2025-12-08 18:44:00,227 - INFO - src.core.orchestrator - Initializing modules...
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - Using dynamic contract extraction mode (no static configuration file)
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - Using dynamic data semantics analysis (no static configuration file)
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - AnalysisOrchestrator initialized
2025-12-08 18:44:00,277 - INFO - api_server - Task 9d429bfb-87c6-4426-8a27-3dd6df2b0034 log file: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/analysis_20251208_184400.log
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - Starting statistical analysis process...
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:44:00,277 - INFO - src.core.orchestrator - Stage 1: Parse research protocol document, generate sub prompts
2025-12-08 18:44:00,277 - INFO - src.modules.document_processor - Starting to parse research plan document...
2025-12-08 18:44:00,400 - INFO - src.modules.document_processor - Successfully read Word document: protocol.docx
2025-12-08 18:44:00,400 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/data.csv
2025-12-08 18:44:00,404 - INFO - src.modules.data_profiler - Data analysis completed: 22 variables
2025-12-08 18:44:00,404 - INFO - src.modules.document_processor - Calling LLM to parse research plan...
2025-12-08 18:44:00,404 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:44:03,999 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:47:39,261 - INFO - src.modules.llm_client - LLM response completed, time taken: 218.9 seconds
2025-12-08 18:47:39,262 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 39107)
2025-12-08 18:47:39,263 - INFO - src.modules.document_processor - LLM response saved to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/llm_response_20251208_184739.txt
2025-12-08 18:47:39,263 - INFO - src.modules.document_processor - LLM response length: 46361 characters
2025-12-08 18:47:39,263 - INFO - src.modules.document_processor - LLM response first 500 characters: # Statistical Analysis Task: SAP 7.1 - Data Preparation and Quality Control

## Core Statistical Methods
**Verbatim from Protocol Section 7.1:**
- Multi-source data integration from: (1) Bone density screening system; (2) Health questionnaire system; (3) Regional health big data platform; (4) Primary healthcare archives
- Data linkage via unique identifier combinations (ID card, file number, name, DOB)
- Non-destructive cleaning: Read-only raw data, version-controlled scripts (R/Python)
- Unifie
2025-12-08 18:47:39,265 - INFO - src.modules.document_processor - Extracted 7 sub prompts
2025-12-08 18:47:39,266 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.1_Data Preparation and Quality Control.md (section: 7.1)
2025-12-08 18:47:39,266 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.2_Missing Data Handling.md (section: 7.2)
2025-12-08 18:47:39,267 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.3_Descriptive Statistics (Table 1).md (section: 7.3)
2025-12-08 18:47:39,267 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.4_Bivariate Exploratory Analysis.md (section: 7.4)
2025-12-08 18:47:39,267 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.5_Multivariable Modeling and Model Diagnostics.md (section: 7.5)
2025-12-08 18:47:39,268 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.7_Interaction and Effect Modification Analysis.md (section: 7.7)
2025-12-08 18:47:39,269 - INFO - src.modules.document_processor - Saved sub prompt: prompt_7.8_Sensitivity Analysis.md (section: 7.8)
2025-12-08 18:47:39,269 - INFO - src.modules.document_processor - Successfully generated 7 sub prompt files
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - Successfully generated 7 sub prompts
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - Stage 2: Process each analysis module
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - Stage 1/7: 7.1 - Data Preparation and Quality Control
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/data.csv
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:47:39,269 - INFO - src.core.orchestrator - [7.1] Extract dynamic contract...
2025-12-08 18:47:39,270 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.1 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 18:47:39,270 - INFO - src.core.orchestrator - [7.1] Dynamic contract: methods={}, recommended files=[]
2025-12-08 18:47:39,270 - INFO - src.core.orchestrator - [7.1] Generate R code...
2025-12-08 18:47:39,270 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.1_Data Preparation and Quality Control.md...
2025-12-08 18:47:39,270 - INFO - src.modules.data_profiler - Using cached data profile: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/data.csv
2025-12-08 18:47:39,275 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/data.csv)
- Sample size: 1265 rows
- Number of variables: 22 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: float64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: float64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 18:47:39,276 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 18:47:39,283 - WARNING - src.modules.code_generator - [7.1] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases']
2025-12-08 18:47:39,283 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:47:41,538 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:49:10,340 - INFO - src.modules.llm_client - LLM response completed, time taken: 91.1 seconds
2025-12-08 18:49:10,341 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 11831)
2025-12-08 18:49:10,342 - INFO - src.modules.code_generator - Code generation successful (attempt 1/3)
2025-12-08 18:49:10,343 - INFO - src.core.orchestrator - [7.1] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.1_Data Preparation and Quality Control.R
2025-12-08 18:49:10,343 - INFO - src.core.orchestrator - [7.1] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/data.csv
2025-12-08 18:49:10,343 - INFO - src.core.orchestrator - [7.1] Execute R code...
2025-12-08 18:49:10,344 - INFO - src.modules.code_executor - Executing R code for Data Preparation and Quality Control (section 7.1)...
2025-12-08 18:49:10,344 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1
2025-12-08 18:49:11,708 - INFO - src.modules.code_executor - Data Preparation and Quality Control (section 7.1) execution successful, generated 12 files
2025-12-08 18:49:11,709 - INFO - src.modules.decision_manager - Global decisions updated: 7.1
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - [7.1] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1/main_output.csv
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - [7.1] Execution successful
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - Stage 2/7: 7.2 - Missing Data Handling
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1/main_output.csv
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:49:11,709 - INFO - src.core.orchestrator - [7.2] Extract dynamic contract...
2025-12-08 18:49:11,709 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.2 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 18:49:11,710 - INFO - src.core.orchestrator - [7.2] Dynamic contract: methods={}, recommended files=[]
2025-12-08 18:49:11,710 - INFO - src.core.orchestrator - [7.2] Generate R code...
2025-12-08 18:49:11,710 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.2_Missing Data Handling.md...
2025-12-08 18:49:11,710 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1/main_output.csv
2025-12-08 18:49:11,713 - INFO - src.modules.data_profiler - Data analysis completed: 24 variables
2025-12-08 18:49:11,714 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 24 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 18:49:11,714 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 18:49:11,718 - WARNING - src.modules.code_generator - [7.2] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 18:49:11,718 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:49:13,123 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:50:46,752 - INFO - src.modules.llm_client - LLM response completed, time taken: 95.0 seconds
2025-12-08 18:50:46,753 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 12193)
2025-12-08 18:50:46,756 - INFO - src.core.orchestrator - [7.2] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.2_Missing Data Handling.R
2025-12-08 18:50:46,756 - INFO - src.core.orchestrator - [7.2] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.1/main_output.csv
2025-12-08 18:50:46,756 - INFO - src.core.orchestrator - [7.2] Execute R code...
2025-12-08 18:50:46,756 - INFO - src.modules.code_executor - Executing R code for Missing Data Handling (section 7.2)...
2025-12-08 18:50:46,757 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2
2025-12-08 18:51:01,682 - INFO - src.modules.code_executor - Missing Data Handling (section 7.2) execution successful, generated 11 files
2025-12-08 18:51:01,683 - INFO - src.modules.decision_manager - Global decisions updated: 7.2
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - [7.2] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2/main_output.csv
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - [7.2] Execution successful
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - Stage 3/7: 7.3 - Descriptive Statistics (Table 1)
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2/main_output.csv
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:51:01,683 - INFO - src.core.orchestrator - [7.3] Extract dynamic contract...
2025-12-08 18:51:01,684 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.3 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 18:51:01,684 - INFO - src.core.orchestrator - [7.3] Dynamic contract: methods={}, recommended files=[]
2025-12-08 18:51:01,684 - INFO - src.core.orchestrator - [7.3] Generate R code...
2025-12-08 18:51:01,684 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.3_Descriptive Statistics (Table 1).md...
2025-12-08 18:51:01,684 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2/main_output.csv
2025-12-08 18:51:01,688 - INFO - src.modules.data_profiler - Data analysis completed: 24 variables
2025-12-08 18:51:01,689 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 24 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 18:51:01,689 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 18:51:01,693 - WARNING - src.modules.code_generator - [7.3] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 18:51:01,693 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:51:04,484 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:52:28,325 - INFO - src.modules.llm_client - LLM response completed, time taken: 86.6 seconds
2025-12-08 18:52:28,325 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 12207)
2025-12-08 18:52:28,327 - INFO - src.core.orchestrator - [7.3] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.3_Descriptive Statistics (Table 1).R
2025-12-08 18:52:28,327 - INFO - src.core.orchestrator - [7.3] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.2/main_output.csv
2025-12-08 18:52:28,327 - INFO - src.core.orchestrator - [7.3] Execute R code...
2025-12-08 18:52:28,327 - INFO - src.modules.code_executor - Executing R code for Descriptive Statistics (Table 1) (section 7.3)...
2025-12-08 18:52:28,328 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3
2025-12-08 18:52:29,268 - WARNING - src.modules.code_executor - Descriptive Statistics (Table 1) execution failed (attempt 1/10): Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'survey'

