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Disclaimer

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The following resources are provided for reference purposes only. Their inclusion on this Web page, created by EcoC²S/Irucka Embry, does not represent any endorsement on the part of EcoC²S/Irucka Embry nor does it represent their endorsement of EcoC²S/Irucka Embry. The use of any of the listed software libraries, programs, tools, etc. and the interpretation of any results obtained remains the responsibility of the user. As well, the use of any of the resources and the interpretation of any results obtained remains the responsibility of the user. [This disclaimer is a revised version of the one found online at Internet Finite Element Resources (IFER).]



Irucka Embry’s R Packages & R Contributions to Existing Projects

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Irucka Embry’s R Examples

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Irucka Embry’s R Trainings

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R Applications

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The R programming language can be used in a variety of ways, such as, but not limited to:



R Resources

R Introduction and Tutorials

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Applications built with R as a back-end

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Other R Resources

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CRAN Task Views

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R GUIs (Graphical User Interface) — Using R with a GUI

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R for Users of other Statistical Software

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R for Users of other Applications & Programming Languages (GNU Octave/MATLAB®, Python, Databases, Spreadsheet Applications, etc.)

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Why you should ditch Microsoft Excel

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Connecting R to and from other Programming Languages & Applications

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R and GNU/Linux / *NIX Command Line Tools (R can process system commands too)

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Data Analysis and Large Data with R

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Data Visualization (Plotting/Graphing) with R

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GIS and R Resources

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Creating Documents, Presentations, and Reports with R and friends

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R and Reproducible Research

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Programming with R

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Regular Expressions (Advanced Find/Replace)

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Develop R (G)UIs [(Graphical) User Interface]

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R Packages

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Creating R Packages

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R Package Repositories

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Software Testing and Debugging

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STEM (Science, Technology, Engineering, and Mathematics) and R

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Time Series Analysis and R

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Probability, Statistics, and R

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Multivariate Statistics and R

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USGS and R

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EGRET/WRTDS

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(Eco)Hydrology Applications with R

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Non-R software and resources

