Data Upload

Upload Heat Pulse Data

Supported formats: ICT JSON, CSV, Legacy text files (.txt, .csv, .json, .dat)

Clock Drift Correction (Optional)

Correct clock drift assuming the first pulse time was correct (synced at data collection start).

Device Time (at collection end)

What time did the logger show?

Actual Time (at collection end)

What was the actual time?

Trim Incomplete Days (Optional)

Remove first and/or last day if they contain less than 23 hours of data. This is recommended for daily aggregation analyses.

Upload Weather Data (Optional)

CSV format with datetime, temperature, and relative humidity columns

VPD Calculation
to

Data Summary


                    

                  

                

              

            

            

              
Probe & Wood Configuration

              
              

                

                  

                    

                      

                        
Probe Configuration

                        

                          
                        

                      

                      

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        

                          

                            
                            

                              
                              
                            

                            

                              

                            

                          

                        

                        

                          

                        

                        

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Wood Properties

                        

                          
                        

                      

                      

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                        

                          

                            
                             Using default generic softwood properties.
                          

                        

                        

                          

                          

                            

                              

                                

                                  
Load Existing Configuration (Optional)

                                

                                

                                  
Upload an existing wood properties YAML file to edit.

                                  

                                    
                                    

                                      
                                      
                                    

                                    

                                      

                                    

                                  

                                  

                                

                              

                            

                            

                              

                                

                                  
Configuration Status

                                

                                

                                  

                                

                              

                            

                          

                          

                            

                              

                                

                                  
Wood Properties Configuration

                                

                                

                                  

                                    
                                    

                                      

                                        

                                        

                                        

                                          
                                          

                                            

                                              
                                            

                                            

                                              
                                            

                                          

                                        

                                        

                                        

                                          
Measure fresh weight immediately after sampling, then oven-dry until weight is stable.

                                          

                                            
                                            
                                          

                                          

                                            
                                            
                                          

                                          

                                            
                                            
                                          

                                          

                                          

                                            
Auto-calculated Densities:

                                            
These are calculated automatically from your weight and volume measurements.

                                            

                                              

                                                

                                                  
                                                  
                                                

                                              

                                              

                                                

                                                  
                                                  
                                                

                                              

                                            

                                          

                                        

                                        

                                          
Dual Density Measurements:

                                          
Measure BOTH densities on the same sample. Volume cancels out!

                                          

                                            
                                            
                                          

                                          

                                            
                                            
                                          

                                        

                                      

                                      

                                        

                                        

                                        
Physical constants for wood and sap. Defaults from Burgess et al. (2001).

                                        
Basic Properties:

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                        

                                          
                                          

                                            
                                            
                                          

                                        

                                        

                                        
Thermal Constants:

                                        

                                          

                                            

                                              
                                              
                                            

                                            

                                              
                                              
                                            

                                          

                                          

                                            

                                              
                                              
                                            

                                            

                                              
                                              
                                            

                                            

                                              
                                              
                                            

                                          

                                        

                                      

                                      

                                        

                                        

                                        
Initial Wound Configuration:

                                        
The wound around the probe affects the measured sapwood area.

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                        

                                        

                                        
Temporal Wound Tracking (Optional):

                                        

                                          

                                            
                                          

                                        

                                        

                                          

                                            
                                            
                                          

                                          

                                            
                                            
                                          

                                          

                                            
                                            
                                          

                                        

                                        

                                          

                                            
                                             Dates auto-populate from loaded heat pulse data range (after any trimming). 
                                            Adjust manually if needed to match original sensor installation dates.
                                          

                                          Initial wound = drill bit + 2 × wound addition. Default: 2.0 + 2(0.3) = 2.6 mm
                                        

                                      

                                      

                                        

                                        

                                        
Calculate wood properties based on your measurements. Requires Method 1 or Method 2 measurements.

                                        

                                      

                                      

                                        

                                        

                                        
Optional - tree-specific measurements for scaling calculations.

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                      

                                      

                                        

                                        

                                        
Set acceptable ranges for quality control.

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                        

                                          
                                          
                                        

                                      

                                    

                                  

                                

                              

                            

                          

                          

                            

                              

                                

                                  
Export Configuration

                                

                                

                                  

                                    Download your wood properties configuration as a YAML file. 
                                    Derived properties will be automatically calculated if measurements are provided.
                                  

                                  

                                    
                                    
                                  

                                  
                                

                              

                            

                          

                        

                        

                        

                      

                    

                  

                

              

              

                

                  

                    

                      
Probe Configuration Visualisation

                      

                        
                      

                    

                    

                      
Visual representation of probe placement relative to tree anatomy.