The following object is masked from ‘package:graphics’:

    dotchart


Loading package: 'dplyr'

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Loading package: 'tidyr'

The following objects are masked from ‘package:Matrix’:

    expand, pack, unpack

Warning messages:
package 'ggplot2' was built under R version 4.5.2 
There are more than 50 warnings (use warnings() to see the first 50)
Warning messages:
1: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
2: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
3: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
4: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
5: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
6: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
Error: unexpected symbol in
"cat(sprintf("Categorical variables processed: %d\n", length(unique(categorical_summary$Variable[categorical_summary$Variable != ""])))
cat"
Execution halted

2025-12-08 18:52:29,268 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 1)
2025-12-08 18:52:29,271 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 18:52:29,271 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=False, has_llm_function=True)
2025-12-08 18:52:29,271 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 18:52:29,271 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 18:52:29,271 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 32789 characters
2025-12-08 18:52:29,271 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 18:52:29,271 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:52:32,873 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:53:54,409 - INFO - src.modules.llm_client - LLM response completed, time taken: 85.1 seconds
2025-12-08 18:53:54,409 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 16966)
2025-12-08 18:53:54,409 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 18:53:54,409 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'surv...
2025-12-08 18:53:54,409 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 18:53:54,411 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 18:53:55,392 - WARNING - src.modules.code_executor - Descriptive Statistics (Table 1) execution failed (attempt 2/10): Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'survey'

The following object is masked from ‘package:graphics’:

    dotchart


Loading package: 'dplyr'

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Loading package: 'tidyr'

