Application Papers

Recognising the need for a citable description of new methods and techniques in ecology and evolution, our Application papers describe new software, equipment, or other practical tools, with the intention of promoting and maximising the uptake of these new approaches.

In order to disseminate the newest advances as broadly as possible, we are pleased to be able to offer free access to all Application papers published in Methods in Ecology and Evolution.

Newest Applications

ControllingCrossesIndividual chambers for controlling crosses in wind-pollinated plants

Online 30 January 2017

A flexible chamber system for controlling pollen flow in wind-pollenated plant species capable of housing hundreds of plants simultaneously in individual chambers through the reproductive portion of their life cycles. This system is affordable and widely applicable to other wind-pollinated plants, or applications in which the distribution of highly mobile species, individuals, spores or gametes must be controlled.
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ClickPointsOpenMEE: Intuitive, open-source software for meta-analysis in ecology and evolutionary biology

Online 30 January 2017

Open Meta-analyst for Ecology and Evolution (OpenMME) addresses the need for advanced, easy-to-use software for meta-analysis and meta-regression. It has a cross-platform, graphical user interface that gives researchers access to the diverse and advanced statistical functionalities offered in R, without requiring knowledge of R programming.
Read the full description
Download OpenMEE

ClickPointsClickPoints: an expandable toolbox for scientific image annotation and analysis

Online 17th November 2016

ClickPoints combines and streamlines the three main steps of image analysis – visualization, annotation and evaluation – in one program. It is designed to simplify repetitive and labour-intensive scientific tasks, especially when dealing with large image and video time-series recordings.
Read the full description
Download ClickPoints

gflowgflow: software for modelling circuit theory-based connectivity at any scale

Online 18th November 2016

gflow is an open-source software , which massively parallelizes the computation of circuit theory-based connectivity. It allows large-extent and high-resolution connectivity problems to be calculated over many iterations and at multiple scales.
Read the full description
Download gflow

deBInferdeBInfer: Bayesian inference for dynamical models of biological systems in R

Online 17th November 2016

deBInfer, a package for the statistical computing environment R, implementing a Bayesian framework for parameter inference in differential equations. deBInfer provides templates for the differential equation model, the observation model and data likelihood, and the model parameters and their prior distributions.
Read the full description
Download deBInfer

BarcodingRBarcodingR: an integrated r package for species identification using DNA barcodes

Online 14th November 2016

BarcodingR is an integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages.
Read the full description
Download BarcodingR

MatlabHTKMatlabHTK: a simple interface for bioacoustic analyses using hidden Markov models

Online 10th November 2016

MatlabHTK is a software interface to a popular speech recognition system that makes it possible for non-experts to implement hidden Markov models for bioacoustic signal processing. Octave/Matlab functions are used to simplify the set-up and the definition of a bioacoustic signal recogniser as well as the analysis of the results.
Read the full description
Download MatlabHTK

PrimerMinerPrimerMiner: an r package for development and in silico validation of DNA metabarcoding primers

Online 10th November 2016

PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI data bases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species.
Read the full description
Download PrimerMiner

SQoloSolo: an open source, customizable and inexpensive audio recorder for bioacoustic research

Online 7th November 2016

The Solo audio recorder is an inexpensive, user-serviceable and easily customized audio recording device which has been extensively field tested in temperate and tropical regions, with over 50,000 hours of audio collected to date. A video tutorial showing hardware assembly and documentation is available via a supporting website.
Read the full description
Find out more about Solo

3DThe third dimension: a novel set-up for filming coelacanths in their natural environment

Online 7th November 2016

The authors describe a novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140 m. It consists of two synchronized high-speed cameras fixed to two articulated arms and can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.
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SQuIDStatistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models

Online 17th October 2016

Statistical Quantification of Individual Differences (SQuID) creates a virtual world inhabited by subjects whose phenotypes are generated by a user-defined phenotypic equation, which allows easy translation of biological hypotheses into quantifiable parameters.
Read the full description
Download SQuID

NoiseEggThe noise egg: a cheap and simple device to produce low-frequency underwater noise for laboratory and field experiments

Online 13th October 2016

The noise egg is a device that can produce a low-frequency sound, which can be used as an experimental source of noise. The device is completely self-contained, easy to assemble and inexpensive. Because the sound from the egg attenuates quickly, it can be used in aquaria and in the field to target study species without affecting the surrounding area.
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EMDSimilarity in spatial utilization distributions measured by the earth mover's distance

Online 6th October 2016

The earth mover's distance (EMD) is a spatially explicit method that quantifies similarity between utilization distributions by calculating the effort it takes to shape one utilization distribution landscape into another. It is a consistent, useful, versatile measure of overlap and provides an easy to use implementation in the R package move.
Read the full description
Download move

GGTreeggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Online 22nd September 2016

ggtree is an R package which provides programmable visualization and annotation of phylogenetic trees. The package allows colouring and annotation of a tree, manipulating a tree by rotating, highlighting clades or operational taxonomic units, exploration of a large tree by zooming into a selected portion and more.
Read the full description
Download ggtree

warbleRwarbleR: an r package to streamline analysis of animal acoustic signals

Online 8th September 2016

warbleR is a new package for the analysis of animal acoustic signal structure. The package offers functions for displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals, conducting cross-correlations, measuring acoustic parameters and analysing interactive vocal signals, among others.
Read the full description
Download warbleR

meteRmeteR: an R package for testing the maximum entropy theory of ecology

Online 6th September 2016

meteR directly calculates all of the maximum entropy theory of ecology's predictions from a variety of data formats; automatically handles approximations and other technical details; and provides high-level plotting and model comparison functions to explore and interrogate models. 
Read the full description
Download meteR

tempchamLow-cost fluctuating-temperature chamber for experimental ecology

Online 30th August 2016

A programmable fluctuating-temperature chamber design based on a relatively small commercially manufactured constant temperature chamber modified with a customized, user-friendly microcontroller. It's cheap and simple to assemble in large numbers, enabling replication of highly complex, many treatment study designs. 
Read the full description
Download the operational code

iNEXTiNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

Online 6th August 2016

iNEXT (iNterpolation/EXTrapolation) is an R package which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity).  
Read the full description
Download iNEXT

inbreedRinbreedR: an R package for the analysis of inbreeding based on genetic markers

Online 21st July 2016

inbreedR estimates the impact of inbreeding on marker heterozygosity and fitness within the framework of Heterozygosity–fitness correlations theory. It also implements user-friendly simulations to explore the precision and magnitude of estimates based on different numbers of genetic markers. 
Read the full description
Download inbreedR

RPhyloparsRphylopars: fast multivariate phylogenetic comparative methods for missing data and within-species variation demogenetics

Online 21st July 2016

Rphylopars provides expanded capabilities over the original PhyloPars interface including a fast linear-time algorithm, allowing for extremely large data sets (which were previously computationally infeasible) to be analysed in seconds or minutes rather than hours. 
Read the full description
Download RPhylopars

CDMetaPOPCDMetaPOP: an individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

Online 16th July 2016

Cost–Distance Meta-POPulation (CDMetaPOP) is a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers. 
Read the full description
Download CDMetaPOP

rotlrotl: an R package to interact with the Open Tree of Life data

Online 11th July 2016

rotl is an R package that can search and download data from the Open Tree of Life directly in R. It uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies. In the article, the authors demonstrate how rotl can be used with other R packages to analyse biodiversity data.
Read the full description
Download rotl

camtrapRcamtrapR: an R package for efficient camera trap data management

Online 11th July 2016

camtrapR allows for streamlined and flexible camera trap data management and should be most useful to researchers and practitioners who regularly handle large amounts of camera trapping data. The functions provide extensive automation to minimize data entry mistakes and require minimal manual user input.
Read the full description
Download camtrapR

BORISBORIS: a free, versatile open-source event-logging software for video/audio coding and live observations

Online 28th May 2016

BORIS allows a user-specific coding environment to be set for a computer-based review of previously recorded videos or live observations. The program allows a project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified.
Read the full description
Download BORIS

moveHMMmoveHMM: an R package for the statistical modelling of animal movement data using hidden Markov models

Online 28th May 2016

moveHMM allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit a hidden Markov model to these data, allowing,for the incorporation of environmental covariates. The package includes assessment and visualization tools for the fitted model.
Read the full description
Download moveHMM

TPATerrestrial Precipitation Analysis (TPA): A resource for characterizing long-term precipitation regimes and extremes

Online 24th May 2016

The TPA package contains Precipitation Trends (P-Trend), Precipitation Attributes (P-Att) and Precipitation Manipulation (P-Man) tools. Combined, these web tools allow researchers to easily calculate fundamental precipitation statistics for past, present and projected future precipitation regimes for any terrestrial location in the world.
Read the full description
Download TPA

Trappertrapper: an open source web-based application to manage camera trapping projects

Online 24th May 2016

A flexible data base driven web application to manage, classify, integrate, share and re-use data in camera trapping projects. This software is open source.
Read the full description
Download trapper

Geometric MorphometricsTuning Geometric Morphometrics: an r tool to reduce information loss caused by surface smoothing

Online 18th May 2016

This work aims to develop a method to assess the amount of information loss or recovery after the application of 3D surface smoothing to virtual objects.
Read the full description
Download the tool

CodynCODYN: an r package of community dynamics metrics

Online 18th May 2016

New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. The R package, codyn helps ecologists easily implement these metrics to gain broader insights.
Read the full description
Download CODYN

ctmmctmm: an R package for analyzing animal relocation data as a continuous-time stochastic process

Online 5th May 2016

ctmm implements all of the continuous-time stochastic processes currently in use in the ecological literature and couples them with powerful statistical methods for autocorrelated data adapted from geostatistics and signal processing.
Read the full description
Download ctmm

ThrowLineA simple and effective method to collect leaves and seeds from tall trees

Online 19th April 2016

An arborist throw-line launcher can be used to collect leaves and seeds from trees without the need for climbing. This is a cost-effective, simple alternative for collecting leaves and seeds from tall trees.
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Watch the Video Tutorials

RCloneRClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in R

Online 16th March 2016

RClone handles clonal data sets, allowing you to (1) check for data set reliability to discriminate multilocus genotypes (MLGs), (2) ascertain MLG and semi-automatic determination of clonal lineages (MLL), (3) calculate genotypic richness & evenness indices based on MLGs or MLLs & (4) describe spatial components of clonality.
Read the full description
Download RClone