                      

                        

                          

                        

                        

                          

                        

                      

                      

                      

                    

                  

                

              

            

            

              
Heat Pulse Velocity Calculations

              

                

                  

                    

                      

                        
Select Calculation Methods

                        

                          
                        

                      

                      

                        
Select one or more heat pulse velocity calculation methods:

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                      

                    

                  

                  

                    

                      

                        
Quality Check Settings

                        

                          
                        

                      

                      

                        
Configure quality control checks applied after calculation:

                        

                          
Illogical Values

                          

                            

                              

                                

                                  
                                

                              

                              

                                

                                  
                                

                              

                            

                            

                              

                                
                                
                              

                            

                          

                        

                        

                          
Statistical Outliers

                          

                            

                              

                                

                                  
                                

                              

                              

                                

                                  
                                

                              

                            

                            

                              

                                
                                
                              

                              

                                
                                
                              

                              

                                
                                
                              

                            

                          

                        

                        

                          
                           These settings control outlier detection sensitivity and data validation. 
                          Lower thresholds are more strict, higher are more lenient.
                        

                      

                    

                  

                

                

                  

                    

                      

                        
Run Calculations

                      

                      

                        

                        

                        
                        

                        

                      

                    

                  

                

                

                  

                    

                      

                        

                          
Calculation Results

                          

                            
                          

                        

                        

                          

                        

                      

                    

                  

                

              

            

            

              
Interactive Visualisation - Raw (Uncorrected) HPV

              
View raw heat pulse velocity calculations to identify outliers, missing data, and quality issues before applying corrections.

              

                

                  

                    

                      

                        
Plot Controls

                        

                          
                        

                      

                      

                        
Methods to Display

                        

                        

                        
Sensor Position

                        Tip: Select only one sensor for faster plot rendering with large datasets
                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Quality Flags to Display

                        

                        

                        
Time Range

                        
Set the date/time range to display. Updates automatically when you use the range slider.

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        
                        

                        
Display Options

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Data Cleaning & Filtering

                        

                          
                        

                      

                      

                        
Interpolation Settings

                        

                          
                          

                            
                            
                          

                        

                        

                          
Creates a straight line between valid points. For single missing points, this is the simple average of before/after values.

                        

                        

                          
Uses weighted average of surrounding valid points. Window size is automatically determined based on gap size. Good for noisy data.

                        

                        

                          
                          
                        

                        

                          

                            
                             Warning: Gaps > 3 hours are not recommended
                          

                        

                        

                        
Quality Flags to Interpolate

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Filter by Method/Sensor (optional)

                        
Leave all unchecked to apply to all methods/sensors

                        

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        

                        
                        
                        

                          

                          

                            

                              
                            

                          

                        

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Heat Pulse Velocity Time Series

                      

                      

                        
                      

                    

                  

                  

                    

                      

                        
Plot Information & Quality Control

                        

                          
                        

                      

                      

                        

                          

                            
Plot Information

                            

                          

                          

                            
Quality Control Summary

                            

                          

                        

                      

                    

                  

                

              

              

              

                

                  

                    

                      

                        
Pulse Trace Controls

                      

                      

                        
Selected Pulse

                        

                        

                        
Sensor Position

                        

                          
                          

                            
                            
                          

                        

                        

                        
Calculation Windows

                        
Show calculation windows used by each method. Heat pulse injection is at t=0.

                        

                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
Pulse Temperature Trace

                      

                      

                        
                      

                    

                  

                

              

            

            

              
Spacing Correction

              

                

                  

                    

                      

                        
About Changepoint-Based Correction

                        

                          
                        

                      

                      

                        

                          Note:
                           View Tab 4 (Visualise Raw HPV) first to identify data quality before correction.
                        

                        

                        
This approach detects baseline shifts in daily minimum velocities caused by probe movement (tree swelling/shrinkage).

                        
    
                          
  • 
                            Step 1:
                             Detect changepoints that divide data into segments
                          
    • 
                          
  • 
                            Step 2:
                             Apply separate Burgess corrections per segment
                          
    • 
                          
  • 
                            Step 3:
                             Review segment-specific results
                          
    • 
                        

                        

                          
                            Based on Burgess et al. (2001) with PELT changepoint detection
                          
                        

                      

                    

                  

                  

                  

                    

                      

                        
Define Zero-Flow Changepoints

                        

                          
                        

                      

                      

                        Changepoints mark dates where probe alignment shifts, dividing data into segments for separate calibration.
                        

                          
                          

                            

                              

                              

                                
                                 Recommended Method
                                

                                Detects changepoints when 
                                BOTH
                                 VPD 
                                AND
                                 sap flow are stable during pre-dawn periods. This dual-criterion approach eliminates false positives from stem refilling and provides higher confidence in baseline detection.
                              