The following objects are masked from ‘package:Matrix’:

    expand, pack, unpack

Warning messages:
package 'ggplot2' was built under R version 4.5.2 
There are more than 50 warnings (use warnings() to see the first 50)
Warning messages:
1: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
2: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
3: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
4: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
5: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
6: In tapply(X = nPSU, INDEX = as.numeric(strata), FUN = head, 1) :
  NAs introduced by coercion
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 18:53:55,393 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 2)
2025-12-08 18:53:55,395 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 18:53:55,395 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=False, has_llm_function=True)
2025-12-08 18:53:55,395 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 18:53:55,395 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 18:53:55,395 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 32337 characters
2025-12-08 18:53:55,395 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 18:53:55,395 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:53:59,874 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:55:19,815 - INFO - src.modules.llm_client - LLM response completed, time taken: 84.4 seconds
2025-12-08 18:55:19,815 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 16874)
2025-12-08 18:55:19,816 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 18:55:19,816 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'surv...
2025-12-08 18:55:19,816 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 18:55:19,817 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 18:55:20,897 - INFO - src.modules.code_executor - Descriptive Statistics (Table 1) (section 7.3) execution successful, generated 6 files
2025-12-08 18:55:20,898 - INFO - src.modules.decision_manager - Global decisions updated: 7.3
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - [7.3] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3/main_output.csv
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - [7.3] Execution successful
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - Stage 4/7: 7.4 - Bivariate Exploratory Analysis
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3/main_output.csv
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - [7.4] Extract dynamic contract...
2025-12-08 18:55:20,898 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.4 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - [7.4] Dynamic contract: methods={}, recommended files=[]
2025-12-08 18:55:20,898 - INFO - src.core.orchestrator - [7.4] Generate R code...
2025-12-08 18:55:20,898 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.4_Bivariate Exploratory Analysis.md...
2025-12-08 18:55:20,898 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3/main_output.csv
2025-12-08 18:55:20,901 - INFO - src.modules.data_profiler - Data analysis completed: 26 variables
2025-12-08 18:55:20,903 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 26 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]
  - Exercise_Group: object, 2 levels → ['Below Recommended', 'At/Above Recommended']
  - PSU_ID: int64, 5 levels → [np.int64(1), np.int64(2), np.int64(3), np.int64(4), np.int64(5)]

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 18:55:20,903 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 18:55:20,907 - WARNING - src.modules.code_generator - [7.4] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 18:55:20,907 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:55:24,672 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:57:03,999 - INFO - src.modules.llm_client - LLM response completed, time taken: 103.1 seconds
2025-12-08 18:57:03,999 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 16094)
2025-12-08 18:57:04,002 - INFO - src.core.orchestrator - [7.4] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.4_Bivariate Exploratory Analysis.R
2025-12-08 18:57:04,002 - INFO - src.core.orchestrator - [7.4] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.3/main_output.csv
2025-12-08 18:57:04,002 - INFO - src.core.orchestrator - [7.4] Execute R code...
2025-12-08 18:57:04,003 - INFO - src.modules.code_executor - Executing R code for Bivariate Exploratory Analysis (section 7.4)...
2025-12-08 18:57:04,003 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4
2025-12-08 18:57:06,153 - INFO - src.modules.code_executor - Bivariate Exploratory Analysis (section 7.4) execution successful, generated 10 files
2025-12-08 18:57:06,154 - INFO - src.modules.decision_manager - Global decisions updated: 7.4
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - [7.4] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4/main_output.csv
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - [7.4] Execution successful
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - Stage 5/7: 7.5 - Multivariable Modeling and Model Diagnostics
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4/main_output.csv
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - ============================================================
2025-12-08 18:57:06,154 - INFO - src.core.orchestrator - [7.5] Extract dynamic contract...
2025-12-08 18:57:06,155 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.5 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 18:57:06,155 - INFO - src.core.orchestrator - [7.5] Dynamic contract: methods={}, recommended files=[]
2025-12-08 18:57:06,155 - INFO - src.core.orchestrator - [7.5] Generate R code...
2025-12-08 18:57:06,155 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.5_Multivariable Modeling and Model Diagnostics.md...
2025-12-08 18:57:06,155 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4/main_output.csv
2025-12-08 18:57:06,160 - INFO - src.modules.data_profiler - Data analysis completed: 26 variables
2025-12-08 18:57:06,162 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 26 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]
  - Exercise_Group: object, 2 levels → ['Below Recommended', 'At/Above Recommended']
  - PSU_ID: int64, 5 levels → [np.int64(1), np.int64(2), np.int64(3), np.int64(4), np.int64(5)]