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  • EcoC²S [Irucka Embry): Alternatives to Proprietary, Freedom- and Privacy-Deleting Technologies: Business Intelligence (BI)
  • The National Network of Reference Watersheds is a collaborative and multipurpose network of minimally disturbed watersheds and monitoring sites. The purpose of this website is to allow users to search the NNRW database of reference watersheds, to identify watersheds of interest, and download watershed information and water quality data. The current scope of the network is limited to freshwater streams. Membership in the network is voluntary and open to individuals, agencies, and institutions interested in participating in monitoring and (or) research in minimally disturbed and pristine watersheds.
  • PEST: Model-Independent Parameter Estimation and Uncertainty Analysis. PEST is the industry standard software package for parameter estimation and uncertainty analysis of complex environmental and other computer models.
  • The OpenFLUID project aims at building and distributing a software platform dedicated to modelling of complex landscape systems, mainly focused on fluxes.
  • Community Surface Dynamics Modeling System (CSDMS)
  • Data Science Toolkit
  • NASA Goddard Institute for Space Studies (GISS): Software Tools
  • US EPA: Water Quality Analysis Simulation Program (WASP)
  • MHYDAS (Modélisation Hydrologique Des AgroSystèmes) is an hydrological model for water exchanges, pollutants and erosion transport in cultivated landscapes
  • AGricultural Non-Point Source Pollution Model (AGNPS) is a joint USDA - Agricultural Research Service (ARS) and - Natural Resources Conservation Service system of computer models developed to predict non point source pollutant loadings within agricultural watersheds. It contains a continuous simulation surface runoff model designed to assist with determining BMPs, the setting of TMDLs, and for risk & cost/benefit analyses.
  • USGS Software
  • USGS Water Software: Explore all water resources applications software to include general use, water quality and chemistry, groundwater, statistics and graphics, and surface water.
  • USGS Water Resources: Applications Software
  • PyFlo is an open-source library written in Python for performing hydraulic and hydrology stormwater analysis. Features include network hydraulic grade analysis and time/iteration based storage and flood routing simulations.
  • Precipitation Runoff Modeling System (PRMS) is a deterministic, distributed-parameter, physical process based modeling system developed to evaluate the response of various combinations of climate and land use on streamflow and general watershed hydrology.
  • Aquatic Informatics: Water Monitoring & Analysis Software
  • Aquatic Informatics: AQUARIUS lets you understand the hydrology hiding within your data by providing powerful tools that are easy to deploy and use. By allowing you to manage all of your environmental monitoring data in one place, AQUARIUS enables higher data integrity and defensibility, greater confidence in your data and decisions, ongoing open and flexible control of your data and customized reporting and publishing that matches your requirements.
  • Kentucky Water Science Center: Water Availability Tool for Environmental Resources (WATER) is a spatially distributed, object oriented, decision support system that combines the expertise of numerous hydrologists, pedologists, computer scientists, and other discipline experts into a user-friendly computer application for managing water resources. The application is an expandable and flexible platform that allows future modifications or extensions, to be added (the hydrologic model “TOPMODEL” is the first of these); thereby, continually increasing the power and utility of the application. WATER was developed within the USGS Center for Applied Hydrologic Solutions (CAHS).
  • Bayesian hydraulic rating curve programs
  • British Geological Survey (BGS): AquiMod is a simple, lumped-catchment groundwater model. It simulates groundwater level time-series at a point by linking simple algorithms of soil drainage, unsaturated zone flow and groundwater flow. It takes time-series of rainfall and potential evapotranspiration as input, and produces a time-series of groundwater level. Hydrographs of flows through the outlets of the groundwater store are also generated, which can potentially be related to river flow measurements. The software is easy to use and should be accessible to users who are new to the field of groundwater/hydrological modelling. The model is configured using a series of text files and run through the command line.
  • Notepad++ is a free (as in “free speech” and also as in “free beer”) source code editor and Notepad replacement that supports several languages. Running in the MS Windows environment, its use is governed by GPL License.
  • Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is distributed free as charityware. If you find Vim a useful addition to your life please consider helping needy children in Uganda.
  • Vimdoc: the online source for Vim documentation
  • GNU Emacs is an extensible, customizable text editor—and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
  • Crimson Editor is a professional source code editor for Windows. (It is no longer developed, but it is still very useful.)
