Open Source Statistics Software - Page 13
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knowceans
Utility classes from maps to search engine to random samplers
Collection of several multi-purpose Java libraries. --- knowceans-tools = collection of Java utility classes. --- Highlights: --- org.knowceans.util: IndexQuickSort, TableList: apply order of one array/list to others +++ Vectors, ArrayUtils: array convenience +++ RandomSamplers, CokusRandom, ArmSampler, Densities: random sampling and distributions +++ Arguments: command line parser +++ StopWatch, Which, ExternalProcess: runtime stuff +++ ParallelFor: OpenMP workalike +++ PatternString, NamedGroupRegex: regex convenience --- org.knowceans.corpus: CorpusSearcher: full-text search engine +++ LabelNumCorpus: svmlight corpus storage and filtering +++ NIPS corpus with text, authors, labels and citations --- org.knowceans.map: InvertibleHashMultiMap, BijectiveHashMap: implement n:m and 1:1 relations. --- Other libs: knowceans-arms = port of the Adaptive Rejection Metropolis Sampler (ARMS) for arbitrary distributions +++ lda-j = port of lda-c, implementing Latent Dirichlet Allocation (LDA) -
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leave-kojack
Leave-k-out-Jackknife Pearson correlation
In general, Pearson correlation coefficients can be quite error-prone to outliers, thus Jackknifing may be helpful. I could not find any useful implementation for calculating more than leave-1-out Jackknife Pearson correlation coefficients. 'leave-kojack' offers an implementation for Jackknife Pearson correlation with dynamic values of k, i.e. leave-k-out Pearson correlation. -
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libcomposition
A C library to handle compositional (=closed) data, like proportions.
Inspired by Aitchison 2003 (http://www.amazon.com/The-Statistical-Analysis-Compositional-Data/dp/1930665784/) this library aims to make compositional data analysis rigorously. -
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libfgen
Library for optimization using a genetic algorithm or particle swarms
libfgen is a library that implements an efficient and customizable genetic algorithm (GA). It also provides particle swarm optimization (PSO) functionality and an interface for real-valued function minimization or model fitting. It is written in C, but can also be compiled with a C++ compiler. Both Linux and Windows are supported. -
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mapgraph
Massively Parallel Graph processing on GPUs -- now part of Blazegraph
Mapgraph is SYSTAP’s disruptive new technology to exploit the main memory bandwidth advantages of GPUs. The early work was co-developed with the University of Utah SCI Institute and has its pedigree in the UINTAH software running on over 750M cores on the TITAN Super Computer. Today, SYSTAP has commercialized this technology into it’s Blazegraph Accelerator and Blazegraph HPC products. Checkout our options for GPU acceleration of graphs or contact us to learn more: https://www.blazegraph.com/product/gpu-accelerated/. The early work was released under the Apache 2 open source license and is available on here at Sourceforge. This work was (partially) funded by the DARPA XDATA program under AFRL Contract #FA8750-13-C-0002 and DARPA Contract #D14PC00029. -
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mathSuite
Powerful Calculus Environment and Matrices Handling Engine
mathSuite is a very powerful Mathematical Suite which deals principally with complex algebric and geometric operations. It is powered by the fabulous ExprEval C Parser. The main purpose of this project is fast math-oriented algorithm virtualization, with an optimized direct text interface. Also it gives you a very powerful and fast Calculus Environment which let you handle easily interchangeable variable lists, matrices, LOGS and Settings Layouts with optimized Items Lists Managing Engine. You'll also be able to execute your own scriptfiles with a basic math-oriented beta script language. Some feature regarding Matrices and Linear Algebra Operations are LU-Factorization, SVD Decomposition, Rank Calculator, Ill Condition Checking and more... There are also a very powerful Linear System Solver and Basic PRELoaded Functions Integrator Engine. -
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Python module to track the overall median of a stream of values "on-line" in reasonably efficient fashion.
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An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.