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 18:57:06,162 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 18:57:06,166 - WARNING - src.modules.code_generator - [7.5] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 18:57:06,166 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:57:09,060 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 18:59:51,382 - INFO - src.modules.llm_client - LLM response completed, time taken: 165.2 seconds
2025-12-08 18:59:51,382 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 20886)
2025-12-08 18:59:51,384 - INFO - src.modules.code_generator - Code generation successful (attempt 1/3)
2025-12-08 18:59:51,386 - INFO - src.core.orchestrator - [7.5] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.5_Multivariable Modeling and Model Diagnostics.R
2025-12-08 18:59:51,386 - INFO - src.core.orchestrator - [7.5] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.4/main_output.csv
2025-12-08 18:59:51,386 - INFO - src.core.orchestrator - [7.5] Execute R code...
2025-12-08 18:59:51,387 - INFO - src.modules.code_executor - Executing R code for Multivariable Modeling and Model Diagnostics (section 7.5)...
2025-12-08 18:59:51,388 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5
2025-12-08 18:59:52,316 - WARNING - src.modules.code_executor - Multivariable Modeling and Model Diagnostics execution failed (attempt 1/10): Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 18:59:52,316 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 1)
2025-12-08 18:59:52,320 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 18:59:52,320 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=False, has_llm_function=True)
2025-12-08 18:59:52,320 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 18:59:52,321 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 18:59:52,321 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 56700 characters
2025-12-08 18:59:52,321 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 18:59:52,321 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 18:59:55,233 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:01:58,108 - WARNING - src.modules.llm_client - LLM call failed (attempt 1/10): JSONDecodeError - API response parsing error (usually temporary network problem, retrying automatically)
2025-12-08 19:01:58,109 - INFO - src.modules.llm_client - Waiting 1 seconds to retry...
2025-12-08 19:01:59,114 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=2/10)...
2025-12-08 19:02:01,295 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:04:46,371 - INFO - src.modules.llm_client - LLM response completed, time taken: 167.3 seconds
2025-12-08 19:04:46,371 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=2, tokens: 31541)
2025-12-08 19:04:46,372 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:04:46,372 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(depars...
2025-12-08 19:04:46,372 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:04:46,373 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:04:47,325 - WARNING - src.modules.code_executor - Multivariable Modeling and Model Diagnostics execution failed (attempt 2/10): Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 19:04:47,326 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 2)
2025-12-08 19:04:47,328 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 19:04:47,329 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=False, has_llm_function=True)
2025-12-08 19:04:47,329 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 19:04:47,329 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 19:04:47,329 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 56759 characters
2025-12-08 19:04:47,329 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 19:04:47,329 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:04:49,773 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:07:35,957 - INFO - src.modules.llm_client - LLM response completed, time taken: 168.6 seconds
2025-12-08 19:07:35,958 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 31772)
2025-12-08 19:07:35,958 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:07:35,958 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(depars...
2025-12-08 19:07:35,958 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:07:35,959 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:07:36,900 - WARNING - src.modules.code_executor - Multivariable Modeling and Model Diagnostics execution failed (attempt 3/10): Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 19:07:36,901 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 3)
2025-12-08 19:07:36,904 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 19:07:36,904 - INFO - src.modules.code_executor - Enabling enhanced LLM repair strategy (including data snapshot)
2025-12-08 19:07:36,904 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=True, has_llm_function=True)
2025-12-08 19:07:36,904 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 19:07:36,904 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 19:07:36,904 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 57289 characters
2025-12-08 19:07:36,904 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 19:07:36,904 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:07:40,044 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:10:28,891 - INFO - src.modules.llm_client - LLM response completed, time taken: 172.0 seconds
2025-12-08 19:10:28,891 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 32152)
2025-12-08 19:10:28,891 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:10:28,891 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(depars...
2025-12-08 19:10:28,891 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:10:28,892 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:10:29,829 - WARNING - src.modules.code_executor - Multivariable Modeling and Model Diagnostics execution failed (attempt 4/10): Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 19:10:29,829 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 4)
2025-12-08 19:10:29,832 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 19:10:29,832 - INFO - src.modules.code_executor - Enabling enhanced LLM repair strategy (including data snapshot)
2025-12-08 19:10:29,832 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=True, has_llm_function=True)
2025-12-08 19:10:29,832 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 19:10:29,832 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 19:10:29,832 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 57969 characters
2025-12-08 19:10:29,832 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 19:10:29,832 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:10:32,478 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:13:22,077 - INFO - src.modules.llm_client - LLM response completed, time taken: 172.2 seconds
2025-12-08 19:13:22,078 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 32526)
2025-12-08 19:13:22,078 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:13:22,078 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(depars...
2025-12-08 19:13:22,078 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:13:22,079 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:13:23,009 - WARNING - src.modules.code_executor - Multivariable Modeling and Model Diagnostics execution failed (attempt 5/10): Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(deparse.level, ...): number of columns of arguments do not match
Calls: rbind -> rbind
Execution halted

2025-12-08 19:13:23,009 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 5)
2025-12-08 19:13:23,012 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 19:13:23,012 - INFO - src.modules.code_executor - Enabling enhanced LLM repair strategy (including data snapshot)
2025-12-08 19:13:23,012 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=True, has_llm_function=True)
2025-12-08 19:13:23,012 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 19:13:23,012 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 19:13:23,012 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 58389 characters
2025-12-08 19:13:23,012 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 19:13:23,012 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:13:25,148 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:16:09,741 - INFO - src.modules.llm_client - LLM response completed, time taken: 166.7 seconds
2025-12-08 19:16:09,741 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 32126)
2025-12-08 19:16:09,742 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:16:09,742 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Error in rbind(depars...
2025-12-08 19:16:09,742 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:16:09,743 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:16:11,408 - INFO - src.modules.code_executor - Multivariable Modeling and Model Diagnostics (section 7.5) execution successful, generated 16 files
2025-12-08 19:16:11,409 - INFO - src.modules.decision_manager - Global decisions updated: 7.5
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - [7.5] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5/main_output.csv
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - [7.5] Execution successful
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - Stage 6/7: 7.7 - Interaction and Effect Modification Analysis
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5/main_output.csv
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:16:11,409 - INFO - src.core.orchestrator - [7.7] Extract dynamic contract...
2025-12-08 19:16:11,410 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.7 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 19:16:11,410 - INFO - src.core.orchestrator - [7.7] Dynamic contract: methods={}, recommended files=[]
2025-12-08 19:16:11,410 - INFO - src.core.orchestrator - [7.7] Generate R code...
2025-12-08 19:16:11,410 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.7_Interaction and Effect Modification Analysis.md...
2025-12-08 19:16:11,410 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5/main_output.csv
2025-12-08 19:16:11,413 - INFO - src.modules.data_profiler - Data analysis completed: 27 variables
2025-12-08 19:16:11,415 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 27 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]
  - Exercise_Group: object, 2 levels → ['Below Recommended', 'At/Above Recommended']
  - PSU_ID: int64, 5 levels → [np.int64(1), np.int64(2), np.int64(3), np.int64(4), np.int64(5)]
  - Osteoporosis_Binary: int64, 2 levels → [np.int64(1), np.int64(0)]