  • Emerald Editor is (being) designed to be an open-source multi-purpose, functional text editor, inspired heavily by Crimson Editor. It is available under the GNU General Public License. (It is no longer developed, but it is still very useful.)
  • Antiword is a free MS Word reader for Linux and RISC OS. There are ports to FreeBSD, BeOS, OS/2, Mac OS X, Amiga, VMS, NetWare, Plan9, EPOC, Zaurus PDA, MorphOS, Tru64/OSF, Minix, Solaris and DOS. Antiword converts the binary files from Word 2, 6, 7, 97, 2000, 2002 and 2003 to plain text and to PostScript™.
  • Pandoc: a universal document converter
  • LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents. LaTeX is available as free software.
  • MiKTeX is an up-to-date implementation of TeX/LaTeX and related programs for Windows (all current variants). TeX is a typesetting system written by Donald Ervin Knuth who says that it is “intended for the creation of beautiful books - and especially for books that contain a lot of mathematics”.
  • Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.
  • Scribus is an Open Source program that brings professional page layout to Linux, BSD UNIX, Solaris, OpenIndiana, GNU/Hurd, Mac OS X, OS/2 Warp 4, eComStation, Haiku and Windows desktops with a combination of press-ready output and new approaches to page design. Underneath a modern and user-friendly interface, Scribus supports professional publishing features, such as color separations, CMYK and spot colors, ICC color management, and versatile PDF creation.
  • Inkscape: An Open Source vector graphics editor, with capabilities similar to Illustrator, CorelDraw, or Xara X, using the W3C standard Scalable Vector Graphics (SVG) file format. Inkscape supports many advanced SVG features (markers, clones, alpha blending, etc.) and great care is taken in designing a streamlined interface. It is very easy to edit nodes, perform complex path operations, trace bitmaps and much more. We also aim to maintain a thriving user and developer community by using open, community-oriented development.
  • GIMP is an acronym for GNU Image Manipulation Program. It is a freely distributed program for such tasks as photo retouching, image composition and image authoring. It has many capabilities. It can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible. It is designed to be augmented with plug-ins and extensions to do just about anything. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.
  • Hierarchical Data Format: From Wikipedia, the free encyclopedia
  • The HDF Group: Information, Support, and Software
  • The HDF Group: Why use HDF?
  • The HDF Group: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
  • NetCDF: From Wikipedia, the free encyclopedia
  • NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
  • NoSQL Databases
  • Structured Query Language (SQL): From Wikibooks, open books for an open world
  • SQLCourse.com: This unique introductory SQL tutorial not only provides easy-to-understand SQL instructions, but it allows you to practice what you learn using the on-line SQL interpreter. You will receive immediate results after submitting your SQL commands. You will be able to create your own unique tables as well as perform selects, inserts, updates, deletes, and drops on your tables. This SQL tutorial currently supports a subset of ANSI SQL. The basics of each SQL command will be covered in this introductory tutorial. Unless otherwise stated, the interpreter will support everything covered in this course. If you’re already familar with the basics of SQL, you can still use this as a refresher, and practice some SQL statements.
  • SQLCourse2.com: This unique SQL Tutorial is the “sequel” to the highly successful SQLCourse.com site and will provide you with more advanced easy-to-follow SQL Instruction and the ability to practice what you learn on-line with immediate feedback! You will receive immediate results on a web page after submitting your SQL Commands. This continuation course will provide you with critical need-to-know advanced features and clauses of the SELECT statement that weren’t supported in the previous SQLCourse.com site. Everything you learn here will be ANSI SQL compliant and should work with most SQL databases such as Oracle, SQL Server, mySQL, MS Access, Informix, Sybase, or any other ANSI SQL compliant database. If you’re already familar with the basics of SQL, you can still use this as a refresher, and practice some SQL statements.
  • PostgreSQL: The world’s most advanced open source database
  • PostGIS is a spatial database extender for PostgreSQL object-relational database. It adds support for geographic objects allowing location queries to be run in SQL.
  • Converting MySQL to PostgreSQL: From Wikibooks, open books for an open world
  • MariaDB: An enhanced, drop-in replacement for MySQL.
  • MySQL Big Resource Forum
  • MySQL: From Wikibooks, open books for an open world
  • MariaDB: AskMonty KnowledgeBase
  • MariaDB Crash Course by Ben Forta
  • MariaDB: From Wikibooks, open books for an open world
  • H2 is a Java SQL database
