TranCIT: Transient Causal Interaction Toolbox
Getting Started
Installation
Prerequisites
Install from PyPI
Install from Source
Verify Installation
Optional Dependencies
Quickstart
Installation Check
Basic Causality Analysis
Pipeline-Based Event Analysis
Different Types of Analysis
Working with Real Data
Common Troubleshooting
What’s Next?
Tutorials
Tutorial 1: Basic DCS Analysis
Understanding the Data Format
Step-by-Step DCS Analysis
Visualizing Results
Tutorial 2: Event-Based Analysis with Pipeline
Understanding Event Detection
Configuring the Pipeline
Running the Event-Based Analysis
Visualizing Event-Based Results
Tutorial 3: Advanced Configuration and Optimization
Model Order Selection
Handling Different Data Types
Performance Optimization
Statistical Validation
Tutorial 4: Real-World Applications
Neural Data Analysis
Economic Time Series Analysis
Multi-Scale Analysis
Tutorial 5: Best Practices and Troubleshooting
Data Quality Assessment
Robust Analysis Pipeline
Common Issues and Solutions
Performance Monitoring
User Guide
Examples
Basic Usage Script
Reproducing a Scientific Figure (Jupyter Notebook)
Advanced Pipeline Example
More Coming Soon!
API Reference
Core Module (
trancit.core
)
Base Classes
Exception Classes
Causality Analysis (
trancit.causality
)
Dynamic Causal Strength (DCS)
Transfer Entropy
Granger Causality
Relative Dynamic Causal Strength (rDCS)
Utility Functions
Pipeline System (
trancit.pipeline
)
Pipeline Orchestration
Pipeline Stages
Configuration (
trancit.config
)
Main Configuration
Parameter Classes
Model Estimation (
trancit.models
)
VAR Model Estimation
BIC Model Selection
Model Validation
Simulation (
trancit.simulation
)
Signal Generation
AR Event Simulation
VAR Simulation
Utilities (
trancit.utils
)
Data Processing
Core Analysis Functions
Signal Processing
Residual Analysis
Visualization
Helper Functions
Complete Usage Examples
Basic Analysis Workflow
Event-Based Analysis Workflow
Performance Notes
Troubleshooting
Event Detection Preprocessing Pipeline
Overview
Preprocessing Stages
1. Event Detection
2. Border Removal
3. Snapshot Extraction
4. Artifact Rejection
5. Statistics Computation
Software Architecture
Pipeline Design Pattern
State Management
API Design
Configuration-Driven Architecture
User Interface
Configuration Flexibility
Implementation Details
Event Detection Algorithm
Snapshot Extraction Details
Error Handling
Integration with Causality Analysis
References
Software Architecture
Package Structure
Core Module (
trancit.core
)
Causality Module (
trancit.causality
)
Pipeline Module (
trancit.pipeline
)
Models Module (
trancit.models
)
Simulation Module (
trancit.simulation
)
Utilities Module (
trancit.utils
)
Dependencies
Core Dependencies
Design Choices
Configuration-Driven Architecture
Extensibility Through Abstract Base Classes
Comprehensive Error Handling
Reproducibility and Logging
Testing and Quality Assurance
Performance Considerations
Version Management
Community & Legal
Contributing
TL;DR - How to Contribute
Reporting Issues
Feature Requests
Contributing Code
More Guidelines
License
TranCIT: Transient Causal Interaction Toolbox
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
V
_
__init__() (trancit.causality.dcs.DCSCalculator method)
(trancit.causality.dcs.DCSResult method)
(trancit.causality.granger.GrangerCausalityCalculator method)
(trancit.causality.granger.GrangerCausalityResult method)
(trancit.causality.rdcs.RelativeDCSCalculator method)
(trancit.causality.rdcs.RelativeDCSResult method)
(trancit.causality.transfer_entropy.TransferEntropyCalculator method)
(trancit.causality.transfer_entropy.TransferEntropyResult method)
(trancit.config.BicParams method)
(trancit.config.CausalParams method)
(trancit.config.DetectionParams method)
(trancit.config.MonteCParams method)
(trancit.config.OutputParams method)
(trancit.config.PipelineConfig method)
(trancit.config.PipelineOptions method)
(trancit.core.base.BaseAnalyzer method)
(trancit.core.base.BaseConfig method)
(trancit.core.base.BaseResult method)
(trancit.core.exceptions.ComputationError method)
(trancit.core.exceptions.ConfigurationError method)
(trancit.core.exceptions.DCSError method)
(trancit.core.exceptions.ValidationError method)
(trancit.models.bic_selection.BICSelector method)
(trancit.models.model_validation.ModelValidator method)
(trancit.models.var_estimation.VAREstimator method)
(trancit.pipeline.orchestrator.PipelineOrchestrator method)
(trancit.pipeline.orchestrator.PipelineResult method)
__post_init__() (trancit.config.PipelineConfig method)
__repr__() (trancit.core.base.BaseConfig method)
(trancit.core.base.BaseResult method)
A
align_type (trancit.config.DetectionParams attribute)
,
[1]
analyze() (trancit.causality.dcs.DCSCalculator method)
(trancit.causality.granger.GrangerCausalityCalculator method)
(trancit.causality.rdcs.RelativeDCSCalculator method)
(trancit.causality.transfer_entropy.TransferEntropyCalculator method)