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 19:16:11,416 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 19:16:11,420 - WARNING - src.modules.code_generator - [7.7] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 19:16:11,420 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:16:12,590 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:17:55,147 - INFO - src.modules.llm_client - LLM response completed, time taken: 103.7 seconds
2025-12-08 19:17:55,147 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 15037)
2025-12-08 19:17:55,149 - INFO - src.core.orchestrator - [7.7] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.7_Interaction and Effect Modification Analysis.R
2025-12-08 19:17:55,149 - INFO - src.core.orchestrator - [7.7] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.5/main_output.csv
2025-12-08 19:17:55,149 - INFO - src.core.orchestrator - [7.7] Execute R code...
2025-12-08 19:17:55,150 - INFO - src.modules.code_executor - Executing R code for Interaction and Effect Modification Analysis (section 7.7)...
2025-12-08 19:17:55,150 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7
2025-12-08 19:17:56,444 - INFO - src.modules.code_executor - Interaction and Effect Modification Analysis (section 7.7) execution successful, generated 6 files
2025-12-08 19:17:56,445 - INFO - src.modules.decision_manager - Global decisions updated: 7.7
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - [7.7] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7/main_output.csv
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - [7.7] Execution successful
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - 
============================================================
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - Stage 7/7: 7.8 - Sensitivity Analysis
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - Current data path: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7/main_output.csv
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - [7.8] Extract dynamic contract...
2025-12-08 19:17:56,445 - INFO - src.modules.contract_extractor - Extract method contracts from sub prompt: 7.8 - Required methods=0, Alternative method groups=0, Recommended methods=0, Files=0
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - [7.8] Dynamic contract: methods={}, recommended files=[]
2025-12-08 19:17:56,445 - INFO - src.core.orchestrator - [7.8] Generate R code...
2025-12-08 19:17:56,445 - INFO - src.modules.code_generator - Generating R code for /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_temp/prompt_7.8_Sensitivity Analysis.md...
2025-12-08 19:17:56,445 - INFO - src.modules.data_profiler - Reading data file for analysis (first 100 rows): /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7/main_output.csv
2025-12-08 19:17:56,448 - INFO - src.modules.data_profiler - Data analysis completed: 28 variables
2025-12-08 19:17:56,450 - INFO - src.modules.code_generator - Current stage data snapshot:
Current stage data snapshot (/Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7/main_output.csv)
- Sample size: 1265 rows
- Number of variables: 28 columns

Available variables (only use these):
  - Gender: object, 2 levels → ['Female', 'Male']
  - Age: int64, continuous variable
  - BMI: float64, continuous variable
  - Self_Rated_Health: object, 2 levels → ['Satisfied', 'Basically_Satisfied']
  - Self_Care_Ability: object, 1 levels → ['Independent']
  - Exercise_Frequency: object, 2 levels → ['No_Exercise', 'Daily']
  - Dietary_Habits: object, 2 levels → ['Balanced', 'Mainly_Vegetarian']
  - Smoking_Status: object, 2 levels → ['Smoker', 'Non_Smoker']
  - Alcohol_Frequency: object, 3 levels → ['Never', 'Frequent', 'Daily']
  - Physical_Function: object, 1 levels → ['Normal']
  - Hemoglobin: int64, continuous variable
  - Fasting_Glucose: float64, continuous variable
  - Total_Bilirubin: float64, continuous variable
  - Serum_Creatinine: int64, continuous variable
  - Blood_Urea_Nitrogen: float64, continuous variable
  - Total_Cholesterol: float64, continuous variable
  - Triglycerides: float64, continuous variable
  - Cerebrovascular_Disease: object, 1 levels → ['Other']
  - Other_Neurological_Diseases: float64, 0 levels → []
  - Bone_Mineral_Density: float64, continuous variable
  - Osteoporosis_Status: object, 3 levels → ['Osteoporosis', 'Normal', 'Low_Bone_Mass']
  - Geographic_Region: object, 3 levels → ['Pingyi', 'Boxing', 'West_Coast']
  - study_id: object, 50 levels → ['ID_0001', 'ID_0002', 'ID_0003', 'ID_0004', 'ID_0005']
  - survey_weight: int64, 1 levels → [np.int64(1)]
  - Exercise_Group: object, 2 levels → ['Below Recommended', 'At/Above Recommended']
  - PSU_ID: int64, 5 levels → [np.int64(1), np.int64(2), np.int64(3), np.int64(4), np.int64(5)]
  - Osteoporosis_Binary: int64, 2 levels → [np.int64(1), np.int64(0)]
  - Age_Group: object, 3 levels → ['65-74', '75-84', '≥85']