                              

                                

                                  
                                   Weather data required
                                  

                                  Please upload weather data in Tab 1 and calculate VPD before using this method.
                                

                              

                              

                                
VPD Stability Criteria

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                
Sap Flow Stability Criteria

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                
Detection Settings

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                  
                                  

                                    
                                    
                                  

                                

                                

                                
                                

                                

                                

                                  
Detected Dual-Stable Changepoints:

                                  
                                    
                                     Changepoints where 
                                    BOTH
                                     VPD and sap flow are stable. Shown as 
                                    purple dotted lines
                                     on plot.
                                  
                                  

                                  

                                  
                                

                              

                            

                            

                              

                              
                                
                                 Detect extended periods of stable low VPD conditions suitable for spacing correction.
                              
                              

                                

                                  
                                   Weather data required
                                  

                                  Please upload weather data in Tab 1 and calculate VPD before using this method.
                                

                              

                              

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                
                                

                                

                                

                                  
Detected Stable VPD Changepoints:

                                  
                                    
                                     Detected changepoints shown as 
                                    green dotted lines
                                     on plot. Click 
                                    [+]
                                     to add individually or use button below to add all.
                                  
                                  

                                  

                                  
                                

                              

                            

                            

                              

                              
                                
                                 Automatically detect baseline shifts in daily minimum velocities using PELT changepoint detection.
                              
                              

                                
                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                              

                                

                                  
                                  
                                

                              

                              

                                

                                  

                                    
                                    
                                  

                                  

                                    
                                    

                                      
                                      
                                    

                                  

                                

                                

                                  

                                    
                                    

                                      
                                      
                                    

                                  

                                  

                                    

                                      
                                    

                                  

                                

                              

                              

                              
                              

                              

                              

                                
Detected Changepoints:

                                
                                  
                                   Detected changepoints shown as 
                                  orange dotted lines
                                   on plot. Click 
                                  [+]
                                   to add individually or use button below to add all.
                                
                                

                                

                                
                              

                            

                            

                              

                              Add a changepoint at a specific date/time where you know the baseline shifted.
                              

                                

                                  

                                    
                                    
                                  

                                

                                

                                  

                                    
                                    
                                  

                                

                              

                              
                            

                          

                        

                        

                        
Current Changepoints:

                        
                          Confirmed changepoints shown as 
                          red dashed lines
                           with baselines. Click 
                          [X]
                           to remove.
                        
                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Apply Spacing Correction

                      

                      

                        
Baseline Correction Method

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        
                          Segment Minimum:
                           Traditional approach - uses minimum value in each segment between changepoints. Creates step-wise corrections.
                          

                          Gradient Interpolation:
                           Advanced - linearly interpolates between changepoint values for smooth, continuous correction. Eliminates artificial jumps. 
                          
                            
                             Use with Caution
                          
                        
                        

                          

                            
                             Edge Period Limitation
                            

                            Gradient interpolation requires empirical baseline values. Only data 
                            between the first and last changepoints
                             can be scientifically corrected.
                            

                            

                            Data outside this range:
                            

                            • Before first changepoint: No empirical support
                            

                            • After last changepoint: No empirical support
                            

                            

                            Recommendation: Exclude edge periods or use Segment Minimum method for full dataset coverage.
                          

                        

                        

                        
Burgess Correction Method

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        
                          Burgess:
                           Uses Burgess et al. (2001) physics-based correction. Most accurate for HRM with offsets ≤ ±5 cm/hr.
                          

                          Linear:
                           Simple empirical offset subtraction. Works for all methods (HRM, MHR, Tmax) and large offsets.
                        
                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
Daily Minimum Velocities with Changepoints

                        

                          
                        

                      

                      

                        Visualise daily minimum velocities and changepoints. Click on the plot to add a changepoint at that date.
                        

                          
                          

                            
                            
                          

                        

                        

                          

                            

                              

                                
                              

                            

                          

                          

                            

                              

                                

                                  
                                

                              

                            

                          

                        

                        

                        
                        

                        

                          
                            
                             Tip: Click any date on the plot to populate the Manual tab for adding a changepoint.
                          
                        

                      

                    

                  

                  

                    

                      

                        
Spacing Correction Results

                        

                          
                        

                      

                      

                        

                          

                            No results yet. Define changepoints and run spacing correction.
                          

                        

                        

                          

                            
                            

                              

                                

                                

                                  

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                  

                                  

                                    

                                      

                                        
                                      

                                    

                                  

                                

                                
                              

                              

                                

                                Each segment between changepoints gets separate Burgess correction coefficients.
                                

                              

                              

                                

                                

                              

                            

                          

                        

                      

                    

                  

                

              

            

            

              
Wound Correction

              
Apply wound correction for probe reinstallations.

