Softwares

Software platforms ( Computer platforms)


CAPSIS is a platform for the development of forest growth and forest dynamics models allowing the construction and evaluation of silvicultural scenarios, intended for researchers, forest managers or education.
Pl@ntnet is a participatory botany infrastructure.

Software suites


AMAPStudio is a software suite dedicated to edition, visualisation, exploration and multi-scale simulation of 3D plant architectural development , at the scale of individuals or vegetation stands. In particular:

  • Xplo, a software for exploring plant architecture at different scales.
  • Scan, an interactive software to build and edit plant architecture recon,structiont from TLS point clouds.
  • AMAPSim, is a simulation core of 3D plant architectural development, which can be connected to external applications.
  • Archimed, a platform biophysical processes modeling from 3D vegetation models.

ForestRS brings together tools dedicated to the use of remote sensing products for the study of individual trees and tree stands.

  • AlloStand, an R package for generating 3D forest mock-ups from forest inventory data.
  • AMAPVox, a LiDAR data voxelisation software.
  • FOTO, a python package for predicting stand structure parameters in tropical forests, based on texture analysis of satellite images.
  • PyTools4DART, python API for the DART radiative transfer simulator, developed at UMR TETIS.

Softwares


C++ applications

  • CMMP, offers continuous mathematical models of plant growth.
  • TROLL, an individual-based forest dynamics simulator, developed in collaboration with UMR EDB in Toulouse.

Mobile applications

  • DiagARCHI, a mobile app for architectural diagnosis.

R packages

  • ADS, ADS, an R package for the analysis of spatial point processes.
  • BIOMASS, an R package for estimating above-ground biomass and associated uncertainty in tropical forests.
  • ConR, an R package for estimating species conservation status according to criterion B of the International Union for the Conservation of Nature (IUCN).
  • JDSM, R package includes for estimating parameters of Joint Species Distribution Models (JSDM). Thses models use information on species co-occurrences to predict their potential distributions.
  • hSDM, an R package for estimating parameters of hierarchical species distribution models in a Bayesian framework. These models make it possible to interpret observations (occurrence and abundance of a species) according to hierarchical processes combining ecological (habitat suitability, spatial dependence and anthropogenic disturbances) and observation processes (species detectability). Hierarchical species distribution models are essential to accurately characterise the environmental response of species, predict their probability of occurrence and assess model uncertainty.
  • Mimetic Point Process,an R package to help generate mimetic spatial point patterns.
  • SSDM, an R package to predict the distribution of species richness and composition from stacked species distribution models.

Python packages

  • forestatrisk, Python module to model tropical deforestation and predict future forest cover under various deforestation scenarios. It allows estimating the spatial probability of deforestation as a function of environmental variables describing the accessibility of the forest (distance to roads, villages and rivers, distance to the forest edge, topography), its protection status (belonging to the network of natural protected areas) and its history (distance to past deforestation). Through spatially correlated random effects, the model also takes into account the residual spatial variability of the deforestation process. This residual variability is not explained by the environmental variables included in the model.
  • pywdpa, a Python package providing an interface with the World Database on Protected Areas (WDPA) hosted on the Protected Planet website athttps://www.protectedplanet.net. The pywdpa package provides functions to download protected area (PA) shapefiles for all countries from an iso code using the Protected Planet API at https://api.protectedplanet.net. The pywdpa package translates into Python some of the functions in the R worldpa package (https://github.com/FRBCesab/worldpa)

Miscellaneous

  • GreenLab, collection of models of plant development and growth, in Matlab.
  • IDAO, a plant identification tool based on a multimedia approach, in Visual Basic.