Validation tips:
- The number of levels of factor variables may be different from expectations
- Do not assume that variables are always binary or have specific number of levels
- Use friendly data processing rather than strict stop() validation
2025-12-08 19:17:56,450 - INFO - src.modules.code_generator - Preflight check: passed, issues=[]
2025-12-08 19:17:56,454 - WARNING - src.modules.code_generator - [7.8] Detected sparse variables: ['Self_Rated_Health', 'Self_Care_Ability', 'Dietary_Habits', 'Physical_Function', 'Cerebrovascular_Disease', 'Other_Neurological_Diseases', 'study_id']
2025-12-08 19:17:56,454 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:17:58,065 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:20:17,983 - INFO - src.modules.llm_client - LLM response completed, time taken: 141.5 seconds
2025-12-08 19:20:17,983 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 18793)
2025-12-08 19:20:17,984 - INFO - src.core.orchestrator - [7.8] R code saved: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/02_r_scripts/7.8_Sensitivity Analysis.R
2025-12-08 19:20:17,984 - INFO - src.core.orchestrator - [7.8] R will read data: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.7/main_output.csv
2025-12-08 19:20:17,984 - INFO - src.core.orchestrator - [7.8] Execute R code...
2025-12-08 19:20:17,984 - INFO - src.modules.code_executor - Executing R code for Sensitivity Analysis (section 7.8)...
2025-12-08 19:20:17,985 - INFO - src.modules.code_executor - Stage execution environment prepared: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.8
2025-12-08 19:20:19,150 - WARNING - src.modules.code_executor - Sensitivity Analysis execution failed (attempt 1/10): Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'survey'

The following object is masked from ‘package:graphics’:

    dotchart


Loading package: 'dplyr'

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Loading package: 'tidyr'

The following objects are masked from ‘package:Matrix’:

    expand, pack, unpack


Loading package: 'mice'

The following object is masked from ‘package:stats’:

    filter

The following objects are masked from ‘package:base’:

    cbind, rbind


Loading package: 'EValue'

The following object is masked from ‘package:survey’:

    HR

Warning messages:
package 'ggplot2' was built under R version 4.5.2 
Warning messages:
In sqrt(pr_lower * (pr_lower - 1)) : NaNs produced
Error in plot.window(xlim, ylim, log = log, ...): 'ylim' values must be finite
Calls: barplot -> barplot.default -> plot.window
Execution halted

2025-12-08 19:20:19,151 - INFO - src.modules.code_executor - Attempting to fix R code error... (attempt 1)
2025-12-08 19:20:19,154 - INFO - src.modules.code_executor - Current data snapshot obtained for error repair
2025-12-08 19:20:19,154 - INFO - src.modules.code_executor - Calling attempt_fix (force_llm=False, has_llm_function=True)
2025-12-08 19:20:19,155 - INFO - src.modules.error_fix_manager - Using LLM repair
2025-12-08 19:20:19,155 - INFO - src.modules.error_fix_manager - Building fix prompt...
2025-12-08 19:20:19,155 - INFO - src.modules.error_fix_manager - Fix prompt built, length: 47656 characters
2025-12-08 19:20:19,155 - INFO - src.modules.error_fix_manager - Calling LLM fix function...
2025-12-08 19:20:19,155 - INFO - src.modules.llm_client - Starting LLM call (model=anthropic/claude-sonnet-4, attempt=1/10)...
2025-12-08 19:20:21,784 - INFO - httpx - HTTP Request: POST https://openrouter.ai/api/v1/chat/completions "HTTP/1.1 200 OK"
2025-12-08 19:22:40,812 - INFO - src.modules.llm_client - LLM response completed, time taken: 141.7 seconds
2025-12-08 19:22:40,812 - INFO - src.modules.llm_client - LLM call successful (model=anthropic/claude-sonnet-4, attempt=1, tokens: 26387)
2025-12-08 19:22:40,813 - INFO - src.modules.code_executor - attempt_fix returned: success=True, method=llm_fix
2025-12-08 19:22:40,813 - INFO - src.modules.error_fix_manager - Repair successful: llm_fix - Loading required package: sysfonts
Loading required package: showtextdb

