Data and code
A complete and up-to-date overview of our open source products is on GitHub here.
As a group, we are committed to an Open Science Practice. We’re building an environment of open source tools for ecosystem data and modelling. This should empower the community to use latest methodological innovations, developed in our group. Here is a list of our most important contributions:
Code
rpmodel
An implementation of the P-model for leaf-level acclimation of photosynthesis Stocker et al., 2019 GMD). Implemented as an R package (fully in R). This is used as reference code for P-model implementations in other modelling frameworks and for experimental model development. For efficient time series simulations use its implementation within rsofun.
rsofun
A modelling framework for site-scale simulations of ecosystem processes, implemented as an R package (back-end in Fortran 90). Implements the following models:
- P-model for leaf-level acclimation of photosynthesis, Stocker et al., 2019 GMD
- SPLASH for bioclimatic variables, including the surface radiation budget and the soil water balance, Davis et al., 2017 GMD
- LM3-PPA for comprehensive simulations of ecosystem carbon and water cycling, tree growth, and tree cohort-explicit forest dynamics following the Perfect Plasticity Approximation, Weng et al., 2015
ingestr
Functions to extract (ingest) environmental point data from large global files or remote data servers and create time series at user-specified temporal resolution. Facilitates forcing and evaluation data preparation for rsofun. The main functionalities are:
- Temporal downscaling from montly to daily resolution
- Quality filtering, temporal interpolation and smoothing of remote sensing data
- Handling of different APIs and file formats, returning ingested data in tidy format.
SOFUN
A modular modelling framework for global-scale simulations of ecosystem processes, implemented in Fortran 90. . Implements the following models:
- P-model for leaf-level acclimation of photosynthesis, Stocker et al., 2019 GMD
- SPLASH for bioclimatic variables, including the surface radiation budget and the soil water balance, Davis et al., 2017 GMD
DYPTOP
A cost-efficient TOPMODEL implementation to simulate sub-grid spatio-temporal dynamics of global wetlands and peatlands (Stocker et al., 2014 GMD). Written in Fortran.
cwd
A light R package for deriving cumulative water deficits, given time series of evapotranspiration and precipitation.
Data and outputs
- fLUE: Fractional reduction in light use efficiency due to soil moisture stress, estimated at FLUXNET2015 Tier 1 sites, as described in Stocker et al., (2018) New Phytologist.
- SCWDX80 and zCWDX80: Global rooting zone water storage capacity (SCWDX80, mm) and rooting depth (zCWDX80, mm) estimates from Stocker et al., (2021) BiorXiv.
- GPP at FLUXNET Tier 1 sites from P-model: Gross primary production, simulated by the P-model for each FLUXNET 2015 Tier 1 site. From stocker et al. (2020) GMD
Please note:
The authors of these packages are open to collaborate. Where substantial intellectual inputs are provided by us, we ask for credit. Intellectual input can take the form of (but is not limited to) custom code, data manipulation, or methodological advice (including experimental design). The form of credit is to be determined in mutual agreement, considering contributions, and may include the authorship on manuscripts or on other research products resulting from respective work. For simple questions regarding the functioning of our open source software, please refer first to the extensive documentation on respective websites (see links above), our YouTube channel, and related published papers. For remaining questions, please raise an issue on Github (in the respective repository). Of course, for such types of support and issue resolution, we do not expect co-authorships. Fair acknowledgements and properly cited software and literature is appreciated.