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analysis-and-writing-tools

Software for research, analysis and writing is often costly to purchase but high quality free and/or Open Source software is available and is often as good as, and sometimes better, than the commercial equivalent. Here we provide information on some of the best software tools of which we are aware. The Editor's pick is marked with **. If you know of good tools that we haven't mentioned, please let us know!

Analysis & statistics
Bibliography, writing & research tools
Data
Geographical information systems
Graphics
Operating systems


Analysis & statistics

Density estimates the density or size of a population from capture–recapture data collected using an array of detectors (such as camera-traps).  Requires Windows (or can be run as the R package secr under Windows, Mac or Linux).

Distance allows you to design and analyse distance sampling surveys of wildlife populations.  Requires Windows (but many of the components are R packages, which can be run under Windows, Mac or Linux).

EstimateS computes a variety of biodiversity functions, estimators and indices based on biotic sampling data. Some features require species relative abundance data, others only species presence/absence data.   Requires Windows or Mac.

Genstat for Teaching and Learning is a free version of GenStat designed to cover the statistical analyses that are needed in schools or in a university undergraduate course.  Requires Windows.

Instat is a general statistical package that is simple to use. Includes special facilities for the processing of climatic data.  Requires Windows.

MARK is for parameter estimation using data from marked individuals. Requires Windows (but known to run under emulation or on a virtual machine on Mac or Linux).

MYSTAT is statistical software designed specifically for use by students. It has many of the core statistical functions available in SYSTATRequires Windows.

R** is a software environment for statistical computing and graphics. Widely used by conservationists and ecologists, it provides a variety of statistical and graphical techniques and has many additional packages, including some for ecological analysis. R is complex but much help is available, both with the system itself and from elsewhere. The RStudio graphical desktop is our favourite way of accessing RRequires Windows, Mac or Linux.

SSC-Stat is a statistical add-in for Excel, strengthening the its data management, graphics and descriptive statistics.  Requires Windows and Excel.

Veusz** is our favourite scientific plotting and graphing package. It is easy to learn and use and produces publication-ready SVG, postscript and PDF output.  Requires Windows, Mac or Linux.

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Bibliography, writing & research tools

Beall's List of Potential, possible or probable predatory scholarly open-access journals.

Directory of Open Access Journals is a directory of open access journals, defined as journals that do not charge readers or their institutions to access content. The list aims to include all open access scientific and scholarly journals that use a quality control system (but note that some of the journals on this list are also on Beall's List).

Google Docs** is a system to create documents, spreadsheets and presentations online, and is useful for sharing and collaboration. Files can be uploaded and downloaded in many standard formats.

Google Scholar provides a simple way to search for scholarly literature across many disciplines and sources (but beware that it also indexes material from journals on Beall's List).

Mendeley is a bibliography tool for organizing and citing articles and for storing PDFs.  Requires Windows, Mac or Linux.

LibreOffice** and the related OpenOffice are office software suites. They can read and write files from many office software packages and can be used with ZoteroRequires Windows, Mac or Linux.

Zotero** is one of our favourite software tools. It helps you collect, manage and cite research sources, can capture citation information from web pages, store PDFs, document files, images, links and web pages, integrates with LibreOffice and Microsoft Word, and can download references directly from Google Scholar and other resources.  Requires Windows, Mac or Linux.

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Data

Many of the following sources provide data, in shape file, GeoTIFF and other formats for use with QGIS or other Geographical Information Systems.

ARKive is a collection of thousands of videos, images and fact-files illustrating the world's species.

Free spatial data** includes country and continental level, global climate, species occurrence and elevation data, and LandSat images. If you require only administrative areas use the Global Administrative Areas spatial database, which is more recent.

Freshwater Ecoregions of the World provides a global biogeographic regionalization of the Earth's freshwater biodiversity.

Global 200 is an analysis of global patterns of biodiversity to identify the terrestrial, freshwater and marine ecoregions that harbour exceptional biodiversity.

