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Revision as of 14:35, 22 March 2014

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Apophenia 'Apophenia' is a statistical library for C. It provides functions on the same level as those of the typical stats package (OLS, probit, singular value decomposition, &c.) but doesn't tie the user to an ad hoc language or environment. It uses the GNU Scientific Library for number crunching and SQLite for data management, so the library itself focuses on model estimation and quickly processing data. GPLv2
Autoclass AutoClass solves the problem of automatic discovery of classes in data (sometimes called clustering or unsupervised learning), as distinct from the generation of class descriptions from labeled examples (called supervised learning). It aims to discover the 'natural' classes in the data. AutoClass is applicable to observations of things that can be described by a set of attributes, without referring to other things. The data values corresponding to each attribute are limited to be either numbers or the elements of a fixed set of symbols. With numeric data, a measurement error must be provided. PublicDomain
Bc 'Bc' is an arbitrary precision numeric processing language. Its syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements. 'Bc' is a utility included in the POSIX P1003.2/D11 draft standard. This version does not use the historical method of having bc be a compiler for the dc calculator (the POSIX document doesn't specify how bc must be implemented). This version has a single executable that both compiles the language and runs the resulting 'byte code.' The byte code is not the dc language. GPLv2orlater
Cl-ana cl-ana is a library of modular utilities for reasonably high performance data analysis & visualization using Common Lisp. (Reasonably means I have to be able to use it for analyzing particle accelerator data). The library is made of various sublibraries and is designed in a very bottom-up way so that if you don't care about some feature you don't have to load it.

The functionality support so far are

  • Tabular data analysis: Read-write of large datasets stored in HDF5 files are supported, along with ntuple datasets, CSVs, and in-memory data tables. Users can add their own table types by defining 4 methods and extending the table CLOS type.
  • Histograms: Binned data analysis is supported with both contiguous and sparse histogram types; functional interface is provided via map (which allows reduce/fold) and filter.
  • Plotting: Uses gnuplot for plotting dataset samples, plain-old lisp functions, histograms, strings-as-formulae, and anything else the user wishes to add via methods on a couple of generics.
  • Fitting: Uses GSL for non-linear least squares fitting. Uses plain-old lisp functions as the fit functions and can fit against dataset samples, histograms, and whatever the user adds.
  • Generic mathematics: CL doesn't provide extendable math functions, so cl-ana provides these as well as a convenient mechanism (a single function) for using these functions instead of the non-extendable versions. Already included are error propogation and quantities (values with units, e.g. 5 meters) as well as a GNU Octave-style handling of sequences (e.g. (+ (1 2) (3 4)) --> (4 6)). GPLv3
Dap Dap is a small statistics and graphics package, based on C, that provides core methods of data management, analysis, and graphics commonly used in statistical consulting practice. Anyone familiar with basic C syntax can learn Dap quickly and easily from the manual and the examples in it. Advanced features of C are not necessary, although they are available. As of Version 3.0, Dap can read SBS programs, thereby freeing the user from having to learn any C at all to run straightforward analyses. The manual contains a brief introduction to the C syntax needed for C-style programming for Dap. Because Dap processes files one line at a time, rather than reading entire files into memory, it can be, and has been, used on data sets that have very many lines and/or very many variables. GPLv2orlater
Data Frame In the R language, a dataframe object is a way to group tabular data. The functions in this package allow the manipulation of data in a similar way in Octave. Dataframe objects in Octave can be created in a variety of ways (from other objects or from tabular data in a file) and then can be accessed either as matrix or by column name. This Octave add-on package is part of the Octave-Forge project. GPLv3orlater
DataStatix DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5.

Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come);

graphs from every data. GPLv3
Datamash Datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. it is designed to be portable and reliable, and aid researchers to easily automate analysis pipelines, without writing code or even short scripts. GPLv3orlater
Dinrhiw2 Primary aim of the dinrhiw is to be linear algebra library and machine learning

library. For this reason dinrhiw implements PCA and neural network codes. Currently, the neural network code only supports:

