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s2.1_set_missing_to_simulation_data.R
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# s2.1 get missing pattern which combine 1 T1surf and psytool
# using bootstrap to get n sample
rm(list = ls())
source('/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/programm/imp_compare_utils.R')
time_op <- Sys.time()
sprintf('Start time: %s\n', time_op) %>% cat
# set parameter
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/combine_data/choose_psy_1.5.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/psytool/single/choose_1.5_pattern/'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/test'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/cog_newgroup/s1.4_Cognative_T1surf_Combine_Data.Rdata'
# # source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/cog_newgroup//s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/cog_TrueMiss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/cog_TrueMiss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/Reho_age/s1.4_zRehoAAL116_Gender_CorCombine_Data.Rdata'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/Reho_age_20miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/Reho_age_20miss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/cog_newgroup/s1.4_Cog5_ZsHarQCT1_CorCombine_Data.Rdata'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/Cog5_ZsHarQCT1_TrueMiss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/Cog5_ZsHarQCT1_TrueMiss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1_data/cog_newgroup/s1.4_CVLT_ZsHarQCT1_CorCombine_Data.Rdata'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_ZsHarQCT1_80Miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_ZsHarQCT1_80Miss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/cog_newgroup/cvlt/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_SimuY_80Miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_SimuY_80Miss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/reho/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_SimuY_80Miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_SimuY_80Miss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/reho_UnNorm/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_UnNormSimuY_TrueMiss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_UnNormSimuY_TrueMiss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/cog_newgroup/cvlt_UnNorm/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_UnNormSimuY_TrueMiss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_UnNormSimuY_TrueMiss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/reho_TCoef/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_TCoefSimuY_80Miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/ReHo_TCoefSimuY_80Miss_NoRep0.8'
# source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/cog_newgroup/cvlt_TCoef/s1.7_SimulationOutcomeData.RData'
# img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_TCoefSimuY_80Miss_NoRep0.8/img'
# save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_TCoefSimuY_80Miss_NoRep0.8'
source_path <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s1.7_simulation_y/cog_newgroup/cvlt_IntTCoef/s1.7_SimulationOutcomeData.RData'
img_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_IntTCoefSimuY_TrueMiss_NoRep0.8/img'
save_dir <- '/gpfs/lab/liangmeng/members/liyifan/R/imp_compare/s2_simulation/CVLT_IntTCoefSimuY_TrueMiss_NoRep0.8'
is_out_pattern_img <- F
boot_num <- 100
is_replace <- F # if T, sample is back up, F mean no repetition
sample_size <- 0.8 # 0~1 means sample_size * data_size, >1 means size number
pattern_num <- -1 # -1 means all pattern
add_missing_rate <- NULL # 0~1, if true rate, setting to NULL
save_dir <- file.path(save_dir, basename(source_path))
# print log
sprintf('add_missing_rate: %.3f\nsample_size: %.3f\n',
add_missing_rate, sample_size) %>% cat
# mkdir out dir
{
if (!file.exists(img_dir)){
dir.create(img_dir, recursive = T)
sprintf('Create img dir! %s\n', img_dir) %>% cat()
}
if (!file.exists(save_dir)){
dir.create(save_dir, recursive = T)
sprintf('Create save dir! %s\n', save_dir) %>% cat()
}
}
# load data
{
load_name <- load(source_path)
eval(parse(text=sprintf("data_save_list <- %s", load_name)))
miss_data_list <- data_save_list
complete_data_list <- lapply(data_save_list, function(psy){
psy[complete.cases(psy), ]
})
}
# out patten image of each scales
if (is_out_pattern_img){
for (name_i in names(miss_data_list)){
out_path = file.path(img_dir, paste(name_i, '_pattern.png', sep=''))
png(out_path, width=1200, height=1200)
md.pattern(miss_data_list[[name_i]], rotate.names = T)
dev.off()
print(name_i)
}
}
# bootstrap
{
boot_op_time <- Sys.time()
# miss_data_boot_list <- lapply(miss_data_list, get_bootstrap_data,
# sample_number=boot_num, sample_size=sample_size, is_replace=is_replace)
#
# complete_data_boot_list <- lapply(miss_data_boot_list, function(x){
# lapply(x, function(x){x[complete.cases(x),]})
# })
complete_data_boot_list <- lapply(complete_data_list, get_bootstrap_data,
sample_number=boot_num, sample_size=sample_size, is_replace=is_replace)
sprintf('bootstrap end, time used: %.4f %s\n',
Sys.time() - boot_op_time, attr(Sys.time() - boot_op_time, 'units')) %>% cat()
}
# add simulation missing pattern in complete data
{
simu_op_time <- Sys.time()
# # 2021.01.12, using total missing pattern rather than boot missing pattern
# simulation_missing_data_list <- map2(complete_data_boot_list, miss_data_list, function(c, m, pattern_num, add_missing_rate){
# return(lapply(c, function(c, m, pattern_num, add_missing_rate){
# sprintf('simulation end %s\n', Sys.time()) %>% cat()
# return(simulation_missing_pattern(c, m, pattern_num=pattern_num, add_missing_case_rate=add_missing_rate))
# }, m, pattern_num, add_missing_rate))
# }, pattern_num=pattern_num, add_missing_rate=add_missing_rate)
sprintf('Simulation Pattern...\n') %>% cat()
simulation_missing_data_list <- list()
scale_i <- 0
scale_number <- length(complete_data_boot_list)
for (scale_name in names(complete_data_boot_list)){
scale_op_time <- Sys.time()
scale_i = scale_i + 1
boot_number <- length(complete_data_boot_list[[scale_name]])
for (boot_i in 1:boot_number){
boot_op_time <- Sys.time()
simulation_missing_data_list[[scale_name]][[boot_i]] <-
simulation_missing_pattern(complete_data_boot_list[[scale_name]][[boot_i]],
miss_data_list[[scale_name]],
pattern_num=pattern_num,
add_missing_case_rate=add_missing_rate)
scale_time <- Sys.time() - scale_op_time
boot_time <- Sys.time() - boot_op_time
total_time <- Sys.time() - time_op
sprintf(' Scale: %d/%d(%s %.4f %s), Boot: %d/%d(%.4f %s), total: %.4f %s\n',
scale_i, scale_number, scale_name,
scale_time, attr(scale_time, 'units'),
boot_i, boot_number,
boot_time, attr(boot_time, 'units'),
total_time, attr(total_time, 'units')) %>% cat()
}
}
sprintf('Simulation end, time used: %.4f %s\n',
Sys.time() - simu_op_time, attr(Sys.time() - simu_op_time, 'units')) %>% cat()
}
# save data
save_list <- list(simulation_missing_data_boot_list=simulation_missing_data_list,
complete_data_boot_list=complete_data_boot_list,
total_complete_data_list=complete_data_list)
save_path <- file.path(save_dir, sprintf('simulation_boot_%d_%s.RData', boot_num,
strftime(Sys.time(),format='%Y-%m-%d-%H:%M:%S')))
save(save_list, file=save_path)
sprintf('simulation data saved!: %s\n', save_path) %>% cat()
sprintf('save end, total time used: %.4f %s\n',
Sys.time() - time_op, attr(Sys.time() - time_op, 'units')) %>% cat()