  • HSQLDB (HyperSQL DataBase) is the leading SQL relational database engine written in Java. It offers a small, fast multithreaded and transactional database engine with in-memory and disk-based tables and supports embedded and server modes. It includes a powerful command line SQL tool and simple GUI query tools. HSQLDB supports the widest range of SQL Standard features seen in any open source database engine: SQL:2011 core language features and an extensive list of SQL:2011 optional features. It supports nearly full Advanced ANSI-92 SQL (BNF format). Many extensions to the Standard, including syntax compatibility and features of other popular database engines, are also supported.
  • Poppler is a PDF rendering library based on the xpdf-3.0 code base.
  • Extract tables from PDF files. tabula-extractor is the table extraction engine that powers Tabula, now available as a library and command line program.
  • Tabula: Extract Tables from PDFs
  • Tesseract is probably the most accurate open source OCR engine available. Combined with the Leptonica Image Processing Library it can read a wide variety of image formats and convert them to text in over 60 languages. It was one of the top 3 engines in the 1995 UNLV Accuracy test. Between 1995 and 2006 it had little work done on it, but since then it has been improved extensively by Google. It is released under the Apache License 2.0.
  • Cognitive OpenOCR (Cuneiform)
  • YAGF is a graphical front-end for cuneiform and tesseract OCR tools. With YAGF you can open already scanned image files or obtain new images via XSane (scanning results are automatically passed to YAGF). Once you have a scanned image you can prepare it for recognition, select particular image areas for recognition, set the recognition language and so no. Recognized text is displayed in a editor window where it can be corrected, saved to disk or copied to clipboard. YAGF also provides some facilities for a multi-page recognition.
  • FreeOCR is a free Optical Character Recognition Software for Windows and supports scanning from most Twain scanners and can also open most scanned PDF’s and multi page Tiff images as well as popular image file formats. FreeOCR outputs plain text and can export directly to Microsoft Word format.
  • OCRopus™ is an OCR system written in Python, NumPy, and SciPy focusing on the use of large scale machine learning for addressing problems in document analysis.
  • GOCR is an OCR (Optical Character Recognition) program, developed under the GNU Public License. It converts scanned images of text back to text files. Joerg Schulenburg started the program, and now leads a team of developers. GOCR can be used with different front-ends, which makes it very easy to port to different OSes and architectures. It can open many different image formats, and its quality have been improving in a daily basis.
  • PDF OCR Wrapper: This is a wrapper written in Java that allows to recursively iterate a directory structure and call an OCR engine on each found PDF on the condition that it hat not yet been called for that PDF. It works well with the ABBYY OCR Engine for Linux.
  • EcoC²S [Irucka Embry): EcoC²S Online Resources: Free and Open Source Software for Architects, Designers, Engineers, Mathematicians, Scientists, and Statisticians (Irucka Embry)
  • Perl 5 is a highly capable, feature-rich programming language with over 27 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
  • PDL (“Perl Data Language”) gives standard Perl the ability to compactly store and speedily manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing. PDL turns Perl in to a free, array-oriented, numerical language similar to (but, we believe, better than) such commerical packages as IDL and MatLab. One can write simple perl expressions to manipulate entire numerical arrays all at once. A simple interactive shell (perldl) is provided for use from the command line and a module (PDL) for use in Perl scripts.
  • Python is a programming language that lets you work quickly and integrate systems more effectively
  • SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
  • GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.
  • Scilab: The Free Software for Numerical Computation
  • Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. Julia’s Base library, largely written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace. IJulia, a collaboration between the Jupyter and Julia communities, provides a powerful browser-based graphical notebook interface to Julia.
  • Julia for R programmers by Douglas Bates, U. of Wisconsin-Madison, July 18, 2013 — [Requires PDF Software]
  • Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, sets, lists, vectors, matrices and tensors. Maxima yields high precision numerical results by using exact fractions, arbitrary-precision integers and variable-precision floating-point numbers. Maxima can plot functions and data in two and three dimensions.
  • The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more.
  • Beaker is a notebook-style development environment for working interactively with large and complex datasets. Its plugin-based architecture allows you to switch between languages or add new ones with ease, ensuring that you always have the right tool for any of your analysis and visualization needs.
  • The FEniCS Project is a collection of free software with an extensive list of features for automated, efficient solution of differential equations.
  • MATLAB program for plotting a Simplified Psychrometric Chart