Loading package: 'surv...
2025-12-08 19:22:40,813 - INFO - src.modules.code_executor - Error repair successful, method: llm_fix
2025-12-08 19:22:40,814 - INFO - src.modules.code_executor - R code corrected and file updated
2025-12-08 19:22:42,152 - INFO - src.modules.code_executor - Sensitivity Analysis (section 7.8) execution successful, generated 14 files
2025-12-08 19:22:42,153 - INFO - src.modules.decision_manager - Global decisions updated: 7.8
2025-12-08 19:22:42,153 - INFO - src.core.orchestrator - [7.8] Update data path to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results/7.8/main_output.csv
2025-12-08 19:22:42,153 - INFO - src.core.orchestrator - [7.8] Execution successful
2025-12-08 19:22:42,153 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Analysis execution completed
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Total modules: 7
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Successful modules: 7
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Failed modules: 0
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Duration: 2321.88 seconds
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:22:42,154 - INFO - api_server - Task 9d429bfb-87c6-4426-8a27-3dd6df2b0034 starting post-processing in main thread...
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Starting post-processing: cleanup and report generation
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:22:42,154 - INFO - src.core.orchestrator - Running data_cleaner as subprocess: /usr/local/bin/python3 /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/src/modules/data_cleaner.py /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c --verbose
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] returncode=0
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] ============================================================
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Data cleanup completed 
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] ============================================================
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Moved sensitive files: 9 files
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Kept safe files: 63 files
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Skipped files: 0 files
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Failed files: 0 files
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Moved to /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_private:
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.1/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.1/outlier_report.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.2/imputed_datasets.rds
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.2/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.3/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.4/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.5/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.7/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner]   - 7.8/main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] ============================================================
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Data cleanup completed
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,377 - INFO - ============================================================
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,377 - INFO - Starting data cleanup process...
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,377 - INFO - Results directory: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,377 - INFO - Private directory: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_private
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,377 - INFO - ============================================================
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO - Found 9 stage directories to process
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO - 
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 1/9: 7.0
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Found 0 files in 7.0
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Stage 7.0 has no files, skipping
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO - 
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 2/9: 7.1
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Found 12 files in 7.1
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Processing file 1/12: plot_categorical_distribution.png
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Safe file: plot_categorical_distribution.png (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Processing file 2/12: plot_outliers_continuous.png
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Safe file: plot_outliers_continuous.png (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,378 - INFO -   Processing file 3/12: table_data_dimensions.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,379 - INFO -   Safe file: table_data_dimensions.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,379 - INFO -   Processing file 4/12: main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,379 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,379 - INFO -     Moved
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,379 - INFO -   Processing file 5/12: table_variable_summary.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,380 - INFO -   Safe file: table_variable_summary.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,380 - INFO -   Processing file 6/12: table_range_violations.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,380 - INFO -   Safe file: table_range_violations.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,380 - INFO -   Processing file 7/12: table_duplicate_records.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,381 - INFO -   Safe file: table_duplicate_records.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,381 - INFO -   Processing file 8/12: data_dictionary.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,381 - INFO -   Safe file: data_dictionary.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,381 - INFO -   Processing file 9/12: outlier_report.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Sensitive file: outlier_report.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -     Moved
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Processing file 10/12: missing_pattern.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Safe file: missing_pattern.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Processing file 11/12: analysis_summary.json
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Processing file 12/12: plot_missing_pattern.png
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Safe file: plot_missing_pattern.png (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Completed processing stage 7.1
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO - 
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 3/9: 7.2
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Found 9 files in 7.2
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Processing file 1/9: table_cca_comparison.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Safe file: table_cca_comparison.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Processing file 2/9: imputed_datasets.rds
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,382 - INFO -   Sensitive file: imputed_datasets.rds
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -     Moved
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Processing file 3/9: main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -     Moved
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Processing file 4/9: plot_trace_convergence.png
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Safe file: plot_trace_convergence.png (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Processing file 5/9: table_convergence_check.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Safe file: table_convergence_check.csv (retained)
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,383 - INFO -   Processing file 6/9: table_imputation_methods.csv
2025-12-08 19:22:42,418 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Safe file: table_imputation_methods.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Processing file 7/9: table_missing_summary.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Safe file: table_missing_summary.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Processing file 8/9: analysis_summary.json
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Processing file 9/9: plot_missing_pattern.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Safe file: plot_missing_pattern.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Completed processing stage 7.2
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 4/9: 7.3
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Found 6 files in 7.3
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,384 - INFO -   Processing file 1/6: table1_baseline_characteristics.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: table1_baseline_characteristics.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 2/6: plot_smd_loveplot.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: plot_smd_loveplot.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 3/6: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -     Moved
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 4/6: table1_smd_summary.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: table1_smd_summary.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 5/6: plot_baseline_distributions.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: plot_baseline_distributions.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 6/6: analysis_summary.json
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Completed processing stage 7.3
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 5/9: 7.4
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Found 10 files in 7.4
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Processing file 1/10: table_bivariate_exposure_covariates.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,385 - INFO -   Safe file: table_bivariate_exposure_covariates.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 2/10: table_correlation_continuous.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Safe file: table_correlation_continuous.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 3/10: plot_correlation_matrix.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Safe file: plot_correlation_matrix.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 4/10: plot_bmd_vs_glucose_loess.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Safe file: plot_bmd_vs_glucose_loess.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 5/10: plot_bivariate_exercise_osteoporosis.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Safe file: plot_bivariate_exercise_osteoporosis.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 6/10: table_bivariate_exposure_outcome.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Safe file: table_bivariate_exposure_outcome.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 7/10: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -     Moved
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,386 - INFO -   Processing file 8/10: table_bivariate_outcome_covariates.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Safe file: table_bivariate_outcome_covariates.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Processing file 9/10: analysis_summary.json
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Processing file 10/10: plot_bivariate_exercise_bmd.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Safe file: plot_bivariate_exercise_bmd.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Completed processing stage 7.4
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 6/9: 7.5
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Found 16 files in 7.5
