Open Science
Open source software
We produce different software tools for the analysis of ecosystem properties. Some of the open source sofware tools we have developed are:
| Name | Purpose | More information |
|---|---|---|
| SoilR | SoilR is an R package for modeling soil organic matter dynamics. It can be used to implement any type of soil carbon model and compare output between different model structures or parameterizations. | SoilR site Download from GitHub . |
| LAPM | The Linear Pool Models LAPM python package implements a set of system diagnostics for compartment models expressed as linear autonomous systems. The package computes density distributions for system and pool ages as well as transit times using as input a compartmental matrix and a vector of inputs to a system. | Read the documentation and clone from GitHub |
| CompartmentalSystems | CompartmentalSystems is a python package for the analysis of smooth nonautonomous nonlinear compartmental systems. This package can run simulations and also computes time-dependent density distributions for system, pool ages as well as transit time. | Read the documentation and clone from GitHub |
| BGC-MD | This is a collection of biogeochemical models expressed in symbolic mathematics and implemented in Python. | Clone the development repository , or check the static website with the current set of models. |
| measuRing | measuRing is an R package developed by Wilson Lara for the detection and control of tree-ring widths from dendrochronological images. It processes the image section and computes luminance data from images producing a matrix of gray values and a time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders, or control of automatic detection. The package provides functions to visually include/exclude ring borders on the R graphical device, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to negative extreme values in the smoothed time-series of gray values. | A paper describing the package is available here . Download from CRAN |
Visit our GitHub organization site for more tools
Our software has been recognized by the Dynamical Systems section of the Society for Industrial and Applied Mathematics. See the results of the DSWeb 2018 Software Contest for more details.
Open data
We have developed a number of databases and contribute data to larger projects. Here are some of the most relevant open data projects.
| Name | Description | More information |
|---|---|---|
| ATTO flasks | We are in charge of the high precision monitoring program for 14CO2, greenhouse gases, and stabe isotopes at the Amazon Tall Tower Observatory. This record of atmospheric data, is unique in South America, and provides background data for a number of studies at the regional and continental scales. | The data can be obtain from the ATTO data portal. |
| SIDb | The Soil Incubation Database SIDb contains time series of carbon release from incubation experiments under controlled conditions. An R package is available to process the data and obtain useful diagnostics. | SIDb is hosted in GitHub |
| ISRaD | We contribute to the development of ISRaD, an open community repository for soil radiocarbon data. ISRaD is a major collaboration between the USGU Powell Center and the Max Planck Institute for Biogeochemistry. | A website describing the database in associated tools can be found in ISRaD. The main publication that describes the database can be found here |
| Aridec | In collaboration with Agustín Sarquís from the University of Buenos Aires, we developed a database of litter decomposition studies from arid regions. | The data can be obtained from GitHub . An article describing the database can be found here |