              

                

                  

                    

                      

                        
About Wound Correction

                        

                          
                        

                      

                      

                        
Wound correction accounts for the wound created by probe installation, which expands over time as wound tissue forms.

                        
    
                          
  • 
                            Initial Installation:
                             First date of data with initial wound size (drill bit + wound tissue)
                          
    • 
                          
  • 
                            Reinstallations:
                             Add dates when probe was removed and reinstalled with measured wound diameter
                          
    • 
                          
  • 
                            Temporal Tracking:
                             Wound diameter is interpolated linearly between dates
                          
    • 
                        

                        

                          
                            Based on Burgess et al. (2001) and ICT International Appendix 23.1
                          
                        

                      

                    

                  

                  

                  

                    

                      

                        
Initial Installation

                      

                      

                        
                          
                           Initial installation date is automatically set to the first date of your data.
                           Initial wound diameter is calculated from drill bit size and wound tissue addition.
                        
                        

                        

                        
Wood Properties Configuration:

                        Drill bit diameter and wound tissue addition are loaded from your wood properties YAML file.
                        

                      

                    

                  

                  

                    

                      

                        
Manage Reinstallations

                        

                          
                        

                      

                      

                        
                          
                           Add dates when the probe was removed and reinstalled.
                           The wound diameter will reset to the initial size at each reinstallation.
                        
                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                        

                          
                          
                        

                        
                        

                        
Current Reinstallations:

                        
                          Click 
                          [X]
                           to remove a reinstallation.
                        
                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Final Measurement (Growth Rate)

                      

                      

                        
                          Define the final wound diameter at the end of the experiment (or a specific date).
                           This determines the daily growth rate applied to all installation periods.
                        
                        

                          

                            

                              
                              
                            

                          

                          

                            

                              
                              
                            

                          

                        

                      

                    

                  

                  

                    

                      

                        
Apply Wound Correction

                      

                      

                        
                          Apply wound correction to spacing-corrected velocity data.
                           Correction uses temporal wound diameter tracking if reinstallations are defined.
                        
                        

                          
                          

                            
                            
                          

                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
Temporal Wound Diameter

                        

                          
                        

                      

                      

                        Visualize how wound diameter changes over time based on initial installation and reinstallation dates.
                        

                          

                            No temporal wound tracking defined. Set final measurement date and diameter to see wound growth over time.
                          

                        

                        

                          
                        

                      

                    

                  

                  

                    

                      

                        
Wound Correction Results

                        

                          
                        

                      

                      

                        

                          

                            No results yet. Apply wound correction to see results.
                          

                        

                        

                          

                            
                            

                              

                                

                                

                                  

                                    

                                      
                                      

                                        
                                        
                                      

                                    

                                  

                                  

                                    

                                      

                                        
                                      

                                    

                                  

                                  

                                    

                                      

                                        
                                      

                                    

                                  

                                

                                
                              

                              

                                

                                Wound correction coefficients (B) applied over time.
                                

                              

                              

                                

                                

                              

                            

                          

                        

                      

                    

                  

                  

                    

                      

                        
Active Wound Correction Status

                      

                      

                        

                          

                            No wound correction applied.
                          

                        

                        

                          
Wound correction is active and will be used in downstream analyses:

                          

                          

                          
                        

                      

                    

                  

                

              

            

            

              
Method Calibration

              
Calibrate secondary methods to a primary method using linear regression.

              

                

                  

                    

                      

                        
About Calibration

                        

                          
                        

                      

                      

                        
Review the diagnostic plots on the right to evaluate calibration quality for each method.

                        
The segmented regression plot shows the breakpoint where methods diverge.

                        
You can use auto-detected thresholds or set manual values per method.

                        

                          
                            Recommended: Apply AFTER spacing and wound corrections
                          
                        

                      

                    

                  

                  

                  

                    

                      

                        
Configuration

                      

                      

                        

                          
                          

                            
                            
                          

                        

                        
                          
                           Primary method is HRM. All secondary methods will be calibrated against HRM.
                        
                      

                    

                  

                  

                    

                      

                        
Threshold Settings

                      

                      

                        
                          Review the segmented regression plots, then set thresholds for each method below.
                          The auto-detected value is the statistically identified breakpoint.
                        
                        

                      

                    

                  

                  

                    

                      

                        
Apply Calibration

                      

                      

                        
                        

                        

                          

                            Calibration Applied
                          

                          

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Calibration Diagnostics - Review Before Applying

                      

                      

                        
                          
                           Review these plots to understand calibration quality and threshold selection.
                          