  • hamiltonian monte carlo sampling (HMC) and simple bayesian neural network
  • second order L-BFGS search
  • gradient descent (backpropagation)
As well as mathematical routines for arbitrary precision mathematics, hermite curve interpolation and many other things. GPLv3
KNIME KNIME [naim] is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. GPLv3 with exception
MLPACK MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. MLPACK contains the following algorithms: Collaborative Filtering, Density Estimation Trees, Euclidean Minimum Spanning Trees, Fast Exact Max-Kernel Search (FastMKS), Gaussian Mixture Models (GMMs), Hidden Markov Models (HMMs), Kernel Principal Component Analysis (KPCA), K-Means Clustering, Least-Angle Regression (LARS/LASSO), Local Coordinate Coding, Locality-Sensitive Hashing (LSH), Logistic regression, Naive Bayes Classifier, Neighbourhood Components Analysis (NCA), Non-negative Matrix Factorization (NMF), Principal Components Analysis (PCA), Independent component analysis (ICA), Rank-Approximate Nearest Neighbor (RANN), Simple Least-Squares Linear Regression (and Ridge Regression), Sparse Coding, Tree-based Neighbor Search (all-k-nearest-neighbors, all-k-furthest-neighbors), Tree-based Range Search. LGPLv3orlater
Mastrave Mastrave is a free software library written to perform vectorized scientific computing and to be as compatible as possible with both GNU Octave and Matlab computing frameworks, offering general purpose, portable and freely available features for the scientific community. Mastrave is mostly oriented to ease complex modeling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series.

Semantic array programming

The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a reasonably well documented wrap around the main incompatibilities between those computing environments and by promoting a reasonably general idiom based on their common, stable syntagms. It also promotes the systematic adoption of data-transformation abstractions and lightweight semantic constraints to enable concise and reliable implementations of models following the paradigm of semantic array programming.

There are a couple of underlying ideas: library design is language design and vice versa (Bell labs); language notation is definitely a "tool of thought" (version), in the sense that there is a feedback between programming/mathematical notation and the ability to think new scientific insights. And perhaps ethic ones.

Science and society

Mastrave is free software, which is software respecting your freedom. As many other free scientific software packages, it is offered to the scientific community to also promote the development of a free society more concerned about cooperation rather than competitiveness, heading toward knowledge and culture freedom.

Such a vision implies the possibility for motivated individuals to freely access, review and contribute even to the cutting-edge academic culture. This possibility relies on the development of tools and methodologies helping to overcome economic, organizational and institutional barriers (i.e. knowledge oligopolies) while systematically promoting reproducible research. This is a long-term goal to which the free software paradigm can and has been able to actively cooperate. GPLv3orlater
Mcsim MCSim is a simulation and statistical inference tool for algebraic or differential equation systems. While other programs have been created to the same end, many of them are not optimal for performing computer intensive and sophisticated Monte Carlo analyses. MCSim was created specifically to perform Monte Carlo analyses in an optimized, and easy to maintain environment. GPLv3orlater
MedianTracker MedianTracker supports efficient median queries on and dynamic additions to a list of values. It provides both the lower and upper median of all values seen so far. Any __cmp__()-able object can be tracked, in addition to numeric types. add() takes log(n) time for a tracker with n items; lower_median() and upper_median() run in constant time. Since all values must be stored, memory usage is proportional to the number of values added (O(n)). Expat
Opennn OpenNN is a class library written in C++ which implements neural networks.

The library is intended for advanced users, with high C++ and machine learning skills. OpenNN provides an effective framework for the research and development of data mining and predictive analytics algorithms and applications.

OpenNN is based on the most popular neural network model, the multilayer perceptron. The package comes with unit testing, many examples and extensive documentation.

The library has been designed to learn from data sets. Some typical applications here are function regression (modelling), pattern recognition (classification) and time series prediction (forecasting).