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Processing file 1/16: table_multivariate_linear.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Safe file: table_multivariate_linear.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,387 - INFO -   Processing file 2/16: table_diagnostics_linear.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Safe file: table_diagnostics_linear.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Processing file 3/16: table_diagnostics_poisson.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Safe file: table_diagnostics_poisson.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Processing file 4/16: plot_influential_points.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Safe file: plot_influential_points.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Processing file 5/16: table_nonlinearity_tests.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Safe file: table_nonlinearity_tests.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Processing file 6/16: plot_forest_osteoporosis.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Safe file: plot_forest_osteoporosis.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,388 - INFO -   Processing file 7/16: table_vif_multicollinearity.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Safe file: table_vif_multicollinearity.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Processing file 8/16: table_bivariate_osteoporosis.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Safe file: table_bivariate_osteoporosis.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Processing file 9/16: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -     Moved
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,389 - INFO -   Processing file 10/16: table_bivariate_bmd.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: table_bivariate_bmd.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 11/16: plot_diagnostics_linear.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: plot_diagnostics_linear.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 12/16: analysis_summary.json
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 13/16: plot_diagnostics_poisson.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: plot_diagnostics_poisson.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 14/16: table_influential_points_summary.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: table_influential_points_summary.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 15/16: table_multivariate_poisson.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: table_multivariate_poisson.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 16/16: plot_forest_bmd.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Safe file: plot_forest_bmd.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Completed processing stage 7.5
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 7/9: 7.6
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Found 0 files in 7.6
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Stage 7.6 has no files, skipping
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 8/9: 7.7
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Found 5 files in 7.7
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,390 - INFO -   Processing file 1/5: table_stratified_effects.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,391 - INFO -   Safe file: table_stratified_effects.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,391 - INFO -   Processing file 2/5: table_interaction_tests.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,391 - INFO -   Safe file: table_interaction_tests.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,391 - INFO -   Processing file 3/5: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,391 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -     Moved
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 4/5: plot_interaction_heatmap.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: plot_interaction_heatmap.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 5/5: analysis_summary.json
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Completed processing stage 7.7
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO - 
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] Processing stage 9/9: 7.8
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Found 14 files in 7.8
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 1/14: table_extreme_values.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: table_extreme_values.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 2/14: plot_extreme_values_impact.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: plot_extreme_values_impact.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 3/14: table_variable_coding.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: table_variable_coding.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 4/14: table_evalue.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Safe file: table_evalue.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,392 - INFO -   Processing file 5/14: table_mnar_sensitivity.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Safe file: table_mnar_sensitivity.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Processing file 6/14: table_cca_comparison.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Safe file: table_cca_comparison.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Processing file 7/14: table_alternative_adjustment.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Safe file: table_alternative_adjustment.csv (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Processing file 8/14: plot_evalue_interpretation.png
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Safe file: plot_evalue_interpretation.png (retained)
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Processing file 9/14: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Sensitive file: main_output.csv
2025-12-08 19:22:42,419 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -     Moved
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,393 - INFO -   Processing file 10/14: table_log_transformation.csv
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Safe file: table_log_transformation.csv (retained)
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Processing file 11/14: table_or_vs_pr.csv
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Safe file: table_or_vs_pr.csv (retained)
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Processing file 12/14: analysis_summary.json
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Safe file: analysis_summary.json (retained)
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Processing file 13/14: plot_mnar_sensitivity.png
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Safe file: plot_mnar_sensitivity.png (retained)
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Processing file 14/14: plot_or_vs_pr_comparison.png
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Safe file: plot_or_vs_pr_comparison.png (retained)
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO -   Completed processing stage 7.8
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Writing cleanup record...
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Preparing to write cleanup record to: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_private/cleanup_record.json
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Writing cleanup record (moved: 9, kept: 63, failed: 0)...
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Cleanup record saved successfully: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/_private/cleanup_record.json
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Cleanup record written successfully
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Printing cleanup summary...
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Cleanup summary printed
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - [data_cleaner] 2025-12-08 19:22:42,394 - INFO - Data cleanup process completed, returning results
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - Data cleanup completed: DataCleaner subprocess finished successfully
2025-12-08 19:22:42,420 - INFO - src.core.orchestrator - Running report_generator as subprocess: /usr/local/bin/python3 /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/src/modules/report_generator.py --protocol /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/protocol.docx --output-dir /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results --config /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/config.json
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] returncode=0
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
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2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Statistical Analysis Report Generator
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] ============================================================
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Research protocol: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/01_uploads/protocol.docx
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Output directory: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/03_results
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Configuration file: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/config.json
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] ============================================================
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating cover and summary...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 1/9: Stage 7.0 (stage 7.0)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 2/9: Analysis Stage 7.1 (stage 7.1)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 3/9: Missing Data Analysis (stage 7.2)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 4/9: Descriptive Statistics (stage 7.3)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 5/9: Analysis Stage 7.4 (stage 7.4)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 6/9: Analysis Stage 7.5 (stage 7.5)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 7/9: Stage 7.6 (stage 7.6)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 8/9: Analysis Stage 7.7 (stage 7.7)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating section 9/9: Analysis Stage 7.8 (stage 7.8)...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating discussion and conclusion...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Generating Word document...
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] ============================================================
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Report generation completed!
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] File location: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/04_reports/statistical_analysis_report.docx
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Number of report sections: 9
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] ============================================================
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] 
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Report generation successful!
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - [report_generator] Location: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/04_reports/statistical_analysis_report.docx
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - Analysis report generated: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/04_reports/statistical_analysis_report.docx
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - ============================================================
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - Post-processing completed
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - Report location: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/04_reports/statistical_analysis_report.docx
2025-12-08 19:31:37,796 - INFO - src.core.orchestrator - Data cleanup: DataCleaner subprocess finished successfully
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2025-12-08 19:31:37,797 - INFO - api_server - Task 9d429bfb-87c6-4426-8a27-3dd6df2b0034 postprocess() returned successfully
2025-12-08 19:31:37,797 - INFO - api_server - Task 9d429bfb-87c6-4426-8a27-3dd6df2b0034 post-processing completed
2025-12-08 19:31:37,797 - INFO - api_server - Task 9d429bfb-87c6-4426-8a27-3dd6df2b0034 analysis execution completed, status: completed
2025-12-08 20:00:36,137 - INFO - api_server - Download report: /Users/bcx/Desktop/Cross-Sectional Study Design and Analysis Agent (AgenMed_CSS)/workspace/analysis_20251208_184400_7548210c/04_reports/statistical_analysis_report.docx