PlantOMaticPlant-O-Matic: a dynamic and mobile guide to all plants of the Americas

Online 10th March 2016

Plant-O-Matic is a free iOS application that combines the species distribution models with the location services built into a mobile device. It provides users with a list of all plant species expected to occur in the 100 × 100 km geographic grid cell corresponding to the user's location.
Read the full description
• Download Plant-O-Matic from iTunes or GitHub

plantplant: A package for modelling forest trait ecology and evolution

Online 21st February 2016

An extensible framework for modelling size- and trait-structured demography, ecology and evolution in simulated forests. At its core, plant is an individual-based model where plant physiology and demography are mediated by traits. Individual plants from multiple species can be grown in isolation, in patches of competing plants or in metapopulations under a disturbance regime.
Read the full description
Download plant

MOPhyloMO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics

Online 5th February 2016

MO-Phylogenetics is a software tool to infer phylogenetic trees optimizing two reconstruction criteria at the same time, integrating a framework for multi-objective optimization with two phylogenetic software packages. It includes multi-objective metaheuristics that can be applied to phylogenetic inference.
Read the full description
Download MO-Phylogenetics

RPANDARPANDA: an R package for macroevolutionary analyses on phylogenetic trees

Online 3rd February 2016

RPANDA is an R package that implements model-free and model-based phylogenetic comparative methods for macroevolutionary analyses. It provides investigators with tools for exploring patterns in phylogenetic trees and fitting various models to these trees.
Read the full description
Download RPANDA

PHYLOMETRICSPHYLOMETRICS: an R package for detecting macroevolutionary patterns, using phylogenetic metrics and backward tree simulation

Online 18th January 2016

PHYLOMETRICS is an efficient algorithm to construct the null distributions by generating phylogenies under a trait state-dependent speciation and extinction model with a fixed number of extant taxa with a given trait state and a fixed sampling fraction of taxa with each trait state. It also includes a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics.
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SIMRSIMR: an R package for power analysis of generalized linear mixed models by simulation

Online 18th January 2016

SIMR allows users to calculate power for generalized linear mixed models from the LME4 package. The power calculations are based on Monte Carlo simulations. It includes tools for running a power analysis for a given model and design and calculating power curves to assess trade-offs between power and sample size.
Read the full description
Download SIMR

taxonlookupA simple approach for maximizing the overlap of phylogenetic and comparative data

Online 5th January 2016

A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that lack data with ‘phylogenetically equivalent’ species that have data. This paper presents algorithms that use topological and taxonomic information to maximize the number of swaps without altering the structure of the phylogeny.
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Download taxonlookup

plantBORAL – Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in R

Online 5th January 2016

An R package available on cran for model-based analysis of multivariate abundance data, with estimation performed using Bayesian Markov chain Monte Carlo methods. A key feature of the boral package is the ability to incorporate latent variables as a parsimonious method of modelling between species correlation.
Read the full description
Download BORAL

piecewiseSEMpiecewiseSEM: Piecewise structural equation modelling in r for ecology, evolution, and systematics

Online 30th December 2015

A practical implementation of confirmatory path analysis for the r programming language. The package extends this method to all current (generalized) linear, (phylogenetic) least-square, and mixed effects models, relying on familiar R syntax.
Read the full description
Download piecewiseSEM

CPWCPW Photo Warehouse: a custom database to facilitate archiving, identifying, summarizing and managing photo data collected from camera traps

Online 18th December 2015

A freely available softwarethat has been customized to identify, archive, and transform photos into data formats required for statistical analyses. Users navigate a series of point-and-click menu items that allow them to input information from camera deployments, automatically import photos related to those deployments, and store data within a relational database.
Read the full description
Download CPW Photo Warehouse

Universal FQAThe Universal Floristic Quality Assessment (FQA) Calculator: an online tool for ecological assessment and monitoring

Online 4th November 2015

Floristic Quality Assessments (FQAs) are measurements of a natural area's ecological integrity based on their plant species composition. The Universal FQA is an open-source web-based FQA Calculator. It offers 30 FQA data bases from across the United States and Canada and has been used to calculate thousands of assessments.
Read the full description
Download the Universal FQA

MetagearFacilitating systematic reviews, data extraction and meta-analysis with the METAGEAR package for R

Online 13th October 2015

A multifunctional toolbox with capabilities ranging from applying a systematic review approach to objectively assemble and screen the literature, to extracting data from studies, and to finally summarize and analyse these data with the statistics of meta-analysis.
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OligonucleotideRecognizing false positives: synthetic oligonucleotide controls for environmental DNA surveillance

Online 26th September 2015

A set of synthetic oligonucleotides for use as species-specific positive PCR controls for several high-profile aquatic invasive species.
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OEZYOEZY: Optimising EnZYme selection for best performing terminal restriction fragment length polymorphism analysis using ARB

Online 16th September 2015

A software tool which utilises ARB and the SILVA database of hundreds of thousands of aligned ribosomal RNA genes or user-submitted sequences as basis for the selection of optimal sets of REs of various sizes.
Read the full description
Download OEZY

BiMatBiMat: a MATLAB package to facilitate the analysis of bipartite networks

Online 13th September 2015

An open-source MATLAB package for the study of the structure of bipartite ecological networks. BiMat enables both multiscale analysis of the structure of a bipartite ecological network and meta-analyses of many bipartite networks simultaneously.
Read the full description
Download BiMat

StagePopstagePop: modelling stage-structured populations in R

Online 28th August 2015

An R-package for predicting the deterministic dynamics and interactions of stage-structured populations (i.e. where the life cycle consists of distinct stages, for example eggs, juveniles and reproductive adults).
Read the full description
Download stagePop

Soil CO2Soil CO2 Efflux and Point Concentration Sensing Systems

Online 21st July 2015

The use of two low-cost, portable CO2 sensing systems to enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.
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CO2 Callibration and Exprimental Data


Online 14th July 2015

mvMORPH is a package of multivariate phylogenetic comparative methods for the r statistical environment. It allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion.New features provided by the package include the possibility of fitting models with changes in the mode of evolution along the phylogeny.
Read the full description
Download mvMORPH


Online 1st July 2015

PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.
Read the full description
Download POPART

SeawaterUsing sea water for cleaning oil from seabird feathers

Online 18th June 2015

For oiled feathers, a sea water wash/rinse produced clean, low BAI/unclumped feathers with minimal particulate residue. Sea water cleaning trials should now be undertaken on live birds to understand links with sea water use and waterproofing.
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Online 25th May 2015

PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.
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Download PIPITS

Online 23rd May 2015 provides maps and graphs for data exploration, download of processed data for modelling and statistical analysis, and tools for sharing results with other users. The tool supports the most frequently used M-Series immersion loggers. Support for a broader range of device types and expanded analysis functionality is planned.
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Online 18th May 2015

letsR is designed to handle and analyse macroecological data such as species’ geographic distributions (polygons in shapefile format and point occurrences) and environmental variables (in raster format).
Read the full description
Download letsR


Online 13th May 2015

LEA enables users to run ecological association studies from the R command line. The package can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets.
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Download LEA


Online 21st April 2015

VirtualCom is a simulation model that generates such data sets. Integrating both ecological and evolutionary processes, it simulates the evolution of the pool of regionally occurring species, the process-based assembly of native communities and the invasion of novel species into native communities.
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Online 3rd April 2015

The fuzzySim package allows a variety of methods for converting (multiple) species presence/absence data into continuous, fuzzy surfaces, including inverse distance to presence raised to any power, trend surface analysis of any given degree and generalized linear models based on presence–absence.
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Download fuzzySim



Online 31st March 2015

The open-source R package, rSPACE, is for implementing a spatially based power analysis for designing monitoring programs. A sampling design can then be implemented to create replicate encounter histories which are subsampled and analysed to estimate the power of the monitoring program to detect changes in population abundance over time, using occupancy as a surrogate.
Read the full description
Download rSPACE


Online 9th February 2015

The TR8 package for R was built to provide plant scientists with a simple tool for retrieving plant functional traits from freely accessible online traitbases.
Read the full description
Download TR8


Online 2nd January 2015

StereoMorph is a new R package for the rapid and accurate collection of 3D landmarks and curves using two standard digital cameras. It provides a complete set of tools for every step in the collection of 3D landmarks and curves using a stereo camera set-up.The image processing tools and digitizing application are readily applicable to 2D morphometrics as well.
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Download StereoMorph
Download the StereoMorph tutorial files


Online 15th December 2014

MotionMeerkat is a new standalone program that identifies motion events from a video stream. After running a video, the user reviews a folder of candidate motion frames for the target organism. This tool reduces the time needed to review videos and accommodates a variety of inputs.
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Download MotionMeerkat (source code run in the python environment)


Online 16th November 2014

The R package BAT - Biodiversity Assessment Tools - performs a number of analyses based on either species identities (TD) or trees depicting species relationships (PD and FD). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components.
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Download BAT


Online 13th November 2014

The authors have developed a Python package that brings together some of the more popular neutral landscape model algorithms using a general numerical framework.
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Download NLMpy


Online 28th October 2014

The authors introduce enaR , an r package for Ecosystem Network Analysis (ENA). ENA is an analytical tool set rooted in ecosystem ecology with over 30 years of development that examines the structure and dynamics of matter and energy movement between discrete ecological compartments (e.g. a food web).
Read the full description
Download enaR [from CRAN]

ENMevalA tool to asses plastics exposure in seabirds

Online 12th Spetember 2014

The authors developed a minimally invasive tool that allows for the detection of exposure to plastics in seabirds.
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Online 12th Spetember 2014

The authors present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees.
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Download PyRate 


Online 3rd Spetember 2014

ENMeval is an R package that: (1) creates datasets for k-fold cross validation using one of several methods for partitioning occurrence data (including options for spatially independent partitions), (2) builds a series of candidate models using Maxent with a variety of user-defined settings, and (3) provides multiple evaluation metrics to aid in selecting optimal model settings.
Read the full description
Download ENMeavel [from CRAN]


Online 29th August 2014

The authors present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing. Multiple fishing gears can be defined and fishing mortality can change through time making it possible to simulate a range of exploitation strategies and management options.
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Download mizer [from CRAN]


Online 6th August 2014

The authors developed the MEMGENE package for R in order to detect and visualize relatively weak or cryptic spatial genetic patterns and aid researchers in generating hypotheses about the ecological processes that may underlie these patterns. MEMGENE provides a flexible set of R functions that can be used to modify the analysis.
Read the full description
Download memgene [from CRAN]

Species ExtinctionA tool to infer species extinction

Online 23rd July 2014

The author uses the Pohnpei Mountain Starling Aplonis pelzelni to describe an Excel spreadsheet which infers extinction from a sighting record. The spreadsheet implements a Bayesian model which includes uncertainty around the prior, uncertain sightings and survey effort.
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Download the spreadsheet


Online 19th July 2014

The authors present Rphylip, a new R interface for the PHYLIP package. Functions of Rphylip interface seamlessly with all of the major analysis functions of the PHYLIP package. This new interface will enable the much easier use of PHYLIP programs in an integrated R workflow.
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Download Rphylip [from CRAN]


Online 18th July 2014

A method and open source R package agTrend for analyzing regional trends of abundance from sites with uneven sample schedules over space and time.
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Download agTrend


Online 30th May 2014

New version ModestR 2.0 makes it easy to download occurrence records from the Global Biodiversity Information Facility (GBIF), to import shape files with species range maps such as those available at the website of the International Union for Conservation of Nature (IUCN), to import KML files, to import CSV files with records of the users, to import ESRI ASCII grid probability files generated by distribution modelling software, and show the resulting records on a map.
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Download ModestR


Online 28th May 2014

MeCa is a user-friendly MATLAB toolbox that contains different options – including the groundwater correction - for the calculation of metabolism.
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Download MeCa


Online 10th May 2014

Occupancy models can be implemented in program E-SURGE, which was initially developed to analyse capture–recapture data in the HMM framework. Replacing individuals by sites provides the user with access to several features of E-SURGE that are not available altogether or just not available in standard occupancy software: i) flexible model specification through a user-friendly syntax without having to write custom code, ii) decomposition of the observation and state processes in several steps to provide flexible parameterisation, iii) up-to-date diagnostics of model identifiability, and iv) advanced numerical algorithms to produce fast and reliable results (including site random effects).
Read the full description
Download E-SURGE


Online 22nd April 2014

SDMtoolbox is a free comprehensive python-based toolbox for macroecology, landscape genetic and evolutionary studies to be used in ArcGIS 10.1 (or higher) with the Spatial Analyst extension. The toolkit simplifies many GIS analyses required for species distribution modeling and other analyses, alleviating the need for repetitive and time consuming climate data pre-processing and post-SDM analyses.
Read the full description
Download SDMtoolbox, a user guide, and example data


Online 22nd April 2014

An R package for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees. BAMMtools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability. Users can compare the fit of alternative diversification models using Bayes factors and by directly comparing model posterior probabilities.
Read the full description
Download BAMMtools [from CRAN]


Online 28th March 2014

Synchrony provides modern parametric and non-parametric methods for (i) quantifying temporal and spatial patterns of auto- and cross-correlated variability in univariate, bivariate and multivariate datasets, and (ii) assessing their statistical significance via Monte Carlo randomizations.
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Online 20th February 2014

MLST@SNaP is a fast, user-friendly and automated process to convert thousands of MLST sequences or sequence types into SNaP profiles and vice-versa
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Download MLST@SNaP


Online 20th January 2014

The authors introduce a novel modelling platform, RangeShifter, which integrates complex population dynamics and dispersal behaviour, includes plastic and evolutionary processes, and simulates scenarios on spatially-explicit landscapes.
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Online 15th January 2014

PopGenReport is a new R-package that simplifies performing population genetics analyses in R, through the use of a new report generating function.
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Download PopGenReport


Online 29th November 2013

The authors introduce and document a set of data analysis tools, implemented within the IsoMAP (Isoscapes Modeling, Analysis, and Prediction) cyber-GIS system, that support basic analysis of sample data for geographic assignment applications.
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Online 12th November 2013

Ecological networks are often composed of different sub-communities (often referred to as modules). Identifying such modules has the potential to develop a better understanding of the assembly of ecological communities and to investigate functional overlap or specialisation. Here, the authors introduce an algorithm to identify modules in quantitative bipartite (or two-mode) networks.
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Online 30th September 2013

This package bridges a gap in the tools that are available to biologists wishing to analyse animal social networks in R.
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Online 24th September 2013

SIDIER is a software package that allows inferring evolutionary relationships from gapped alignments using information contained in both substitutions and insertions/deletions (indels).
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Download SIDIER [from CRAN]


Online 24th September 2013

PASTIS enables a two-stage Bayesian method using MrBayes v.3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage.
Read the full description
Download PASTIS [from CRAN]

Tea Bag IndexTea Bag Index

Online 22nd July 2013

The authors introduce an innovative, cost-effective, well-standardised method to gather data on decomposition rate and litter stabilisation using commercially available teabags as standardised test kits.
Read the full description
Read about the concept and protocol

Tea Bag IndexITSx

Online 19th July 2013

The authors introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets.
Read the full description
Download ITSx


Online 14th June 2013

RInSp provides a comprehensive set of classical and recently proposed indices for quantifying the degree of individual specialisation using both categorical and continuous resource use data. The package also includes tools for ad hoc Monte Carlo and Jackknife resampling procedures for significance testing, plotting, and input/output data manipulation.
Read the full description
Download RInSp [from CRAN]
Download RInSp [from GitHub]


Online 22nd May 2013

pavo provides a cohesive environment for handling spectral data and addressing complex sensory ecology questions, while integrating with R's modular core for a broader and comprehensive analytical framework, automated management of spectral data, and reproducible workflows for colour analysis.
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Download pavo [from CRAN]
Download pavo [from github]


Online 20th May 2013

SimAssem can: 1) simulate assemblages and surveys with user-specified parameters, 2) process existing species encounter history files, 3) generate species richness estimates not available in other programs, and 4) format encounter history data for several other programs.
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Download SimAssem

Curve FitCurve Fit

Online 11th May 2013

Curve Fit is an extension to the application ArcMap that allows users to conduct linear or nonlinear regression analysis on the range of values found within input raster datasets (geo-referenced images), independently for each pixel.
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Download Curve Fit


Online 11th May 2013

The authors present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics, and population differentiation statistics, among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective.
Read the full description
Download diveRsity [from CRAN]


Online 30th April 2013

The authors describe an open source R package, marked, for analysis of mark-recapture data to estimate survival and animal abundance. The package will be most useful to ecologists with large mark-recapture datasets and many individual covariates.
Read the full description
Download marked [from CRAN]


Online 1st April 2013

This R package provides tools for estimating animal density from point transect surveys in which the conventional point transect assumption of uniform animal distribution in the vicinity of the point is violated.
Read the full description
Download nupoint


Online 26th March 2013

PhyloGenerator allows non-specialists to quickly and easily produce robust, repeatable, and defensible phylogenies, without requiring an extensive knowledge of phylogenetics. Experienced phylogeneticists may also find it useful as a tool to conduct exploratory analyses.
Read the full description
Download Phylogenerator


Online 18th March 2013

The authors present a cross-platform R tool that integrates with tree of life efforts by mapping divergence times from an existing timetree (a ‘reference’) to another uncalibrated phylogeny (a ‘target’) that samples from the same lineage. Leveraging existing methods for rate-smoothing phylograms, this tool enables the rapid generation of very large timetrees where direct estimation of the timing of lineage diversification is either impracticable or impossible.
Read the full description
Download Geiger [from CRAN]


Online 14th March 2013

The authors present a publicly available decision support software tool for the comparison of ecological impacts of alternative land-use options.
Read the full description
Download RobOff


Online 11th March 2013

The authors introduce the R package ‘EasyABC’ that enables one to launch a series of simulations from the R platform and to retrieve the simulation outputs in an appropriate format for post-processing. The ‘EasyABC’ package further implements several efficient parameter sampling schemes to speed up the ABC procedure.
Read the full description
Download EasyABC [from CRAN]


Online 9th February 2013

The authors developed a spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton to represent evolutionary processes of adaptation and population dynamics in changing landscapes, using the NetLogo environment.
Read the full description
Download SimAdapt


Online 25th January 2013

Geomorph is a software package for performing geometric morphometric shape analysis in the R statistical computing environment.
Read the full description
Download geomorph from [CRAN]


Online 25th January 2013

SURFACE uses the Ornstein-Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree.
Read the full description
Download SURFACE from [CRAN]



Online 27th December 2012

SPOTG is a user-friendly software for optimizing sampling strategy for five common genetic study topics: hybridization, temporal sampling, bottlenecks, connectivity, and assignment. It facilitates formal evaluation of the expected statistical power of proposed sampling strategies before project implementation
Read the full description


Published online 20th December 2012

BEFdata is a new, open source web platform for the upload, validation and storage of data from a formatted Excel workbook. It allows the harmonization of naming conventions by generating category lists from the primary data, which can be reviewed and managed via the Excel workbook or directly on the platform.
Read the full description


Published online 14th December 2012

This paper describes the link between the trinomial model and the mark–recapture–recovery model of Burnham, and shows how the trinomial model can be implemented in the software package program mark. It provides the user with access to all of the features of program mark including the facilities for model building and model selection without having to write custom code.
Read the full description


Published online 10th December 2012

The authors present IPMpack, a free open-source software (R) package for building IPMs. The package estimates key population characteristics from IPMs, such as population growth rate in both deterministic and stochastic environments, age-specific trajectories of survival and reproduction, and sensitivities and elasticities to changes in underlying vital rates.
Read the full description
Download IPMpack from [CRAN]


Published online 23rd November 2012

The authors introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance.
Read the full description
Download Cheddar from [CRAN]
Download R code for reproducing figures and tables
Download R code for producing more comprehensive versions of Tables 1 and 2


Published online 11th October

The TreeBASE portal is an important and rapidly growing repository of phylogenetic data. The authors of this paper have developed treebase, an open-source software package for the R programming environment, providing simplified, programmatic and interactive access to phylogenetic data in the TreeBASE repository.
Read the full description
Download treebase from [CRAN]


Published online 1st October 2012

The authors have developed GeoLight, an R package which provides basic functions for all steps of determining global positioning and a new approach in analysing movement pattern.
Read the full description
Download Geolight from [CRAN]


Published online 17th September 2012

SPACECAP is an R package implementing Bayesian spatially explicit hierarchical models to analyse spatial capture–recapture data.
Read the full description
Download spacecap from [CRAN]

gibbsGibbs sampler

Published online 20th August 2012

The authors develop a Gibbs sampler for Bayesian analysis of siteoccupancy data that include covariates of species occurrence and species detection probabilities. This Gibbs sampler is based on a class of site-occupancy models in which probabilities of species occurrence and detection are specified as probit-regression functions of site- and survey-specific covariate measurements. They also provide code (based on theRsoftware program) for conducting Bayesian and classical analyses of site-occupancy data.
Read the full description
Download the R code from the supplementary material


Published online 10th August

Currently, parametric curve-fitting requires a priori assumptions of curve trajectories, restricting their use for exploratory analyses. The new r package FlexParamCurve that automates curve selection and provides tools to analyse nonmonotonic curve data in nonlinear least-squares and nonlinear mixed-effects models. Examples include empirical and simulated data sets for the growth of seabird chicks.
Read the full description
Download FlexParamCurve from [CRAN]
• View the accompanying videos: An Introduction, and A Tutorial


Published online 6th August 2012

The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/ extinction rates independently.
Read the full description
Download diversitree from [CRAN]
Download tutorial and worked examples
Watch the video


Published online 5th July 2012

Taxonstand, an R package to automatically standardise plant names using The Plant List. The scripts included in this package allow connection to the online search engine of the Plant List and retrieve information from each species about its current taxonomic status. This tool greatly facilitates the preparation of large vegetation databases prior to their analyses, particularly when they cover broad geographical areas (supranational or even continental scale) or contain data from regions with rich floras where taxonomic problems have not been resolved for many of their taxa.
Read the full description
Download taxonstand from [CRAN]


Published online 18th June 2012

Betapart allows the assessment of spatial patterns of beta diversity using multiple-site dissimilarity measures accounting for compositional heterogeneity across several sites or pairwise measures providing distance matrices accounting for the multivariate structure of dissimilarity. It also allows computing patterns of temporal difference in assemblage composition, and its turnover and nestedness components.
Read the full description
Download betapart from [CRAN]


Published online 18th June 2012

Paleotree is a library of functions for the R statistical computing environment dedicated to analyses that combine paleontological and phylogenetic data sets, particularly the time-scaling of phylogenetic trees, which include extinct fossil lineages.
Read the full description
Download palotree from [CRAN]
Read the blog


Published online 11th June 2012

The R package popdemo provides software tools for novel analytical methods that aim to enhance the predictive power of basic population projection matrix models. These include indices of transient population dynamics and transfer function analyses.
Read the full description
Download popdemo from [CRAN]


Published online 11th May 2012

The Non-Additive InVerses (nadiv) R software package contains functions to create and use non-additive genetic relationship matrices in the animal model of quantitative genetics.This includes functions to create the inverse of the dominance and epistatic relatedness matrices from a pedigree, which are required for estimating these genetic variances in an animal model.
Read the full description
Download nadiv from [CRAN]
Tutorials on how to use nadiv


Published online 10th May 2012

Simapse – Simulation Maps for Ecological Niche Modelling, a free and opensource application written in Python and available to the most common platforms. It uses Artificial Neural Newtowrks (ANNs) with back-propagation to build spatially explicit distribution models from species data (presence ⁄ absence, presence-only and abundance).
Read the full description
Download simapse


jPopGenjPopGen Suite

Published online 2nd March 2012

jPopGen Suite is an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences. It is specially designed for data with a non-negligible error rate, although it serves well for ‘error-free’ data. It implements several methods for estimating the population mutation rate, population growth rate and conducting neutrality tests.
Read the full description
• Download jPopGen Suite from its website


Published online 21st February 2012

mvabund is an R package for model-based analysis of multivariate abundance data. This includes methods for visualising data, fitting predictive models, checking model assumptions, as well as testing hypotheses about the community–environment association.
Read the full description
Download mvabund from [CRAN]


Published online 17th February 2012

Bayesian survival trajectory analysis (BaSTA) is a free open-source software package for estimating age-specific survival from capture–recapture/recovery data under a Bayesian framework. This tool facilitates the analysis of age patterns of survival in long-term animal studies and will enable researchers to robustly infer the effect of covariates, even with large amounts of missing data.
Read the full description
• Download BaSTA from CRAN instal it in R with the following command: install.packages(‘‘BaSTA’’)
BaSTA users mailing list.


Published online 1st February 2012

Approximate Bayesian computation (ABC) is devoted to the analysis of complex models. This application introduces the R package ‘abc’ that implements several ABC algorithms for performing parameter estimation and model selection.
Read the full description
Download abc [CRAN]


Published online 25th January 2012

NichePy are modular tools for estimating the similarity of ecological niche and species distribution models. Those models are used in macroecological studies to investigate the potential geographic distributions of invasive species, the effects of climate change on past, present and future species distributions as well as the evolution of ecological niches.
Read the full description
Download NichePy

Published online 19th January 2012

NetLogo is a free software platform for implementing individual-based and agent-based models. RNetLogo is an R package that links R and NetLogo: any NetLogo program can be controlled and run from R and model results can be transferred back to R for statistical analyses.
Read the full description
Download RNetLogo [CRAN]
and from R-Forge.