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metabnorm
A mixed model normalization method for metabolomics data
In metabolomics the goal is to identify and measure the concentrations of di fferent metabolites (small molecules) in a cell or a biological system. The metabolites form an important layer in the complex metabolic network, and the interactions between di fferent metabolites are often of interest. It is crucial to perform proper normalization of metabolomics data and here we share the code for a normalization approach based on a mixed model, with simultaneous estimation of a correlation matrix. The methodology is implemented in R. -
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minepy
Maximal Information-based Nonparametric Exploration
The minepy homepage has moved to http://minepy.readthedocs.io. The download page is now at https://github.com/minepy/minepy/releases. -
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modnlp-plugins
External plugins for modnlp/teccli
This is a general project for modnlp/teccli plugins, with focus on text visualizaton. -
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montyhall2
Monty Hall Problem (command line)
Monty Hall Problem (command line), written in pure C++, using Visual C++6. It uses another project of mine for random number generation (glhlib - Graphics Library Helper). I also added a JAVA version. The Java version is written with NetBeans. I assume you can get yourself any IDE and compile the .JAVA file. It runs on Windows, Linux, Mac OSX, whatever. -
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msp
mathSuite Speed & Matrix Stream Processor
This program is fundamentally a short-sized version of my mathSuite program: https://sourceforge.net/projects/mathsuite/ It includes all the functionalities of MSCenv (mathSuite Calculus Environment), such as inline variables and functions (mainly thanks to ExprEval), which you can use to perform expensive complex computations and store their results into runtime variables. You can perform also every Linear Algebra Operations included in mathSuite with new optimizations. -
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ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
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Matrix factorization is applied to the B-spline basis to construct an orthonormal basis. Data can be approximated by a linear combination of the orthonormal basis functions. Constraints are imposed such that the fitted function is linear at the boundary points, as in natural cubic spline.
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phcfM
R package for modelling anthropogenic deforestation
phcfM is an R package for modelling anthropogenic deforestation. It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time. -
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portas
Pequeno script em Python para provar o problema de Monty Hall
O jogo consiste no seguinte: Monty Hall (o apresentador) apresentava 3 portas aos concorrentes, sabendo que atrás de uma delas está um carro (prémio bom) e que as outras têm prêmios de pouco valor. Na 1ª etapa o concorrente escolhe uma porta (que ainda não é aberta); De seguida Monty abre uma das outras duas portas que o concorrente não escolheu, sabendo à partida que o carro não se encontra aí; Agora com duas portas apenas para escolher — pois uma delas já se viu, na 2ª etapa, que não tinha o prêmio — e sabendo que o carro está atrás de uma delas, o concorrente tem que se decidir se permanece com a porta que escolheu no início do jogo e abre-a ou se muda para a outra porta que ainda está fechada para então a abrir. Qual é a estratégia mais lógica? Ficar com a porta escolhida inicialmente ou mudar de porta? Com qual das duas portas ainda fechadas o concorrente tem mais probabilidades de ganhar? Por quê? -
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psignifit is a toolbox to fit psychometric functions and test hypotheses on psychometric data. This is version 3 which will now predominantly support python.
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PYthon RELiabilitY A python package implementing state-of-the-art numerical methods arising in the field of uncertainty quantification : from statistical inference to uncertainty propagation for various purposes.
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Implementation in Python of some of the statistical methods provided by "asurv", the survival analysis software.
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r2web
Software for medical statistics based on R
The open source software R enables a large number of statistical analyzes. The software R2web allows to use those R functions that are useful for medical students, with a web interface that facilitates the work of the student (it replaces line commands in R with checkboxes, radio buttons, etc. ). Un logiciel en ligne pour les statistiques pour la médecine, basé sur R. Le logiciel open source R permet de faire un grand nombre d'analyses statistiques. Avec R2web, seules les fonctions R utiles aux étudiants en médecine sont présentes, dans une version web avec une interface qui facilite le travail de l'étudiant (en remplaçant les lignes de commande sous R par des cases à cocher, des boutons radio, etc). -
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rcqp
R interface to the Corpus Query Protocol
Implements the Corpus Query Protocol as a package for the R statistical environment. It allows to query linguistic corpora and manipulate the data as native R objects. It is based on the CWB software.