                          LEFT: Segmented regression - shows breakpoint where methods diverge
                          

                          RIGHT: Residuals plot - shows pattern and fit quality
                        
                        

                      

                    

                  

                

              

            

            

              
Calibration Validation

              
Verify the quality of method calibration by comparing raw vs. calibrated velocities against the HRM baseline.

              

                

                  

                    

                      

                        
Validation Controls

                        

                          
                        

                      

                      

                        
Calibration State

                        Compare raw vs. calibrated velocities
                        

                          
                          

                            
                            
                          

                        

                        

                        
Methods to Display

                        Select methods to compare against HRM baseline
                        

                        

                        
Sensor Position

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Time Range

                        
Select date range to display

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        
                        

                        
Display Options

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Calibration Validation Plot

                      

                      

                        
                          
                          This plot shows how well the calibrated secondary methods align with HRM (the primary/baseline method).
                          Good calibration results in similar patterns between HRM and secondary methods.
                        
                        
                      

                    

                  

                  

                    

                      

                        
Calibration Statistics

                        

                          
                        

                      

                      

                        

                      

                    

                  

                

              

            

            

              
Selectable DMA (sDMA) Method Switching

              
Apply Selectable Dual Method Approach (sDMA) to switch between calibrated methods based on recalculated Peclet numbers and flow conditions.

              

                

                  

                    

                      

                        
About sDMA

                        

                          
                        

                      

                      

                        
sDMA (Selectable Dual Method Approach) automatically switches between methods based on flow conditions.

                        
    
                          
  • 
                            Step 1:
                             Recalculate Peclet numbers using calibrated HRM velocities
                          
    • 
                          
  • 
                            Step 2:
                             Select secondary method and Peclet threshold
                          
    • 
                          
  • 
                            Step 3:
                             Apply sDMA switching logic
                          
    • 
                        

                        

                        

                          
                            Peclet number determines the theoretical validity limit of HRM. When Pe ≥ threshold, sDMA switches to the secondary method.
                          
                        

                      

                    

                  

                  

                  

                  

                    

                      

                        
Step 1: Recalculate Peclet Number

                      

                      

                        
Recalculate Peclet numbers using the latest calibrated HRM velocities.

                        
                          
                           This ensures switching thresholds reflect wound and spacing corrections.
                        
                        
                        

                        

                          

                            
                             Peclet Recalculated
                            

                            

                          

                        

                      

                    

                  

                  

                    

                      

                        
Step 2 & 3: sDMA Configuration

                      

                      

                        
Sensor Positions:

                        

                          
                          

                            
                            
                          

                        

                        

                        
Secondary Methods:

                        
                          
                           Select one or more methods to apply sDMA switching.
                        
                        

                        

                        

                          
                          
                        

                        
                          
                           When Pe ≥ threshold, use secondary method. Otherwise use HRM.
                        
                        

                        
                        
                          
                           sDMA will be applied to all selected sensor/method combinations.
                        
                      

                    

                  

                

                

                  

                    

                      

                        
sDMA Results

                      

                      

                        

                          

                            
                            

                              

                                

                                
                                

                                

                              

                              

                                

                                
Visualize switching points: HRM below threshold, secondary method above.

                                
                              

                            

                          

                        

                        

                          

                            
                            
No sDMA results yet. Follow the steps on the left to apply sDMA switching.

                          

                        

                      

                    

                  

                

              

            

            

              
sDMA Validation - Interactive Time Series

              
Compare HRM baseline, calibrated secondary methods, and sDMA results in an interactive time series plot.

              

                

                  

                    

                      

                        
Plot Controls

                        

                          
                        

                      

                      

                        
Methods to Display

                        Select specific methods to show
                        

                        

                        
Sensor Position

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Time Range

                        
Select date range to display

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        
                        

                        
Display Options

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
sDMA Validation Time Series

                      

                      

                        
                          
                          Compare HRM baseline, calibrated secondary methods, and sDMA results.
                          Click-drag to zoom, double-click to reset zoom.
                        
                        
                      

                    

                  

                

              

            

            

              
Sap Flux Density Conversion & Tree Water Use

              
Convert corrected heat pulse velocity (Vh) to sap flux density (Jv) and integrate across sapwood area for whole-tree water use.

              

                

                  

                    

                      

                        
About Sap Flux Density Conversion

                        

                          
                        

                      

                      

                        
Sap flux density (Jv) represents the volume of sap flowing through a unit area of sapwood per unit time.

