobs_p3;) -robustness_4.RDS: plot_example.R robustness_4.feather +robustness_4.RDS: plot_example.R robustness_4.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@ -# '{"N":${Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --outfile example_4_jobs +# '{"N":${robustness_Ns},"Bxy":[0.7],"Bzy":[-0.7],"m":${ms}, "seed":${seeds}, "outfile":["example_4.feather"], "z_bias":[0.5]}' --example_4_jobs robustness_4_dv_jobs_p1: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_4_dv_jobs_p2: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_4_dv_jobs_p3: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ robustness_4_dv_jobs_p4: grid_sweep.py 04_depvar_differential.R simulation_base.R grid_sweep.py rm -f $@ - ${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 $@ + ${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 $@ -robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3 +robustness_4_dv.feather: robustness_4_dv_jobs_p1 robustness_4_dv_jobs_p2 robustness_4_dv_jobs_p3 robustness_4_dv_jobs_p4 + rm -f $@ $(eval END_1!=cat robustness_4_dv_jobs_p1 | wc -l) $(eval ITEMS_1!=seq $(START) $(STEP) $(END_1)) $(eval END_2!=cat robustness_4_dv_p2 | wc -l) $(eval ITEMS_2!=seq $(START) $(STEP) $(END_2)) $(eval END_3!=cat robustness_4_dv_p3 | wc -l) $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3)) + $(eval END_3!=cat robustness_4_dv_p4 | wc -l) + $(eval ITEMS_3!=seq $(START) $(STEP) $(END_3)) + $(foreach item,$(ITEMS_1),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p1;) $(foreach item,$(ITEMS_2),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p2;) $(foreach item,$(ITEMS_3),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p3;) + $(foreach item,$(ITEMS_4),sbatch --wait --verbose --array=$(shell expr $(item) + $(ONE))-$(shell expr $(item) + $(STEP)) run_simulation.sbatch 0 robustness_4_dv_jobs_p4;) -robustness_4_dv.RDS: plot_dv_example.R robustness_4_dv.feather +robustness_4_dv.RDS: plot_dv_example.R robustness_4_dv.feather summarize_estimator.R rm -f $@ ${srun} Rscript $< --infile $(word 2, $^) --name "robustness_4" --remember-file $@ - clean_main: rm -f remembr.RDS rm -f example_1_jobs @@ -359,5 +405,4 @@ clean_all: # sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_mecor_jobs - .PHONY: supplement diff --git a/simulations/run_job.sbatch b/simulations/run_job.sbatch index 8561788..591b178 100644 --- a/simulations/run_job.sbatch +++ b/simulations/run_job.sbatch @@ -1,8 +1,8 @@ #!/bin/bash #SBATCH --job-name="simulate measurement error models" ## Allocation Definition -#SBATCH --account=comdata -#SBATCH --partition=compute-bigmem +#SBATCH --account=comdata-ckpt +#SBATCH --partition=ckpt ## Resources #SBATCH --nodes=1 ## Walltime (4 hours) @@ -14,4 +14,5 @@ #SBATCH --chdir /gscratch/comdata/users/nathante/ml_measurement_error_public/simulations #SBATCH --output=simulation_jobs/%A_%a.out #SBATCH --error=simulation_jobs/%A_%a.err +echo "$@" "$@" -- 2.39.2