  • Psychropy: A repository of Psychrometric calculation and plotting tools: This is currently a translated Excel VB calculator that I wanted to be able to use in python code with an added funtion to back out Dry bulb temps using humidity ratio and enthalpy. the original calculator can calculate any of 9 psychrometric variables based on two input variables and the pressure
  • CoolProp is an open-source, cross-platform, free property database based in C++ that includes pure fluids, pseudo-pure fluids, and humid air properties. CoolProp is an alternative to NIST REFPROP. Based on reference-accuracy equations of state and transport property correlations for refrigerants Water, CO2, R134a, Nitrogen, Argon, Ammonia, Air, R404a, R410a, Propane and many others. A selection of secondary working fluid properties are also available. Can also make use of REFPROP when available. In addition, calculations for Humid Air Properties based on ASHRAE RP-1485 are provided.
  • jamovi is a new “3rd generation” statistical spreadsheet. designed from the ground up to be easy to use, jamovi is a compelling alternative to costly statistical products such as SPSS and SAS. jamovi is built on top of the R statistical language, giving you access to the best the statistics community has to offer. would you like the R code for your analyses? jamovi can provide that too.
  • Stixbox, developed by Anders Holtsberg, is a statistics toolbox for Matlab, Octave, and Matcom/Mideva.
  • Mastrave is a free software library written to perform vectorized computation 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. 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. 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” (Iverson), in the sense that there is a feedback between programming/mathematical notation and the ability to think new scientific insights. And perhaps ethic ones.
  • Namazu is a full-text search engine intended for easy use. Not only does it work as a small or medium scale Web search engine, but also as a personal search system for email or other files.
  • Linux Basics by Jordan Hayes, Grant Brady & Thomas Girke, UC Riverside
  • EMBOSS (The European Molecular Biology Open Software Suite) is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
  • Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free.
  • Bokeh is a Python interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of novel graphics in the style of D3.js, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.
  • Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don’t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.
  • pyGtkPlot is a pygtk-based front-end for gnuplot. This project aims to a complete graphical front-end for gnuplot, capable not only of handling all its powerful features, but also of extending them by the introduction of new functionalities (like a LaTeX renderer and such…). It is the project owner’s opinion that gnuplot is a handy tool especially for scientists. This means that any major help to this project can come from experienced (python) programmers that are also physicists and/or mathematicians, because these people really need a program like gnuplot, and nobody better than them know what to require from a project like pyGtkPlot.
  • Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs.
  • SWRC Fit: The soil hydraulic parameters for analyzing water movement in variably saturated soil can be determined by fittig soil hydraulic model to a soil water retention curve. SWRC Fit performs nonlinear fitting of 5 soil hydraulic models to measured soil water retention curve; the relationship between the soil water potential and volumetric water content.
  • Cesium is a JavaScript library for creating 3D globes and 2D maps in a web browser without a plugin. It uses WebGL for hardware-accelerated graphics, and is cross-platform, cross-browser, and tuned for dynamic-data visualization. Cesium is open source under the Apache 2.0 license. It is free for commercial and non-commercial use.
  • USGS Global Visualization Viewer
  • NASA Goddard Institute for Space Studies (GISS): Panoply is a cross-platform application that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets.
  • The Open Source Geospatial Foundation (OSGeo)
  • OSGeo4W: This is the web site, wiki and issue tracking database for the OSGeo4W project. OSGeo4W is a binary distribution of a broad set of open source geospatial software for Win32 environments (Windows XP, Vista, etc).
  • OSGeo-Live is a self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything. It is composed entirely of free software, allowing it to be freely distributed, duplicated and passed around. It provides pre-configured applications for a range of geospatial use cases, including storage, publishing, viewing, analysis and manipulation of data. It also contains sample datasets and documentation.
