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.

Software of the UMR AMAP (Duration 2010-2020)

For any question / request about these software, write to amap-dev@cirad.fr

CMP	CMP, for Correlation Map and Profile, is a convenient tool aimed at comparing almost every kind of surface patterns. It focuses on a multiscale comparison of quantitative and qualitative images, and offers multiscale maps and profiles of the mostly used pattern indices. This method is summarized within a coherent open source software that makes analyses very friendly for ecological, remote sensing and even biological or physical studies. CMP is fully complementary to other comparison tools (dedicated to point-pattern analyses or not) such as co-kriging, co-spectra and co-wavelets. CMP software has been developed from Gaucherel’s Matlab® routines (see references) and has been recently transformed into open Java® multiplatform software (see developer forum). CMP works with images saved in raster mode and provides quantified indices in similar formats.
DXM	DXM has been developed at INRA (Institut National de la Recherche Agronomique) in the AMAP laboratory (botAnique et bioinforMatique de l’Architecture des Plantes, France) since 2005, then in the ecology department at IFP (Institut Français de Pondicherry, India) since 2010. DXM is a convenient tool dedicated to researchers of environmental sciences and for education purposes. DXM aims at analyzing and quantifying time series with the help of non stationary signal analysis methods. Starting from a loaded time series (whatever is its length and time resolution), the software is computing various maps and statistics related to its variability and non-stationnarity properties. Among others, it provides computations of Fourier and Autocorrelation spectra, SSA (Singular Spectrum Analysis), wavelet transform and DXM extended auto-correlations (cyclostationnarity).
DYPAL	DYPAL has been developed at INRA (Institut National de la Recherche Agronomique) in the AMAP laboratory (botAnique et bioinforMatique de l'Architecture des Plantes, France) since 2005, then in the ecology department at IFP (Institut Français de Pondichéry, India) since 2010. DYPAL is a convenient tool dedicated to ecologists (researchers), to landscape managers and for education purposes. On the one hand, DYPAL is able to simulate observed dynamics to verify that these dynamics have been correctly understood or to infer the most probable drivers of it. On the other hand, DYPAL provides a computer-aided projection of strategies in landscape ecology and environmental sciences.
MHM	MHM, for Multiscale Heterogeneity Map, is a convenient tool aimed at analysing almost every kind of surface patterns. It focuses on a multiscale analysis and offers multiscale maps and profiles of the most-often used pattern indices. This method is summarized within a coherent open source software that makes analyses very friendly for ecological, remote sensing and even biological or physical studies. MHM is fully complementary to geostatistical tools (dedicated to point-pattern analyses) or to Fragstats modules (generally offering monoscale analyses) and focuses on patchy mosaics. MHM software has been developed from Gaucherel’s Matlab® routines (see references) and has been recently transformed into open Java® multiplatform software (see developer forum). MHM works with images saved in raster mode and provides quantified indices in similar formats.
Pl@ntNote	The Pl@ntNote application is an open source software for researchers to manage ecological field data. It is a modular tool based on individual plants.
SSM	SSM has been developed at INRA (Institut National de la Recherche Agronomique) in the AMAP laboratory (botAnique et bioinforMatique de l’Architecture des Plantes, France) since 2005, then in the ecology department at IFP (Institut Français de Pondicherry, India) since 2010. SSM is a convenient tool dedicated to researchers of environmental sciences, to water resource managers and for education purposes. On the one hand, SSM is able to analyze any observed channel network to quantify its geometry and its topology (to finally infer the most probable drivers of it). On the other hand, SSM provides a simulation tool based on OCN modelling in order to compute confidence levels on observed networks as well as to simulate new (virtual and realistic) river networks.
TOASTER	Toaster (Tree and planT Organs And STructures analysER) is an ImageJ's plugin, which manages different tools developed by Amap teams for the identification and geometrical characterization of anatomical structures from macro to microscopic images