Troubleshooting Tips


A/Ci Curve Fitting 10.0.xls
Provides parameter estimates based on both infinite and optimized mesophyll conductance, the laterfollowing Ethier and Livingston (2004). New version 11 December 2013


Pressure/volume curvefitting based on the approach of Schulte and Hinckley (1985);Schulte,P. J., andT. M. Hinckley. 1985. A Comparison of Pressure-Volume Curve Data-Analysis Techniques. Journal of Experimental Botany 36:1590-1602. Now with uncertainty estimates 6 October 2008


Photosynthetic Light Response curve fitting
Parameter estimates based on fitting a non-rectangular hyperbola following Marshall and Biscoe (1980) and Thornley and Johnson (1990).

Keeling Plot Curve Fitting
Calculates bothType I and Type II regression intercepts. Provides objective criteria to guide removal of user-selectable outliers following Bowling et al. (2002).


Leaf Energy Balance
Calculates leaf energy balance components (e.g. leaf temperature, transpiration, boundary-layer conductance, net radiation) from stomatal resistance, leaf size, shape, angle and solar radiation, windspeed, air temperature and relative humidity. Includes a worksheet for easy sensitivity analysis of different factors.



Two-Pool Decomposition Model 4.0.xls
Includes both a standard 2-pool parallel 1st order model and a reaction-progress variable or "curve-stripping" approach following Cerling et al. (2007).


Uncertainty in Partitioning Using Two-Source Mixing Models
Calculates uncertainty in source partitioning using stable isotopes for two-source mixing models, following Phillips and Gregg (2001).


Green Fraction from Digital Images
Executable program that calculates the green fraction in a digital image, e.g.fractional green cover. Based on the blue (B), green (G) and red (R)bands, 'Fast' gives the fraction of pixels in an image for which G-R>0 and 'Slow 'allows the user to specify the criteria for green pixels (e.g.2*G-R-B>0). The later version also allows for a variable threshold that can be set for different ambient light conditions. Can be run on all files in a list.


Leaf Transpiration Calculator
Calculates leaf transpiration from measurements of stomatal conductance (e.g. from a porometer). Required inputs are humidity, air temperature, leaf temperature and solar radiation at the leaf surface.

Other Useful (and Free) Software


ImageJ - image analysis and processing
R - software environment for statistical computing and graphics
Bio7 - modelling environment with ImageJ and R embedded
SAM - statistical tools for spatial analysis in macroecology
ECOBAS - modular modelling and documentation environment
DIVA-GIS - geographic information system 
Tiberius - neural networks
GP Studio - genetic programming
WinBugs - Bayesian modelling
WinDig - digitizing program to extract data from graphs (also see


This material is based upon work supported by the National Science Foundation under Grant No. 0317139

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation