Biodiversity and conservation planning
CODA (Mike Bedward) provides a greedy algorithm for the design and selection of networks of nature reserves or protected areas. It has been used in earlier reserve planning studies and as a teaching resource.
C-PLAN (Matthew Watts and Bob Pressey) is one the main tools for assisting the design of networks of nature reserves or protected areas. Its main feature is the calculation of continuous surfaces of irreplaceability on maps. It can be coupled with MARXAN and has been used for major reserve planning studies, as a teaching resource and for research into conservation planning methods.
LQGraph (Trevon Fuller and Sahotra Sarkar) presents a graph-theoretic approach to enhance efficiently structural connectivity from a selected scattered set of sites.
MARXAN (Ian R. Ball and Hugh P. Possingham) delivers decision support for reserve system design. It finds reasonably efficient solutions to the problem of selecting a system of spatially cohesive sites that meet a suite of biodiversity targets. Given reasonably uniform data on species, habitats and/or other relevant biodiversity features and surrogates for a number of planning units (as many as 20,000) MARXAN minimizes the cost while meeting user-defined biodiversity targets.
MultCSync (Sahotra Sarkar, Justin Garson, and Alexander Moffett) implements several techniques to deal with trade-offs between alternative biodiversity-valued solutions and social criteria, for use in conjunction with reserve selection software packages that ensure biodiversity surrogate representation. These packages include ResNet (Kelley et al. 2002; Sarkar et al. 2002), C-Plan (Pressey 1999), and Marxan (Ball and Possingham 2000).
NatureServe Vista (Commercial) is built on ESRI’s ArcMAP 9.1, the most widely-used GIS mapping technology. It delivers a decision support system (DSS) that integrates conservation information with land use patterns and policies, providing planners, resource managers, and communities with tools to help manage their natural resources. It enables users to create, evaluate, implement, and monitor land use and resource management plans that operate within the existing economic, social, and political context to achieve conservation goals.
Surrogacy (J. Garson and S. Sarkar) is an evaluation tool to measure the efficiency of a given estimator-surrogate to represent a convention biodiversity measure (true-surrogate) in a given landscape, supporting decisions to establish place prioritizing.
Reserves.xla (Robert A Briers) is an Add-in for Microsoft Excel to implement algorithms for choosing sites to be included in a reserve network. Full details of the algorithms and suggested usages are given in Briers RA (2002) Incorporating connectivity in reserve selection procedures. Biological Conservation 103: 77-83.
ZONATION (Atte Moilanen) is a spatial conservation planning software, which can be used to identify sites important for species conservation. Zonation produces a hierarchical prioritization of the landscape based on the biological values of sites (cells). The software includes several practical features such as aggregation methods, uncertainty analysis, species prioritization and replacement cost analysis for current or proposed reserves. The data requirements are realistic and Zonation can analyse relatively large data sets in reasonable time. Windows software package includes user manual and tutorial.
WORLDMAP (Paul Williams) is easy-to-use software for exploring geographical patterns in diversity, rarity and conservation priorities from large biological datasets. Because diversity is related in part to area extent, WORLDMAP was designed originally to use equal-area gridcells for more robust analyses, although in principle it can be applied to areas of any shape and size, at any spatial scale.
Ecology
EcoSim (Nicholas Gotelli, Gary Entsminger) is an interactive computer program for null model analysis of many aspects of community ecology, including patterns of species co-occurrence, species diversity, niche and size overlap as well as patterns in macroecology. EcoSim performs Monte Carlo randomizations to create “pseudo-communities”, then statistically compares the patterns in these randomized communities with those in the real data matrix. The program is accompanied by a help file, a tutorial and sample data sets.
EstimateS (Rob Colwell) is an essential tool for analysing diversity on the level of the local community, EstimateS 7 is a free software application for Windows and Macintosh operating systems that computes a variety of biodiversity functions, estimators, and indexes. Included are a wide range of species richness estimators for abundance and incidence (presence/absence) data. It also contains diversity indices (Shannon, Simpson, Fisher’s alpha) as well as similarity indices (Jaccard, Sørensen, Bray-Curtis, and Morista-Horn).
GEOSPOD (Walter Jetz) is a Monte Carlo simulation program to model the effect of geometric constraints and area on large-scale patterns in species richness. GEOSPOD calculates both 1-dimensional and 2-dimensional patterns, but sofar 2-dimensional templates are available only for simple circle or quadratic shapes as well as for Subsaharan Africa.
Mid-domain Null (Christy McCain) is a randomisation model similar to RangeModel. It allows for sampling of ranges for randomisation with or without replacement.
PAST (Øyvind Hammer & David A.T. Harper) is a free, easy-to-use data analysis package aimed at paleontology. Inspired by PALSTAT, it includes common statistical, plotting and modelling functions.
RangeModel (Rob Colwell) is a randomisation tool for analysing one-dimensional patterns in species richness. It specifically analyses patterns known as the Mid-domain effect (MDE) by randomising empirical or theoretical species ranges. Simulations can be compared with empirical patterns, and simulated distributions and richness patterns, as well as confidence intervals, can be exported. It is freely downloadable and there is an online users guide on the site.
SAM (Thiago Rangel, Alexandre Diniz-Filho, and Mauricio Bini) is a package of statistical tools for spatial analysis, mainly for applications in Macroecology and Biogeography. SAM runs under Microsoft Windows as as a menu-driven, graphical interface computational program. SAM offers a wide spectrum of statistical methods currently used in Surface Pattern Spatial Analysis. Among the tools are Trend Surface Analysis, PCNM or Eigen-based Spatial Filtering, Spatial Generalised Least Squares, and Simultaneous or Conditional Autoregressive Models.
Geographical analysis
Localiza – Spatial Allocation Software (web page in Spanish only) (Joaquín Bosque Sendra, Francisco Palm Rojas) is a system to help spatially-explicit decision-making processes to allocate social equipments (e.g., hospitals, subway stations, dump sites, etc.), which intends to analyze and find solutions in the allocation of equipments. LOCALIZA is based in the GIS system Idrisi For Windows 2.0, and in inovaGIS (an open source software community for the development of GIS tools). LOCALIZA includes different spatial allocation algorithms, such as MINISUM (minimize the sum of distances), COBEMAX (maximum coverage), etc.
DIVA-GIS (Mapping and analysis of spatial data) (Robert Hijmans, Luigi Guarino, Andy Jarvis, Rachel O’Brien) is a free mapping program (GIS), that can be used for many different purposes. It is particularly useful for mapping and analyzing biodiversity data, such as the distribution of species, or other ‘point-distributions’. With DIVA-GIS you can make maps of the world or of a very small place, integrating, for example, state boundaries, rivers, a satellite image, and the locations of sites where an animal species was observed. You can also make grid maps of the distribution of biological diversity, to identify “hotspots” and areas that have complementary levels of diversity. Finally, you can map and query climate data, predict species distributions using the BIOCLIM or DOMAIN models, or create ESRI shapefiles, import and export grid data.
ENM Tools (Measuring and testing niche overlap) (Dan Warren)
gDefrag (Frederico Mestre, Fernando Ascensão and A. Marcia Barbosa) is an R package providing a set of tools to help the de-fragmentation process. It works by prioritizing the different sections of linear infrastructures (e.g. roads, powerlines) to increase the available amount of a given resource.
MetaLandSim (Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita, Antonio Mira and Pedro Beja) is an R package providing a set of tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
roadHotspots (Bruno Silva) is a Shiny app to visualize hotspots over linear features (e.g. roads) for a set of observations (e.g. animal crossings, roadkills).
Lconnect (Frederico Mestre and Bruno Silva) is an R package providing functions to upload vectorial data and derive landscape connectivity metrics in habitat or matrix systems. Additionally, it includes an approach to assess individual patch contribution to the overall landscape connectivity, enabling the prioritization of habitat patches. The computation of landscape connectivity and patch importance are very useful in Landscape Ecology research. The metrics available are the number of components, number of links, size of the largest component, mean size of components, class coincidence probability, landscape coincidence probability, characteristic path length, expected cluster size, area-weighted flux and integral index of connectivity.
Modelling species distributions
BIOMAPPER (Alexandre Hirzel) is a kit of GIS- and statistical tools designed to build habitat suitability (HS) models and maps for any kind of animal or plant. It is centred on the Ecological Niche Factor Analysis (ENFA) that allows to compute HS models without the need of absence data. More precisely, it can deal with the following tasks: Preparing the ecogeographical maps in order to use them as input for the ENFA (e.g. computing frequency of occurrence map, standardisation, masking, etc.); exploring and comparing them by mean of descriptive statistics (distribution analysis, etc.); computing the Ecological Niche Factor Analysis and exploring its output; computing a Habitat Suitability maps; evaluating it.
BIOMOD (Wilfried Thuiller) is a computer platform for ensemble forecasting of species distributions, enabling explicit treatment of a range of methodological uncertainties and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions with predictor variables. BIOMOD is implemented in R and is a freeware, open source, package.
DesktopGarp (R. Scachetti-Pereira) is a software that uses a genetic algorithm that allows the user to predict and analyze species distributions. This website contains a link to download the DesktopGarp software package and instructions for installing and using the package.
GDM (Ferrier, S., Manion, G., Elith, J. and Richardson, K. 2007) is a software for fitting generalized dissimilarity models with R .
GRASP (A. Lehmann, J.R. Leathwick, and J.McC. Overton) is an add-in to SPLUS and R for generalized regression analysis and spatial prediction.
MAXENT (Phillips et al. 2006) is a computer platform for fitting maximum entropy models to presence-only species distribution data.
ENiRG (Fernando Canovas, Chiara Magliozzi, José António Palazon-Ferrando, Frederico Mestre and Mercedes Gonzalez-Wangüemert) is an R package with a set of tools for the analysis of species ecological niche and calculation of habitat suitability maps resorting to Ecological Niche Factor Analysis.