Global Administrative Areas** is a spatial database (v. 2.0) of global administrative areas and boundaries.

Global Biodiversity and Information Facility provides open access to biodiversity data.

Global Lakes & Wetlands Database contains global spatial information on large lakes and reservoirs, smaller water bodies, and wetlands.

IUCN Red List of Threatened Species provides conservation status information for taxa that have been globally evaluated using the IUCN Red List Categories and Criteria, including spatial data for taxonomic groups that have been comprehensively assessed.

Marine Ecosystems of the World is a biogeographic classification of the world's coasts and shelves.

Natural Earth** is a public domain map dataset available at 1:10m, 1:50m, and 1:110 million scales, with integrated vector and raster data.

Terrestrial Ecoregions of the World is a biogeographical regionalization of the Earth's terrestrial biodiversity.

UNEP Environmental Data Explorer contains >500 variables, as national, subregional, regional and global statistics or as geospatial data sets, covering themes such as freshwater, population, forests, emissions, climate, disasters, health and GDP.

USGS Earth Explorer allows you to query and download satellite images, aerial photographs and digital elevation and other data. To download data you need to create an account, which is free.

World Database on Protected Areas provides a comprehensive dataset on protected areas worldwide, including map layers.

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Geographical Information Systems

ArcGIS Explorer performs basic functions such as view, navigate and query map data.  Requires Windows.

DIVA-GIS is particularly useful for mapping and analysing biodiversity data.  Requires Windows or Mac.

Google Earth lets you view satellite imagery, maps and terrain, and add layers (see, for example, the WWF Project layer).  Requires Windows, Mac or Linux.

GRASS is useful for geospatial data management and analysis, image processing, graphics/map production, spatial modelling, and visualization.  Requires Windows, Mac or Linux.

gvSIG can capture, store, handle, analyse and deploy any kind of referenced geographic information. Requires Windows, Mac or Linux.

OSGeo-Live is a self-contained bootable DVD, USB thumb drive or virtual machine that allows you to try a wide variety of free, open source geospatial software without installing anything. 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. Requires Windows, Mac or Linux.

Quantum GIS** lets you browse and create map data. It supports many common spatial data formats and has plug-ins for a range of tasks, such as obtaining Landsat data and displaying tracks from your GPS. Requires Windows, Mac or Linux.

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Graphics

For editing graphics it is useful to have two pieces of software. A raster (bitmap) graphics editor for photographs and other images that are in raster format, and a vector graphics editor for figures and maps that are in vector format. A raster graphics image is bound to a specific resolution and stores an image as a grid of pixels. Vector graphics is a resolution-independent description of shapes and objects; a rasterization engine uses this information to determine how to plot each line and curve at any resolution or zoom level. Raster graphics are better for photographs and some kinds of artistic drawings, and vector graphics are more suitable for technical illustrations such as scientific figures and maps. It is sometimes useful to export an illustration or figure in vector format (e.g. scalable vector graphics or postscript) from a scientific graphics package or GIS and do final editing in a vector graphics editor.

Gimp** is a raster graphics editor that can edit files in TIF, JPG, PNG and other raster formats.  Requires Windows, Mac or Linux.

Inkscape** is a vector graphics editor that uses the W3C standard scalable vector graphics file format.  Requires Windows, Mac or Linux.

IrfanView is a graphics viewer and converter (it is useful, for example, for viewing or printing a postscript file exported from GIS software, to check that the file has the correct appearance).  Requires Windows.

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Operating systems

Open Source Linux operating systems (including Ubuntu**, Kubuntu, Fedora and openSUSE) are increasingly used by conservationists and ecologists. A Linux system normally include software such as LibreOffice, and many of the software tools mentioned above are available for Linux. If you have an ageing computer with low resources you could use Xubuntu, which is a version of Ubuntu designed to run on older computers. If you need to run Windows software you can use Wine, which can run Windows software under Linux.  Requires A downloaded image for the required operating system, which then needs to be written to a CD or thumb drive and used to install the chosen operating system.

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