                        
    
                          
  • 
                            Formula:
                             Jv = Z × Vh
                          
    • 
                          
  • 
                            Z factor:
                             Wood-specific conversion factor calculated from wood properties
                          
    • 
                          
  • 
                            Units:
                             cm³/cm²/hr (equivalent to cm/hr sap velocity)
                          
    • 
                          
  • 
                            Sensors:
                             Conversion applied to all sensor positions (inner + outer) for radial integration
                          
    • 
                        

                        

                          
                            Based on Burgess et al. (2001) after Barrett et al. (1995)
                          
                        

                        

                        
Recommended Workflow:

                        
    
                          
  1. Calculate raw heat pulse velocity (Vh)
    2. 
                          
  2. Apply spacing correction
    3. 
                          
  3. Apply wound correction (optional)
    4. 
                          
  4. Convert to sap flux density (Jv) - all sensors
    5. 
                          
  5. Integrate across sapwood area → tree-level water use
    6. 
                        

                      

                    

                  

                  

                    

                      

                        
Conversion Settings

                      

                      

                        
                          
                           Select which method(s) to convert to flux density. sDMA methods combine multiple measurement approaches.
                        
                        
Select Methods:

                        

                        

                        
                          
                           Flux density will be calculated for all available sensor positions (inner and outer).
                           Both sensors are required for radial integration across the sapwood.
                        
                        

                        

                        
Wood Properties:

                        Z factor (sap flux conversion factor) is calculated from your wood properties.
                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Tree Water Use Integration

                        

                          
                        

                      

                      

                        
                          
                           Integrate flux density across sapwood area to calculate whole-tree water use (Q).
                        
                        

                          

                            Convert to flux density first.
                          

                        

                        

                          
Tree Dimensions:

                          

                            

                              

                                
                                
                              

                            

                            

                              

                                
                                
                              

                            

                          

                          

                            
                            
                          

                          

                          

                            
                            

                              
                              
                            

                          

                          Weighted average accounts for radial variation in sap flux density.
                          

                          
                        

                      

                    

                  

                  

                    

                      

                        
Export Flux Density Data

                        

                          
                        

                      

                      

                        

                          

                            No flux density data available yet.
                          

                        

                        

                          Export sap flux density data to CSV for further analysis.
                          

                            
                            

                              
                              
                            

                          

                          
                            
                            Download CSV
                          
                        

                      

                    

                  

                

                

                  

                    

                      

                        
1. Flux Density Conversion Summary

                        

                          
                        

                      

                      

                        

                          

                            No flux density data yet. Click 'Convert to Sap Flux Density (Jv)' to begin.
                          

                        

                        

                          

                          

                          

                            
                             Flux density conversion is complete.
                             Proceed to calculate tree water use (Q) below,
                             or go to 
                            Tab 8b: Flux Density Validation
                             to explore interactive plots.
                          

                          

                          
                        

                      

                    

                  

                  

                    

                      

                        
2. Tree Water Use Summary

                        

                          
                        

                      

                      

                        

                          

                            No tree water use data yet. Convert flux density first, then click 'Calculate Tree Water Use (Q)'.
                          

                        

                        

                          

                          

                          

                            
                             Tree water use calculation is complete.
                             Go to 
                            Tab 8b: Flux Density Validation
                             to view interactive plots,
                             or proceed to 
                            Tab 9: Aggregation
                             for temporal summaries.
                          

                        

                      

                    

                  

                  

                    

                      

                        
Active Conversion Status

                        

                          
                        

                      

                      

                        

                          

                            No conversions applied yet.
                          

                        

                        

                          

                        

                      

                    

                  

                

              

            

            

              
Flux Density & Water Use Validation

              
Interactive visualization of flux density and tree water use results with filtering and time range controls.

              

                

                  

                    

                      

                        
Plot Controls

                        

                          
                        

                      

                      

                        
Methods to Display

                        Select specific methods to show
                        

                        

                        
Sensor Position

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Time Range

                        
Select date range to display

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        
                        

                        
Display Options

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
Sap Flux Density Time Series (Jv)

                      

                      

                        
                          
                          Sap flux density over time for all selected methods.
                          Click-drag to zoom, double-click to reset zoom.
                        
                        
                      

                    

                  

                  

                    

                      

                        
Tree Water Use - Hourly (L/hr)

                        

                          
                        

                      

                      

                        
                          
                          Whole-tree water use integrated across sapwood area.
                          Click-drag to zoom, double-click to reset zoom.
                        
                        
                      

                    

                  

                  

                    

                      

                        
Tree Water Use - Daily (L/day)

                        

                          
                        

                      

                      

                        
                          
                          Daily totals of tree water use.
                          Grouped bars show multiple methods side-by-side.
                        
                        
                      

                    

                  

                  

                    

                      

                        
Velocity vs Flux Density Comparison

                        

                          
                        

                      

                      

                        
                          
                          Visualize the conversion from heat pulse velocity (Vh) to sap flux density (Jv).
                          Dashed line shows the Z factor relationship (Jv = Z × Vh).
                        