  • FWTools is a set of Open Source GIS binaries for Windows (win32) and Linux (x86 32bit) systems produced by me, Frank Warmerdam (ie. FW). The kits are intended to be easy for end users to install and get going with. No fudzing with building from source, or having to collect lots of interrelated packages. FWTools includes OpenEV, GDAL, MapServer, PROJ.4 and OGDI as well as some supporting components. The FWTools kits also aims to track the latest development versions of the packages included as opposed to official releases. While this may mean the packages are less stable, it is intended to give folks a chance to use the latest and greatest. FWTools releases also are a means by which I make recent development version bug fixes available to a wider audience than would be prepared to build them from the source. With FWTools releases, I also endeavor to build in as many optional components as possible. Thus, I include support for ECW, JPEG2000, HDF and other file formats that require extra libraries. Linux FWTools releases are intended to be distribution and packaging system agnostic. They should install on pretty much any x86 style Linux system released within the last few years.
  • EcoC²S [Irucka Embry): Alternatives to Proprietary, Freedom- and Privacy-Deleting Technologies: Alternatives to Google Maps, etc. (Online and Offline)
  • USGS Maps: Our programs produce accurate geologic maps and 3-D geologic frameworks that provide critical data for sustaining and improving the quality of life and economic vitality of the Nation. They also organize, maintain, and publish the geospatial baseline of the Nation’s topography, natural landscape, built environment and more.
  • QGIS is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License.
  • QGIS Plugins Repository
  • QGIS Application - Hydrology and Hydraulic modelling: QGIS Issue Tracking
  • Geographic Resources Analysis Support System (GRASS) is a free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. GRASS is an official project of the Open Source Geospatial Foundation.
  • GRASS and Sextante: GRASS-Wiki
  • R statistics: GRASS (Geographic Resources Analysis Support System) GIS-Wiki
  • Hydrological Sciences: GRASS GIS Users Wiki
  • GRASS and SAGA: GRASS GIS Users Wiki
  • System for Automated Geoscientific Analyses (SAGA)
  • Utah Water Research Laboratory, Civil and Environmental Engineering, Utah State University: Terrain Analysis Using Digital Elevation Models (TauDEM) is a suite of Digital Elevation Model (DEM) tools for the extraction and analysis of hydrologic information from topography as represented by a DEM.
  • gvSIG is a Geographic Information System (GIS), that is, a desktop application designed for capturing, storing, handling, analyzing and deploying any kind of referenced geographic information in order to solve complex management and planning problems. gvSIG is known for having a user-friendly interface, being able to access the most common formats, both vector and raster ones. It features a wide range of tools for working with geographic-like information (query tools, layout creation, geoprocessing, networks, etc.), which turns gvSIG into the ideal tool for users working in the land realm.
  • gvSIG Community Edition (CE) is a community driven GIS project fork of gvSIG that will be bundled with SEXTANTE and GRASS GIS. gvSIG CE is a fully functional Open Source Desktop GIS that provides powerful visualization (including thematic maps, advanced symbology and labelling), cartography, raster, vector and geoprocessing in a single, integrated software suite.
  • uDig is an open source (EPL and BSD) desktop application framework, built with Eclipse Rich Client (RCP) technology
  • OpenJUMP GIS: The free, cross-platform and open source GIS for the World
  • Kalypso is an open source application for geospatial modelling and simulation. It is primarily developed to be a user friendly tool for GIS-based modelling and simulation of hydrological and hydraulic numerical models.
  • KalypsoBASE is a Desktop-GIS built on Eclipse. It’s focus lies on modelling gis data using GML Application-Schemata. Features contain generic dialogs based on GML, maps based on OGC’s SLD, and other tools like a charting framework or API for timeseries.
  • British Geological Survey (BGS) Groundhog Desktop GSIS (desktop geoscientific information system) is a graphical software tool developed by the environmental modelling directorate of BGS for the display of geological and geospatial information such as interpreted (correlated) geological cross sections, maps and boreholes. Groundhog Desktop is intended as a basic geoscientific information system (GSIS) — a software tool that facilitates the collation, display, filtering and editing of a range of data relevant to subsurface interpretation and modelling. You can use Groundhog Desktop to load and display certain types of borehole data, geological map linework, interpreted (correlated) cross sections and faults. It also supports reference data such as elevation models and images and has basic editing capabilities.
  • HYdrological Predictions for the Environment (HYPE) Open Source Community (OSC) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modelling and hydrological data prodution. The hypothesis is that more brains and more testing will result in better models and better code.
  • The nofdp Information and Decision Support System (IDSS) is an open source application for the interactive development of flood risk strategies and 1D hydrodynamic flood simulation. Additional modules for ecological and spatial analysis, multicriteria evaluation, flood risk maps, flood frequency, flood duration and communication are included.