OpenNN is being developed by Intelnics, a company specialized in the development and application of neural networks. LGPLv3
OptionMatrix These calculators are real-time multi-model option chain pricers with analytics and interactive controls. optionmatrix is the GTK+ graphical user interface version and optionmatrix_console is the Curses version. Both programs feature: greeks, decimal date to real-date translations, real-date to decimal date translations, real-time time bleeding, configurable option expiration date engines, calendars, strike control systems, tickers and over 168+ option models. optionmatrix also supports: spreads, bonds, term structures, cash flow editing, source code viewing and text exporting. GPLv3orlater
Orange Orange is a GPL visual programming software suite, featuring widgets for interactive data visualization, statistical data analysis, machine learning, text mining, association rules and frequent pattern ming, data fusion, and data mining in general. GPLv3orlater
Papertrail Papertrail is a Ballot Counting Software. It helps scanning and counting regular paper ballots as known from common election situations. It is Free Software, licensed via the GPLv3, to make the election process as dependable as possible, but speeding up the manual counting process a lot. GPLv3orlater
Ploticus Produces full-color lineplots, bargraphs, histograms, scatterplots, pie graphs, rangebars, boxplots, tables, tabular plots etc. Many labeling and style features. Produce graphs for publications, slides, posters, web pages and intranets. Plots from tabular data sets. Handles numeric, date, time, and alphanumeric data. Script-driven, non-interactive. Can render in Postscript, PNG, GIF, or X11. GPLv2orlater
Plotutils The GNU plotutils package contains software for both programmers and technically oriented users. Its centerpiece is the libplot/libplotter, a C/C++ function lib for exporting 2-D vector graphics in many file formats (including WebCGM format, recommended by the graphics Activity of the W3 Consortium). It can also do vector graphics animations, has thread-safe APIs, and supports the use of Posix threads (if available). The program also contains the following command-line programs for plotting scientific data:
  • graph- plots 2-D datasets or data streams in real time
  • plot- translates metafile formats to any of the other formats
  • tek2plot- translates legacy Tektronix data to any of the above formats
  • pic2plot- translates the pic language to any of the other formats
  • plotfont- displays character maps of the fonts available in the above formats.
  • spline- spline interpolation of data
  • ode- numerically integrates ordinary differential equations GPL
PredictionIO PredictionIO is a free software Machine Learning server system. It enables developers and data engineers to build smarter web and mobile applications through a simple set of APIs. Admin UI is provided for developers to select and tune algorithms. AGPLv3
Pspp PSPP is a program for statistical analysis of sampled data. It is a free software replacement for IBM SPSS.

It is a powerfull tool which can be used for exploratory data analysis, hypothesis testing, data preprocessing and visualisation. Available procedures include t-test, anova, linear and logistic regression, non-parametric tests, factor analysis, principle components analysis, cluster analysis, receiver operating characteristic and many more.

It can be used either with a command line or graphical user interface. GPLv3orlater
PuffinPlot PuffinPlot is a user-friendly, cross-platform program which analyses and plots palaeomagnetic data. It provides several plot types and analysis functions commonly used in palaeomagnetism, user-configurable graph layout, CSV data export, and SVG and PDF graph export. It has facilities for both interactive and bulk analysis, and can also be controlled and extended using any JVM-based scripting language (including Python). PuffinPlot is written in Java. GPLv3orlater
PyChem The purpose of this software is to provide a simple to install and easy to use graphical interface to multivariate algorithms.
The package currently supports: storage of supporting experimental data (metadata); data pre-processing; principal components analysis (PCA); discriminant function analysis (DFA,CVA,LDA,DA); cluster analysis; partial least squares regression (PLSR, PLS1); genetic algorithm (GA) based variable selector coupled to PLS and DFA. GPLv2orlater
Sage SAGE is a framework for number theory, algebra, and geometry computation that is initially being designed for computing with elliptic curves and modular forms. The long-term goal is to make it much more generally useful for algebra, geometry, and number theory. SAGE provides a (Python) interpreter interface to several important C/C++ libraries:
  • MPFR -- real number arithmetic,
  • NTL -- Victor Shoup's number theory library,
  • GMP -- arbitrary precision integer and floating point arithmetic package.
  • These systems come with SAGE, and there is an interface to each:
  • GAP -- group theory and combinatorics
  • PARI -- algebraic number theory
  • Singular -- polynomial computations and algebraic geometry
  • Maxima -- symbolic algebra GPLv2
SalStat SalStat is an small application for the statistical analysis of scientific data (with a special concentration on psychology). It can already do 18 kinds of descriptive statistics, t tests (paired, unpaired and one sample), 3 kinds of correlations linear regression and point biserial tests, and single factor anova (both within and between subjects). Data is entered on an easy-to-use datagrid like a spreadsheet, and all the analyses are driven by menus and dialog boxes. Output can be formatted to HTML. GPLv2orlater
Statist Statist is a small and portable statistics program written in C. It is terminal-based, but can utilise GNUplot for plotting purposes. It is simple to use and can be run in scripts. Big datasets are handled reasonably well on small machines. GPLv2orlater
StatistX StatistX is a GUI frontend for the statistics program statist. Currently, it provides about 20 different statistical tests and regressions. Results are presented either as text or Gnuplot graphs. It is not intended to replace tools like R. GPLv2orlater
Statlib The goal of the project is to combine several python statistics modules into a single package. PublicDomain
TensorFlow TensorFlow™ is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well. Apache2.0
Vilno A full-featured statistics package needs data preparation software, to manipulate data and prepare data for analysis. This software package, called Vilno, is data transformation software. It can be used instead of the SAS datastep for data transformation. It can be used to clean and prepare data before importing the derived data into R ( a statistics package using the S programming language ). GPLv2

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