Logiciels scentifiques

ADSSpatial point patterns analysis with R. Perform first- and second-order multi-scale analyses derived from Ripley's K-function, for univariate, multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with test of statitical significance based on Monte Carlo simulations.
AMAPSimAMAPsim propose un noyau de simulation du développement architectural d'une plante interconnectable avec des applications externes.
CMPCMP, 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.
DiogeneDiogene allows an integrated biometrical analysis of observations on annual or perennial plants (in comparative trials or natural populations). It uses multivariable and non-orthogonal models. This sofware also deals with analysis of molecular markers which may be processed separately or jointly with other variables (GLM architecture). This property may be more generally extended to qualitative variables (for instance, architectural category) and quantitative traits (measurements). Graphical outputs in publication quality due to an interface with Gnuplot. Powerful subsets of Spatial Statistics and Data Analysis with associated dendrograms (7 clustering algorithms). The mechanism of resampling (jackknife and bootstrap) is completely automated and very fast. Diogene can simultaneously process up to 9999 variables which may be freely defined by the user, using a syntactic analyzer.
DYPALDYPAL 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.
IDAOIDentification des plantes Assistée par Ordinateur est un procédé utilisant un système de portrait robot, qui permet l'identification de plantes (arbres, adventices, pollens...) même jeunes ou incomplètes, pour des utilisateurs, spécialistes ou non de la botanique.
MHM (for Multiscale Heterogeneity Map)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@ntNoteL'application Pl@ntNote est un logiciel libre destiné au chercheur pour une gestion locale de ses données écologiques collectées sur le terrain. C'est un outil modulable basé sur les individus-plantes.
TOASTERToaster (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