  • ANUGA [Australian National University (ANU) and Geoscience Australia (GA)] is a Free & Open Source Software (FOSS) package capable of modelling the impact of hydrological disasters such as dam breaks, riverine flooding, storm-surge or tsunamis. ANUGA is based on the Shallow Water Wave Equation discretised to unstructured triangular meshes using a finite-volumes numerical scheme. A major capability of ANUGA is that it can model the process of wetting and drying as water enters and leaves an area. This means that it is suitable for simulating water flow onto a beach or dry land and around structures such as buildings. ANUGA is also capable of modelling difficult flows involving shock waves and rapidly changing flow speed regimes (transitions from sub critical to super critical flows).
  • The Penn State Integrated Hydrologic Model (PIHM) is a multiprocess, multi-scale hydrologic model where the major hydrological processes are fully coupled using the semi-discrete finite volume method. The model itself is “tightly-coupled” with PIHMgis, an open-source Geographical Information System designed for PIHM. The PIHMgis provides the interface to PIHM, access to the digital data sets (terrain, forcing and parameters) and tools necessary to drive the model, as well as a collection of GIS-based pre- and post-processing tools. Collectively the system is referred to as the Penn State Integrated Hydrologic Modeling System. The modeling system has been written in C/C++, while the GIS interface is supported by Qt. The Penn State Hydrologic Modeling System is open source software, freely available for download at this site along with installation and user guides.
  • HydroDesktop is a free and open source GIS enabled desktop application that helps you search for, download, visualize, and analyze hydrologic and climate data registered with the CUAHSI Hydrologic Information System.
  • HydroPy is a Python library for computational hydrology. It aims to become a full-featured computational hydrology while keeping the code as simple as possible in order to be comprehensible and easily extensible. HydroPy is written entirely in Python and require some external libraries.
  • OpenEV is a software library and application for viewing and analysing raster and vector geospatial data.
  • spatial-analyst.net is a non-commercial website intended for users interested in advanced use of geocomputational tools. The topics discussed generally belong to spatio-temporal data analysis sciences, digital cartography, geomorphometry, geostatistics, geovisualization, GPS tracking and navigation, raster-based GIS modelling and similar. Most of the articles presented are only supplementary materials to various research publications. Visitors of the website are kindly asked to refer to the peer-reviewed publications, when citing some of the materials, instead of referring to the URL of an article. All materials are prepared on an informative basis only. This is a wiki project, which obviously means that you can edit, extend and modify much of its content.
  • Software: spatial-analyst.net
  • Open Source Software Tools for Soil Scientists: University of California Davis Soil Resource Laboratory
  • GeographicLib is a small set of C++ classes for performing conversions between geographic, UTM, UPS, MGRS, geocentric, and local cartesian coordinates, for gravity (e.g., EGM2008), geoid height and geomagnetic field (e.g., WMM2015) calculations, and for solving geodesic problems. The emphasis is on returning accurate results with errors close to round-off (about 5-15 nanometers). New accurate algorithms for Geodesics on an ellipsoid of revolution and Transverse Mercator projection have been developed for this library. The functionality of the library can be accessed from user code, from the Utility programs provided, or via the Implementations in other languages.
  • libLAS is a C/C++ library for reading and writing the very common LAS LiDAR format. The ASPRS LAS format is a sequential binary format used to store data from LiDAR sensors and by LiDAR processing software for data interchange and archival.
  • rapidlasso GmbH: creators of LAStools, LASzip, and PulseWaves: Our LiDAR processing tools are widely known for their blazing speeds and high productivity. Our software combines robust algorithms with efficient I/O and clever memory management to achieve high throughput for data sets containing billions of points.
  • GeoDa Center for Geospatial Analysis and Computation: School of Geographical Sciences and Urban Planning, College of Liberal Arts and Sciences, Arizona State University (ASU)
  • PCRaster: Software for environmental modelling
  • GDAL (Geospatial Data Abstraction Library): ESRI Shapefile
  • Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf).
  • Python Shapefile Library (pyshp) library reads and writes ESRI Shapefiles in pure Python. You can read and write shp, shx, and dbf files with all types of geometry. Everything in the public ESRI shapefile specification is implemented. This library is compatible with Python versions 2.4 to 3.x.
  • Geo::ShapeFile: Perl extension for handling ESRI GIS Shapefiles.
  • GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. The related OGR library (which lives within the GDAL source tree) provides a similar capability for simple features vector data.