                        
                      

                    

                  

                  

                    

                      

                        
Daily Sap Flux Totals

                        

                          
                        

                      

                      

                        
                          
                          Daily sap flux totals integrated over 24-hour periods.
                        
                        
                      

                    

                  

                

              

            

            

              
Temporal Aggregation

              
Aggregate flux density data to daily/weekly/hourly summaries for temporal analysis.

              

                

                  

                    

                      

                        
Aggregation Settings

                        

                          
                        

                      

                      

                        
Data Type

                        

                          
                          

                            
                            
                          

                        

                        

                        
Temporal Aggregation

                        

                          
                          

                            
                            
                          

                        

                        

                        
Aggregation Function

                        

                          
                          

                            
                            
                          

                        

                        

                        
Plot Type

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Summary Statistics

                        

                          
                        

                      

                      

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Aggregated Data

                      

                      

                        
                      

                    

                  

                  

                    

                      

                        
Aggregated Data

                        

                          
                        

                      

                      

                        

                      

                    

                  

                

              

            

            

              
Interactive Visualisation - Corrected HPV

              
View corrected heat pulse velocity data after applying spacing corrections and/or wound corrections.

              

                

                  

                    

                      

                        
Plot Controls

                        

                          
                        

                      

                      

                        
Methods to Display

                        

                        

                        
Sensor Position

                        Tip: Select only one sensor for faster plot rendering with large datasets
                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Quality Flags to Display

                        

                        

                        
Time Range

                        
Set the date/time range to display. Updates automatically when you use the range slider.

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        

                          
                          

                            
                            

                              
                            

                          

                          
                        

                        
                        

                        
Display Options

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Data Cleaning & Filtering

                        

                          
                        

                      

                      

                        
Interpolation Settings

                        

                          
                          

                            
                            
                          

                        

                        

                          
Creates a straight line between valid points. For single missing points, this is the simple average of before/after values.

                        

                        

                          
Uses weighted average of surrounding valid points. Window size is automatically determined based on gap size. Good for noisy data.

                        

                        

                          
                          
                        

                        

                          

                            
                             Warning: Gaps > 3 hours are not recommended
                          

                        

                        

                        
Quality Flags to Interpolate

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        
Filter by Method/Sensor (optional)

                        
Leave all unchecked to apply to all methods/sensors

                        

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                        

                        
                        
                        

                          

                          

                            

                              
                            

                          

                        

                        

                      

                    

                  

                

                

                  

                    

                      

                        
Heat Pulse Velocity Time Series

                      

                      

                        
                      

                    

                  

                  

                    

                      

                        
Plot Information & Quality Control

                        

                          
                        

                      

                      

                        

                          

                            
Plot Information

                            

                          

                          

                            
Quality Control Summary

                            

                          

                        

                      

                    

                  

                

              

              

              

                

                  

                    

                      

                        
Pulse Trace Controls

                      

                      

                        
Selected Pulse

                        

                        

                        
Sensor Position

                        

                          
                          

                            
                            
                          

                        

                        

                        
Calculation Windows

                        
Show calculation windows used by each method. Heat pulse injection is at t=0.

                        

                        

                        
                      

                    

                  

                

                

                  

                    

                      

                        
Pulse Temperature Trace

                      

                      

                        
                      

                    

                  

                

              

            

            

              
Probe Configuration Builder

              
Create or edit probe configuration YAML files for use in sap flow analysis workflows.

              

                

                  

                    

                      
Probe Configuration Builder

                    

                    

                      

                        Create or edit probe configuration YAML files for use in sap flow analysis workflows. 
                        Upload an existing YAML to edit, or create a new configuration from scratch.
                      

                    

                  

                

              

              

                

                  

                    

                      
Load Existing Configuration (Optional)

                      

                        
                      

                    

                    

                      
Upload an existing probe configuration YAML file to edit.

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      

                    

                  

                

                

                  

                    

                      
Configuration Status

                    

                    

                      

                    

                  

                

              

              

                

                  

                    

                      
Probe Configuration

                    

                    

                      

                        
                        

                          

                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                          

                          

                            

                            
Define the spatial arrangement of thermistor sensors relative to the heater.

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                            

                              Probe Insertion
                            

                            
If probe is not fully inserted (e.g., due to external spacer for thin bark/sapwood), enter spacer thickness.

                            

                              
                              
                            

                            

                          

                          

                            

                            
Physical dimensions and sensor positions.

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                          

                          

                            

                            
Select calculation methods compatible with this probe configuration.

                            
Compatible Methods

                            

                              
                              

                                

                                  
                                

                                

                                  
                                

                                

                                  
                                

                                

                                  
                                

                                

                                  
                                

                              

                            

                            

                            
Recommended Methods

                            
Select the subset of methods recommended for this configuration.

