The following software and packages are generally designed to process/visualize/analyze ancillary data that are often collected at the flux tower site or are relevant in analyzing flux data.
- R package for the derivation of physical and physiological bulk ecosystem properties from eddy covariance data
- functions for calculating surface conductance, aerodynamic conductance, decoupling, surface temperature and humidity, potential evapotranspiration, intrinsic water-use efficiency, bulk intercellular CO2 concentration, etc.
- The package focuses on visualizing large amounts of hourly environmental data
- See examples e.g. here:
- Calculation of Cumulative Basal Area Inflection (CuBI) height. CuBI height is the representative canopy height of a forest stand determined as the height of the inflection point of a sigmoid-shaped relationship between tree height and cumulative basal area.
- Available as R and Matlab software.
- R package for phenology from digital images of vegetation. It contains the most up-to-date processing techniques along with novelties including the combination of different fit/pheno-phase extraction methods
- An open-source, interactive tool for processing sap flux data from thermal dissipation probes. Baseliner enables users to QA/QC data and process data using a combination of automated steps, visualization, and manual editing.
- Matlab software.
- Provides various Excel sheet-based tools mostly with ecophysiological relevance.
- Contains sheets for A/Ci Curve Fitting, Pressure/volume curve-fitting, Photosynthetic Light Response curve fitting, Keeling Plot Curve Fitting, Leaf Energy Balance, Two-Pool Decomposition Model 4.0, Uncertainty in Partitioning Using Two-Source Mixing Models, Green Fraction from Digital Images, Leaf Transpiration Calculator
- An interactive tool that facilitates best practices in data exploration, quality control (e.g., outlier assessment), and flexible processing for multiple tabular data types, including time series and georeferenced data.
- The package is open-source and based on the R programming language. A key functionality of datacleanr is the “reproducible recipe”—a translation of all interactive actions into R code, which can be integrated into existing analysis pipelines.
- Tutorial: https://deep-tools.netlify.app/2020/11/25/datacleanr-intro/
- The R package TREX (TRee sap flow EXtractor), incorporating a wide range of sap flow data-processing procedures to quantify sap flux density from raw thermal dissipation method measurements.
- TREX facilitates the simultaneous application of multiple common data-processing approaches to convert raw sap flow sensor data into physiologically relevant quantities.
- Tutorial: https://deep-tools.netlify.app/2020/11/23/trex-intro/
- A transparent method, compiled in the R package treenetproc, to turn raw dendrometer data into clean, physiologically interpretable information, i.e., stem growth, tree water deficit, growth phenological phases, mean daily shrinkage, and their respective timings.
- Several commonly used characteristics, such as the start and end of stem growth, can be calculated.
- Tutorial: https://deep-tools.netlify.app/2020/11/21/treenetproc-intro/
The list was initially compiled by Ladislav Šigut and Housen Chu and has been updated with inputs from the communities. We thank all the original software/package developers for sharing and maintaining such great services. For details of each software/package, please refer to the developing team through the external links. Please contact the website manager (email@example.com) if you would like to propose any addition or update to the list.