  • The OGR Simple Features Library is a C++ open source library (and commandline tools) providing read (and sometimes write) access to a variety of vector file formats including ESRI Shapefiles, S-57, SDTS, PostGIS, Oracle Spatial, and Mapinfo mid/mif and TAB formats. OGR is a part of the GDAL library.
  • PROJ.4 Cartographic Projections library originally written by Gerald Evenden then of the USGS.
  • AD Model Builder, or ADMB, is a powerful software package for the development of state-of-the-art nonlinear statistical models. ADMB is built around the AUTODIF Library, a C++ language extension which implements reverse mode automatic differentiation. A closely related software package, ADMB-RE, implements random effects in nonlinear models. ADMB was created by David Fournier and now continues to be developed by the ADMB Project, a creation of the non-profit ADMB Foundation. ADMB is free, open source, and available for Windows, Linux, MacOS, and Sun/SPARC.
  • Bayes Net Toolbox for Matlab
  • OpenBUGS (Bayesian inference Using Gibbs Sampling)
  • JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
  • MATJAGS: This interface allows JAGS (“Just Another Gibbs Sampler”) to be used in combination with Matlab. JAGS is a program for Bayesian hierarchical models using Markov chain Monte Carlo (MCMC) inference methods. JAGS is similar to the OpenBUGS and WinBUGS programs but can operate on a number of platforms including Windows and Max OS X.
  • MATBUGS is a Matlab interface for WinBugs and OpenBugs, which are programs for Gibbs sampling applied to hierarchical Bayesian models.
  • PMTK is a collection of Matlab/Octave functions, written by Matt Dunham, Kevin Murphy and various other people. The toolkit is primarily designed to accompany Kevin Murphy’s textbook, Machine learning: a probabilistic perspective, but can also be used independently of this book. The goal is to provide a unified conceptual and software framework encompassing machine learning, graphical models, and Bayesian statistics (hence the logo). (Some methods from frequentist statistics, such as cross validation, are also supported.) The toolbox is currently (December 2011) in maintenance mode, meaning that bugs will be fixed, but no new features will be added (at least not by Kevin or Matt). PMTK supports a large variety of probabilistic models, including linear and logistic regression models (optionally with kernels), SVMs and gaussian processes, directed and undirected graphical models, various kinds of latent variable models (mixtures, PCA, HMMs, etc), etc. Several kinds of prior are supported, including Gaussian (L2 regularization), Laplace (L1 regularization), Dirichlet, etc. Many algorithms are supported, for both Bayesian inference (including dynamic programming, variational Bayes and MCMC) and MAP/ML estimation (including EM, conjugate and projected gradient methods, etc.) PMTK builds on top of several existing packages, available from pmtksupport, and provides a unified interface to them. In addition, it provides readable “reference” implementations of many common machine learning techniques. The vast majority of the code is written in Matlab. (For a brief discussion of why we chose Matlab, Most of the code also runs on Octave, an open-source Matlab clone.) However, in a few cases we also provide wrappers to implementations written in C, for speed reasons. PMTK currently (October 2010) has over 67,000 lines of code. PMTK contains many demos of different methods applied to many different kinds of data sets. The demos are listed here, and the data is available from pmktdata (but will be downloaded automatically when a demo calls loadData).
  • pymc: Markov Chain Monte Carlo sampling toolkit. Bayesian estimation, particularly using Markov chain Monte Carlo (MCMC), is an increasingly relevant approach to statistical estimation. However, few statistical software packages implement MCMC samplers, and they are non-trivial to code by hand. pymc is a python package that implements the Metropolis-Hastings algorithm as a python class, and is extremely flexible and applicable to a large suite of problems. pymc includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics. pymc only requires NumPy. All other dependencies such as matplotlib, SciPy, pytables, sqlite or mysql are optional.
  • agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.
  • csvkit is a suite of utilities for converting to and working with CSV, the king of tabular file formats.
  • pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
  • MetaAnalyst: powerful meta-analysis software
  • Open MetaAnalyst
  • SimLab provides a free development framework for Sensitivity and Uncertainty Analysis. SimLab is a professional tool for model developers, scientists and professionals, to learn, use and exploit global uncertainty and sensitivity analysis techniques. The SimLab license encourages free non-commercial use.
  • GNU MCSim is a simulation package, written in C, which allows you to: design your own statistical or simulation models (eventually dynamic, via ODEs), perform Monte Carlo stochastic simulations, do Bayesian inference through Markov Chain Monte Carlo simulations.
  • MCS-libre Monte-Carlo Simulation Toolkit: Free C++ toolkit to facilitate Monte-Carlo simulation. This is a library covered under the LGPL. “MCS-libre” stands for “Monte Carlo Simulation - libre”.


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