                            
                          

                        

                      

                    

                  

                

              

              

                

                  

                    

                      
Export Configuration

                    

                    

                      
Download your probe configuration as a YAML file.

                      

                        
                        
                      

                      
                    

                  

                

              

            

            

              
Wood Properties Builder

              
Create or edit wood properties YAML files for use in sap flow analysis workflows.

              

              

                

                  

                    

                      
Load Existing Configuration (Optional)

                    

                    

                      
Upload an existing wood properties YAML file to edit.

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      

                    

                  

                

                

                  

                    

                      
Configuration Status

                    

                    

                      

                    

                  

                

              

              

                

                  

                    

                      
Wood Properties Configuration

                    

                    

                      

                        
                        

                          

                            

                            

                            

                              
                              

                                

                                  
                                

                                

                                  
                                

                              

                            

                            

                            

                              
Measure fresh weight immediately after sampling, then oven-dry until weight is stable.

                              

                                
                                
                              

                              

                                
                                
                              

                              

                                
                                
                              

                              

                              

                                
Auto-calculated Densities:

                                
These are calculated automatically from your weight and volume measurements.

                                

                                  

                                    

                                      
                                      
                                    

                                  

                                  

                                    

                                      
                                      
                                    

                                  

                                

                              

                            

                            

                              
Dual Density Measurements:

                              
Measure BOTH densities on the same sample. Volume cancels out!

                              

                                
                                
                              

                              

                                
                                
                              

                            

                          

                          

                            

                            

                            
Physical constants for wood and sap. Defaults from Burgess et al. (2001).

                            
Basic Properties:

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              

                                
                                
                              

                            

                            

                            
Thermal Constants:

                            

                              

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                              

                              

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                                

                                  
                                  
                                

                              

                            

                          

                          

                            

                            

                            
Initial Wound Configuration:

                            
The wound around the probe affects the measured sapwood area.

                            

                              
                              
                            

                            

                              
                              
                            

                            

                            

                            
Temporal Wound Tracking (Optional):

                            

                              

                                
                              

                            

                            

                              

                                
                                
                              

                              

                                
                                
                              

                              

                                
                                
                              

                            

                            

                              

                                
                                 Dates auto-populate from loaded heat pulse data range (after any trimming). 
                                Adjust manually if needed to match original sensor installation dates.
                              

                              Initial wound = drill bit + 2 × wound addition. Default: 2.0 + 2(0.3) = 2.6 mm
                            

                          

                          

                            

                            

                            
Calculate wood properties based on your measurements. Requires Method 1 or Method 2 measurements.

                            

                          

                          

                            

                            

                            
Optional - tree-specific measurements for scaling calculations.

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                          

                          

                            

                            

                            
Set acceptable ranges for quality control.

                            

                              
                              
                            

                            

                              
                              
                            

                            

                              
                              
                            

                          

                        

                      

                    

                  

                

              

              

                

                  

                    

                      
Export Configuration

                    

                    

                      

                        Download your wood properties configuration as a YAML file. 
                        Derived properties will be automatically calculated if measurements are provided.
                      

                      

                        
                        
                      

                      
                    

                  

                

              

            

            

              
Reproducible Code Generation

              
Generate executable R scripts that reproduce your Shiny analysis workflow using sapfluxr functions.

              

                

                  

                    

                      

                        
About Code Generation

                        

                          
                        

                      

                      

                        
This tool generates executable R code that reproduces your entire Shiny analysis workflow.

                        
    
                          
  • 
                            Purpose:
                             Scientific reproducibility
                          
    • 
                          
  • 
                            Output:
                             Self-contained R script
                          
    • 
                          
  • 
                            Usage:
                             Run in R console or RStudio
                          
    • 
                          
  • 
                            Benefits:
                             Publication-ready, auditable, reusable
                          
    • 
                        

                        

                        
Tracked Steps:

                        

                        

                        
                      

                    

                  

                  

                    

                      

                        
Export Options

                      

                      

                        

                          

                            No analysis steps recorded yet. Perform analysis in other tabs.
                          

                        

                        

                          

                            

                              
                            

                          

                          

                            

                              
                            

                          

                          

                            

                              
                            

                          

                          

                          
                            
                            Download R Script
                          
                          
                        

                      

                    

                  

                

                

                  

                    

                      

                        
Generated R Script

                      

                      

                        

                          

                            Code will appear here after you perform analysis steps in the app.
                          

                        

                        

                          
                            
                             This script reproduces your analysis. Copy or download to run in R.
                          
                          

                            
                              

                            

                          

                        

                      

                    

                  

                  

                    

                      

                        
Analysis Steps Breakdown

                        

                          
                        

                      

                      

                        Detailed breakdown of each analysis step: