inst/appliedPAClassificationScripts/runMethods/intensity/createRun_sasaki_lab_intensity_2stage_stage2_ShScripts.R

In elray1/PACwithDDM: Data set applications and simulation study for PACwithDDM paper.

for(setting in c("lab")) {
#	for(location in c("ankle", "hip", "wrist")) {
	for(location in c("hip", "wrist")) {
#	for(location in c("ankle")) {
		for(class_var in c("y_intensity")) {
			for(fit_method in c("RFCRF", "parametricBoostCRF", "baggedFeatureSubsetGradientTreeBoostCRF")) {
#			for(fit_method in c("parametricBoostCRF")) {
#			for(fit_method in c("RFCRF")) {
				# set memory and processig time requirements for each method
				if(identical(fit_method, "RFCRF")) {
					cores_req <- "10"
					mem_req <- "12000"
					time_req <- "4:00"
					queue_req <- "short"
				} else if(identical(fit_method, "RFCRFseqbag")) {
					cores_req <- "10"
					mem_req <- "12000"
					time_req <- "4:00"
					queue_req <- "short"
				} else if(identical(fit_method, "baggedFeatureSubsetGradientTreeBoostCRF")) {
					cores_req <- "10"
					mem_req <- "20000"
					time_req <- "48:00"
					queue_req <- "long"
				} else if(identical(fit_method, "parametricBoostCRF")) {
					cores_req <- "10"
					mem_req <- "5000"
					time_req <- "48:00"
					queue_req <- "long"
				} else if(identical(fit_method, "L2RegularizedCRF")) {
					cores_req <- "10"
					mem_req <- "5000"
					time_req <- "48:00"
					queue_req <- "long"
				} else if(identical(fit_method, "gradientTreeBoostCRF")) {
					cores_req <- "10"
					mem_req <- "15000"
					time_req <- "48:00"
					queue_req <- "long"
				} else if(identical(fit_method, "normalHMM")) {
					cores_req <- "1"
					mem_req <- "8000"
					time_req <- "4:00"
					queue_req <- "short"
				}
				
				for(reduced_trans_mat_parameterization in c(FALSE)) {
					if(reduced_trans_mat_parameterization) {
						update_trans_levels <- TRUE
					} else {
						update_trans_levels <- TRUE
					}
					for(update_trans in update_trans_levels) {
						files_path <- file.path("/home", "er71a", "HMMapplication", "Sasaki", "intensity", setting, "2stage", "stage2", location, class_var, fit_method)
						setwd(files_path)
						
						basefilename <- "run_method_ShScript"
						lsfoutfilename <- "lsfOutput_"
						Routbasefilename <- "sasakiLOSOcrossval"
						if(reduced_trans_mat_parameterization) {
							basefilename <- paste0(basefilename, "ReducedTrans")
							lsfoutfilename <- paste0(lsfoutfilename, "ReducedTrans")
							Routbasefilename <- paste0(Routbasefilename, "ReducedTrans")
						} else {
							basefilename <- paste0(basefilename, "FullTrans")
							lsfoutfilename <- paste0(lsfoutfilename, "FullTrans")
							Routbasefilename <- paste0(Routbasefilename, "FullTrans")
						}
						if(!update_trans) {
							basefilename <- paste0(basefilename, "NoUpdate")
							lsfoutfilename <- paste0(lsfoutfilename, "NoUpdate")
							Routbasefilename <- paste0(Routbasefilename, "NoUpdate")
						}
						basefilename <- paste0(basefilename, "_subject")
						lsfoutfilename <- paste0(lsfoutfilename, ".out")
						Routbasefilename <- paste0(Routbasefilename, "_subject")
						
						requestCmds <- "#!/bin/bash\n"

						requestCmds <- paste0(requestCmds, "#BSUB -n ", cores_req, " # how many cores we want for our job\n")
						requestCmds <- paste0(requestCmds, "#BSUB -R span[hosts=1] # ask for all the cores on a single machine\n")
						requestCmds <- paste0(requestCmds, "#BSUB -R rusage[mem=", mem_req, "] # ask for memory\n")
						requestCmds <- paste0(requestCmds, "#BSUB -o ", lsfoutfilename, " # log LSF output to a file\n",
							"#BSUB -W ", time_req, " # run time\n",
							"#BSUB -q ", queue_req, " # which queue we want to run in\n")
						
						if(identical(setting, "freeliving")) {
							N <- 15
						} else if(identical(setting, "lab")) {
                                                        if(identical(location, "ankle")) {
                                                                N <- 34
                                                        } else {
                                                                N <- 35
                                                        }
                                                }

						
						for(subject in seq_len(N)) {
#						for(subject in c(2)) {
							filename <- paste0(files_path, "/", basefilename, subject, ".sh")
							
							cat(requestCmds, file = filename)
							cat("module load R/3.0.2\n", file = filename, append = TRUE)
							cat(paste0("R CMD BATCH --vanilla \'--args ", subject, " ", setting, " ", location, " ", class_var, " ", fit_method, " ", reduced_trans_mat_parameterization, " ", update_trans,
												 "\' /home/er71a/HMMapplication/Sasaki/intensity/sasakiLOSOcrossval_2stage_stage2.R ", Routbasefilename, subject, ".Rout"),
									file = filename, append = TRUE)
						
							bsubCmd <- paste0("bsub < ", filename)
						
							system(bsubCmd)
						}
					}
				}
			}
		}
	}
}