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
mvabund
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]
BaSTA
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.
abc
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]
NichePy
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
RNetLogo
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.
phytools– 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)
smatr 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]
PMx: 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
REDDcalculator.com: 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 REDDcalculator.com
• Download an offline version [xlsm]
Directed 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
RNCEP: 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
MOTMOT: 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
RBrownie: 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: 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 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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