Published online 15th December 2012

Dynamic Energy Budget-individual-based model can be used to explore properties of both individual life-history traits and population dynamics, which emerge from the set of DEB parameters of a species, and their interaction with environmental variables such as food density. Furthermore, DEB-IBM can be adapted to address specific research questions, for example by including spatial effects. A user manual explains how this can be done.
Read the full description
Download DEB-IBM program and supplementary material from CREAM-ITN.EU

phytoolsphytools– a multifunctional phylogenetics package

Published online 15th December 2011

This R package focuses on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. The author also maintains an active web-log that uses to document present and future developments for phytools.
Read the full description
Phytools web-log
Phylogenetics CRAN Task view
R-sig-phylo email mailing list
• Watch a web seminar about phytools (scroll down to Liam Revell's seminar 15 December 2011)

smatr3smatr 3– an R package for estimation and inference about allometric lines

Published online 29th September 2011

smatr - Standardised Major Axis Tests and Routines - provides a set of tools for estimation and inference about allometric lines, including functions that accept formula input and perform the key inference tasks, the handling of multiple comparisons, robust (S)MA estimation and inference tools, and graphical methods for visualising data and checking (S)MA assumptions.
Read the full description
Download smatr 3 [CRAN]

PMxPMx: software package for demographic and genetic analysis and management of pedigreed populations

Published online 5th September 2011

This C#-based freeware application provides tools for optimal demographic and genetic management of populations of wildlife species, rare domestic breeds, and other populations for which the primary goal is to conserve genetic diversity, and can also be used to characterize the demography and genetics of any captive or wild population for which pedigree and life-history data are available.
• Read the full description
• Download PMx a web-based decision-support tool for implementing Indonesia’s forest moratorium

Published online 5th September 2011

This spatially explicit, web-based application enables analysis of the implications and trade-offs involved in Indonesia’s forest moratorium in Kalimantan, allowing in-depth investigation of the moratorium’s benefits for carbon conservation and its opportunity costs, while serving as a useful framework for understanding the costs and benefits of REDD+ implementation in other forest-rich tropical nations.
• Read the full description
• Go to
• Download an offline version [xlsm]

DRATDirected terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal-restriction fragment length polymorphisms

Published online 29 July 2011

DRAT is a software tool that aids the design of directed terminal-restriction fragment length polymorphism (DT-RFLP) strategies to separate DNA targets based on restriction enzyme polymorphisms, and is available for free download on Windows, Mac OS and Linux for non-commerical purposes.
• Read the full description
• Download DRAT

RNCEPRNCEP: global weather and climate data at your fingertips

Published online 26 July 2011

Recognising the importance of atmospheric data to ecological systems, RNCEP is a package of open-source R functions which access, organise and visualise freely available atmospheric data from two long-term, high-quality, global atmospheric data sets.
Read the full description
Download RNCEP

MOTMOTMOTMOT: models of trait macroevolution on trees

Published online 29 June 2011

MOTMOT is a open-source package, written in the R, that tests for variation in the tempo and mode of continuous character evolution on phylogenetic trees.
• Read the full description
• Download MOTMOT [CRAN]


TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data

Published online 10 June 2011

TempNet is a user-friendly open-source R script that creates customizable, interactive, journal-quality figures within the R graphics window, from genetic data in standard formats such as FASTA and CLUSTAL.
Read the full description
• Download TempNet

RBrownieRBrownie: an R package for testing hypotheses about rates of evolutionary change

Published online 25th May 2011

RBrownie is an interface between the Brownie phylogenetic library and the R software environment, which provides easy access to the main methods in Brownie - including discrete ancestral state reconstruction. In addition, RBrownie supplies a direct interface to Brownie, allowing advanced users to construct more complex combinations of analyses and to execute any newly added Brownie functions
Read the full description
View documentation [pdf]
Download RBrownie [CRAN] or from the author 

PASSaGE v.2PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2

Published online 15th December 2010

PASSaGE has been a popular tool for conducting spatial statistics for the past decade. Now re-written from the ground up with accessibility in mind, PASSaGE v.2 provides broad array of spatial statistical analyses not commonly found in other software packages or GIS software, and is still available to download for free.
Read the full description
View the user manual
Download PASSaGE v.2


FDiversity: a software package for the integrated analysis of functional diversity

Published online 14th December 2010

FDiversity is a free, user-friendly, open source software package for the calculation and integrated statistical analysis of most published functional diversity indices and metrics.
Read the full description
View the user manual
Download FDiversity

Python-based GIS toolsPython based GIS tools for landscape genetics: visualising genetic relatedness and measuring landscape connectivity

Published online 8th July 2010

This collection of freely available, Python-based scripts provides a set of GIS tools developed for use in landscape genetics studies, allowing users to convert files, visualise genetic relatedness, and measure landscape connectivity using least-cost path analysis.
Read the full description
Download the toolbox


WaderMORPH: a user-friendly individual-based model to advise shorebird policy and management

Published online 20th June 2010

WaderMORPH is a user-friendly interface to a shorebird individual-based model (IBM), MORPH, that runs within Microsoft Windows. WaderMORPH hides technical and mathematical details of parameterisation from the user, allowing easy access to the models that have been most successful at predicting the consequences of environmental change for coastal shorebirds.
Read the full description
View the user manual
Download WaderMORPH

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