Add R history file

Author: Buch

code/postprocessing/postprocessing-behavior/.Rhistory

@@ -1,21 +1,3 @@
-source("functions/check_inclusion_criteria.R")
-source("functions/validate_against_eeg.R")
-# === user input: define subject list ===
-# slash-separated string of subject IDs to be processed in this run
-# leave empty ("") to process all available subjects
-# subjects_to_process = "390002/390003/390004/390005/390006/390007/390008/390009/390010/390011/390012/390013/390014/390015/390020/390021/390022/390023/390024/390025/390026/390027/390028/390030/390031/390032/390033/390034/390036/390037/390038/390039/390041/390042";
-subjects_to_process = "390002"
-# parse subject list
-if (subjects_to_process == "") {
-subjects_list <- NULL  # process all subjects
-cat("processing all available subjects\n")
-} else {
-subjects_list <- str_split(subjects_to_process, "/")[[1]]
-subjects_list <- subjects_list[subjects_list != ""]
-cat("processing", length(subjects_list), "specified subjects\n")
-}
-# create output directories
-create_output_dirs()
 # start logging
 log_file <- file.path(logs_dir,
 paste0("console_log_",
@@ -100,6 +82,15 @@ cat("\nsaved validation results to:", validation_file, "\n")
 } else {
 cat("\nwarning: no eeg postprocessing folders found, skipping validation\n")
 }
+# generate final summary report (needs validation results)
+summary_report <- generate_postprocessing_summary(
+behavioral_with_rt,
+inclusion_summary,
+validation_results,
+output_dir,
+processing_params,
+verbose = TRUE
+)
 # batch_behavioral_postprocessing.r - main pipeline for behavioral postprocessing
 # author: marlene buch
 # === setup ===
@@ -118,6 +109,26 @@ source("functions/apply_eeg_exclusions.R")
 source("functions/apply_rt_trimming.R")
 source("functions/check_inclusion_criteria.R")
 source("functions/validate_against_eeg.R")
+source("functions/generate_report.R")
+# batch_behavioral_postprocessing.r - main pipeline for behavioral postprocessing
+# author: marlene buch
+# === setup ===
+cat("=== BEHAVIORAL POSTPROCESSING STARTED ===\n")
+cat("session started:", as.character(Sys.time()), "\n\n")
+# clear environment
+rm(list = ls())
+# load configuration & functions
+source("config/paths.R")
+# get repo root from paths
+repo_root <- file.path(here::here(), "..", "..", "..")
+source("config/settings.R")
+source("functions/load_behavioral_data.R")
+source("functions/load_eeg_trial_info.R")
+source("functions/apply_eeg_exclusions.R")
+source("functions/apply_rt_trimming.R")
+source("functions/check_inclusion_criteria.R")
+source("functions/validate_against_eeg.R")
+source("functions/generate_reports.R")
 # === user input: define subject list ===
 # slash-separated string of subject IDs to be processed in this run
 # leave empty ("") to process all available subjects
@@ -184,7 +195,6 @@ saveRDS(inclusion_summary, inclusion_file)
 cat("saved inclusion summary to:", inclusion_file, "\n")
 # generate reports
 cat("\n=== GENERATING REPORTS ===\n")
-source("functions/generate_reports.R")
 # subject summary table
 subject_table <- generate_subject_summary_table(
 behavioral_with_rt,
@@ -245,25 +255,6 @@ source("functions/apply_eeg_exclusions.R")
 source("functions/apply_rt_trimming.R")
 source("functions/check_inclusion_criteria.R")
 source("functions/validate_against_eeg.R")
-source("functions/generate_report.R")
-# batch_behavioral_postprocessing.r - main pipeline for behavioral postprocessing
-# author: marlene buch
-# === setup ===
-cat("=== BEHAVIORAL POSTPROCESSING STARTED ===\n")
-cat("session started:", as.character(Sys.time()), "\n\n")
-# clear environment
-rm(list = ls())
-# load configuration & functions
-source("config/paths.R")
-# get repo root from paths
-repo_root <- file.path(here::here(), "..", "..", "..")
-source("config/settings.R")
-source("functions/load_behavioral_data.R")
-source("functions/load_eeg_trial_info.R")
-source("functions/apply_eeg_exclusions.R")
-source("functions/apply_rt_trimming.R")
-source("functions/check_inclusion_criteria.R")
-source("functions/validate_against_eeg.R")
 source("functions/generate_reports.R")
 # === user input: define subject list ===
 # slash-separated string of subject IDs to be processed in this run
@@ -373,6 +364,16 @@ output_dir,
 processing_params,
 verbose = TRUE
 )
+cat("\n=== SUMMARY ===\n")
+cat("total subjects processed:", n_distinct(behavioral_data$subject), "\n")
+cat("subjects included:", sum(inclusion_summary$included), "\n")
+cat("subjects excluded:", sum(!inclusion_summary$included), "\n")
+cat("\nprocessed data saved to:", output_dir, "\n")
+# stop logging
+sink()
+cat("\n=== BEHAVIORAL POSTPROCESSING COMPLETE ===\n")
+cat("session ended:", as.character(Sys.time()), "\n")
+cat("log saved to:", log_file, "\n")
 # batch_behavioral_postprocessing.r - main pipeline for behavioral postprocessing
 # author: marlene buch
 # === setup ===
@@ -395,8 +396,7 @@ source("functions/generate_reports.R")
 # === user input: define subject list ===
 # slash-separated string of subject IDs to be processed in this run
 # leave empty ("") to process all available subjects
-# subjects_to_process = "390002/390003/390004/390005/390006/390007/390008/390009/390010/390011/390012/390013/390014/390015/390020/390021/390022/390023/390024/390025/390026/390027/390028/390030/390031/390032/390033/390034/390036/390037/390038/390039/390041/390042";
-subjects_to_process = "390002"
+subjects_to_process = "390002/390003/390004/390005/390006/390007/390008/390009/390010/390011/390012/390013/390014/390015/390020/390021/390022/390023/390024/390025/390026/390027/390028/390030/390031/390032/390033/390034/390036/390037/390038/390039/390041/390042";
 # parse subject list
 if (subjects_to_process == "") {
 subjects_list <- NULL  # process all subjects