Software Map
Tag cloud  Project Tree  Project List
ANOVA Bayesian Bioinformatics Bioinformatics & Biostatistics Biostatistics C++ Cancer Chemoinformatics Classification Clustering Copynumber DNA Ecology Economics Finance Genetics Machine Learning Machine learning Multiple Comparisons Multivariate Analysis Multivariate Regression Multivariate Techniques ODE Phylogeny R RForge Regression Time series Visualization Wholegenome bioinformatics biostatistics break detection categorical change detection classification clustering community ecology data mining database datasets dissimilarity distance distributions diversity dynamic systems ecological models ecology econometrics epidemiology finance gene expression generalized linear models graphics high dimentional data likelihood linear programming machine learning microarray missing data mixed effect models mixed model model comparison model estimation model selection movement multivariate multivariate regression multivariate statistics nonlinear models nonparametric optimization parametric model permutation tests phylogeny plotting political analysis prediction psychology raster regression reporting robust robust statistics simulation social networks soil spatial spatial autocorrelation spatial classes spatial data spatial methods spatial point patterns spatiotemporal species distribution models survival teaching text mining time series trajectory visualization
17 projects in result set.
A cookbook of epidemiological models  This package aims to provide a large, diverse set of mathematical models developed in R, including both deterministic and stochastic models, and approaches to parameter estimation.  
Tags: epidemiology, IBM, ODE, differential equations, dynamic systems, individualbased models, simulation  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20130508 13:59 
EcoVirtual  Tools for ecological model simulations to help teach ecological theory. It comprises two packages. (1) EcoVirtual: feature set of simulations; (2) RcmdrPluginEcoVirtual: plugin for Rcmdr inteface  
Tags: simulation, ecological models, virtual ecology, Rcmdr  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20110205 19:18 
First Passage Times  Simulation and inference for diffusion processes in the presence of thresholds.  
Tags: stochastic differential equations, first passage times, simulation, inference, thresholds, boundaries  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20120522 09:20 
Individualbased metapopulation model  This package provides functions to run an individualbased metapopulation model, which includes genetic dynamics of diploid individuals, and flexibly defined lifehistories.  
Tags: simulation, individualbasedmodel, metapopulation, dispersal, genetics  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20120718 10:30 
NetSim: A social network simulation tool  A tool to simulate social networks and individual behavior by combining different dynamic models.  
Tags: simulation, social networks  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20130110 15:10 
ODE Solvers Compiled OnDemand  The odeintr package generates compiled ODE solvers ondemand. It uses the Boost odeint library and Rcpp.  
Tags: C++, Ecology, Economics, Fast, Fisheries, Forestry, HPC, ODE, R, Rcpp, dynamic systems, ecological models, ordinary differential equations, simulation, solver  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20150506 21:14 
RRBS Simulation, Modeling and Analysis  The project provides scripts for the simulation, modeling, and analysis of RRBS methylation profiles. Users may generate biologically realistic RRBS datasets and apply a genomewide algorithm for the detection of differentially methylated regions.  
Tags: RRBS, methylation, epigenetics, simulation  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20130711 16:35 
Simulation of clustered multistate data  R functions implementing the simulation procedure proposed at http://www.slideshare.net/federicorotolo/acopulabasedsimulationmethodforclusteredmultistatesurvivaldata to generate survival data with a clustered and multistate structure.  
Tags: simulation, copula, frailty models, multistate models, competing risks models, biostatistics, clustering, survival  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20111203 10:40 
SoilR  The objective of this project is the development of an R package for modeling soil organic matter decomposition. The package contains a collection of different functions commonly used to represent soil organic matter dynamics.  
Tags: Ecology, ODE, dynamic systems, ecological models, ecology, simulation, soil  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20120117 15:38 
UMPIRE  UMPIRE provides tools to simulate realistic biological expression data. It includes additive and multiplicative noise, correlated expression, inactive genes, and a link to outcome data that incorporates the multihit cancer model.  
Tags: Bioinformatics, Cancer, Gene expression, bioinformatics, gene expression, simulation, simulations, synthetic dataset  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20140203 16:37 
Visual Inference Software Development  Convenient and readily available software is lacking for visualizing the process of statistical inference for various applications in statistical practice. The "logic" of inference, should be clearly depicted, if possible.  
Tags: Bayesian, likelihood, marginal likelihood, simulation, visualization  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20120411 12:56 
hawkes  Hawkes process simulation in one and several dimensions as well as parametric Hawkes process calibration to data  
Tags: Hawkes, simulation, moment calculation  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20120425 23:03 
memisc  This package provides functionality to present analysis results in (almost) publicationready format. Also some convenience tools for graphics, programming, and simulation are provided.  
Tags: data management, LaTeX, R, graphics, reporting, simulation, tables  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20130208 10:55 
senesceR  Simulation of an in vitro population of cells undergoing stochastic transition from replication to senescence.  
Tags: population, simulation, cell, replicative, senescence, cellular  
This project has not yet categorized itself in the Trove Software Map  Activity Percentile: 0 Activity Ranking: 0 Registered: 20120610 16:44 
simecol  Ecological Models with R  simecol allows to implement ecological models (ODEs, IBMs, ...) using a templatelike objectoriented stucture. It helps to organize scenarios and may also be useful for other areas.  
Tags: dynamic systems, differential equations, individualbased models, ODE, IBM, ecology, simulation, ecological models  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20080220 20:34 
spatial copula  This package is intended to provide the power of copulas to the spatial and spatiotemporal context. It will offer tools and functions to perform spatial analysis exploiting the possibility to fully model the whole dependence structure with copulas.  
Tags: copula, multivariate, simulation, spatial, spatial autocorrelation, spatial classes, spatial data, spatial methods, spatial regression  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20110321 17:39 
xergm  The xergm package implements eXtensions for Exponential Random Graph Models (ERGM), in particular temporal ERGMs via bootstrapped pseudolikelihood ("btergm") and generalized ERGMs for valueedged networks ("gergm").  
Tags: btergm, tergm, ergm, network, bootstrapping, dynamic, model, model estimation, simulation, sna, social networks, social network analysis, ERGM, TERGM, BTERGM, gergm, GERGM, xergm, XERGM  

Activity Percentile: 0 Activity Ranking: 0 Registered: 20140410 08:16 