(trancit.core.base.BaseAnalyzer method)
(trancit.pipeline.orchestrator.PipelineOrchestrator method)
B
BaseAnalyzer (class in trancit.core.base)
BaseConfig (class in trancit.core.base)
BaseResult (class in trancit.core.base)
bic (trancit.config.PipelineConfig attribute)
,
[1]
(trancit.config.PipelineOptions attribute)
,
[1]
BicParams (class in trancit.config)
BICSelectionStage (class in trancit.pipeline.stages)
BICSelector (class in trancit.models.bic_selection)
bootstrap (trancit.config.PipelineOptions attribute)
,
[1]
C
causal (trancit.config.PipelineConfig attribute)
,
[1]
causal_analysis (trancit.config.PipelineOptions attribute)
,
[1]
CausalityAnalysisStage (class in trancit.pipeline.stages)
CausalParams (class in trancit.config)
ComputationError (class in trancit.core.exceptions)
compute_event_statistics() (in module trancit.utils.core)
ConfigurationError (class in trancit.core.exceptions)
D
DCSCalculator (class in trancit.causality.dcs)
DCSError (class in trancit.core.exceptions)
DCSResult (class in trancit.causality.dcs)
debiased_stats (trancit.config.PipelineOptions attribute)
,
[1]
desnap (trancit.config.PipelineConfig attribute)
,
[1]
detection (trancit.config.PipelineConfig attribute)
,
[1]
(trancit.config.PipelineOptions attribute)
,
[1]
DetectionParams (class in trancit.config)
diag_flag (trancit.config.CausalParams attribute)
,
[1]
E
estim_mode (trancit.config.BicParams attribute)
(trancit.config.CausalParams attribute)
,
[1]
estimate_residuals() (in module trancit.utils.residuals)
estimate_var_coefficients() (trancit.models.var_estimation.VAREstimator method)
EventDetectionStage (class in trancit.pipeline.stages)
execute() (trancit.pipeline.stages.BICSelectionStage method)
(trancit.pipeline.stages.CausalityAnalysisStage method)
(trancit.pipeline.stages.EventDetectionStage method)
(trancit.pipeline.stages.InputValidationStage method)
(trancit.pipeline.stages.SnapshotExtractionStage method)
F
file_keyword (trancit.config.OutputParams attribute)
,
[1]
find_peak_locations() (in module trancit.utils.signal)
G
generate_signals() (in module trancit.simulation)
generate_var_nonstat() (in module trancit.simulation)
get_residuals() (in module trancit.utils.residuals)
GrangerCausalityCalculator (class in trancit.causality.granger)
GrangerCausalityResult (class in trancit.causality.granger)
I
InputValidationStage (class in trancit.pipeline.stages)
L
l_extract (trancit.config.DetectionParams attribute)
,
[1]
l_start (trancit.config.DetectionParams attribute)
,
[1]
locs (trancit.config.DetectionParams attribute)
,
[1]
M
mode (trancit.config.BicParams attribute)
,
[1]
ModelValidator (class in trancit.models.model_validation)
momax (trancit.config.BicParams attribute)
,
[1]
monte_carlo (trancit.config.PipelineConfig attribute)
,
[1]
MonteCParams (class in trancit.config)
morder (trancit.config.BicParams attribute)
,
[1]
N
n_btsp (trancit.config.MonteCParams attribute)
,
[1]
normalize_data() (in module trancit.utils.preprocess)
O
old_version (trancit.config.CausalParams attribute)
,
[1]
options (trancit.config.PipelineConfig attribute)
,
[1]
output (trancit.config.PipelineConfig attribute)
,
[1]
OutputParams (class in trancit.config)
P
passband (trancit.config.PipelineConfig attribute)
,
[1]
perform_desnap_analysis() (in module trancit.utils.core)
PipelineConfig (class in trancit.config)
PipelineOptions (class in trancit.config)
PipelineOrchestrator (class in trancit.pipeline.orchestrator)
PipelineResult (class in trancit.pipeline.orchestrator)
R
ref_time (trancit.config.CausalParams attribute)
,
[1]
RelativeDCSCalculator (class in trancit.causality.rdcs)
RelativeDCSResult (class in trancit.causality.rdcs)
remove_artif (trancit.config.DetectionParams attribute)
,
[1]
remove_artif_threshold (trancit.config.DetectionParams attribute)
run() (trancit.pipeline.orchestrator.PipelineOrchestrator method)
S
sampling_rate (trancit.config.PipelineConfig attribute)
,
[1]
save_flag (trancit.config.PipelineOptions attribute)
,
[1]
save_path (trancit.config.OutputParams attribute)
,
[1]
shrink_flag (trancit.config.DetectionParams attribute)
,
[1]
simulate_ar_event() (in module trancit.simulation)
simulate_ar_event_bootstrap() (in module trancit.simulation)
SnapshotExtractionStage (class in trancit.pipeline.stages)
T
tau (trancit.config.BicParams attribute)
,
[1]
thres_ratio (trancit.config.DetectionParams attribute)
,
[1]
time_varying_causality() (in module trancit.causality.rdcs)
to_dict() (trancit.core.base.BaseConfig method)
(trancit.core.base.BaseResult method)
TransferEntropyCalculator (class in trancit.causality.transfer_entropy)
TransferEntropyResult (class in trancit.causality.transfer_entropy)
V
validate() (trancit.core.base.BaseConfig method)
(trancit.models.model_validation.ModelValidator method)
ValidationError (class in trancit.core.exceptions)
VAREstimator (class in trancit.models.var_estimation)