Issue 8.2

Issue 8.2 is now online!

The February issue of Methods is now online!

This issue contains four(!) Applications articles and two Open Access articles. These six papers are freely available to everyone – no subscription required.

 Earth Mover’s Distance: The Earth Mover’s Distance (or EMD) is a method commonly used in image retrieval applications. The authors of this paper propose its use to calculate similarity in space use in the framework of movement ecology. This will be helpful for many questions regarding behavioural ecology, wildlife management and conservation.

 warbleR: The R package warbleR is a new package for the analysis of animal acoustic signal structure. It offers functions for downloading avian vocalisations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, and much more.

– meteR: The open-source R package, meteR directly calculates all of Maximum entropy theory of ecology’s (METE’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.

– Noise Egg: The Noise Egg is a device that can produce a low-frequency sound, which can be used as an experimental source of noise both in aquaria and in the field. It was developed to study the effects of noise on communication and behaviour in small aquatic animals; however, it could be used for other purposes, such as testing the propagation of certain frequencies in shallow-water habitats.

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Issue 8.1

Issue 8.1 is now online!

The January issue of Methods is now online!

All of the articles in this month’s issue of Methods in Ecology and Evolution are free for the whole year. You will not need a subscription to access or download any of them throughout 2017.

Our first issue of this year contains three Applications articles and two Open Access articles. These five papers will be freely available permanently.

– CDMetaPOP: Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

– Rphylopars: An R implementation of PhyloPars, a tool for phylogenetic imputation of missing data and estimation of trait covariance across species (phylogenetic covariance) and within species (phenotypic covariance). Rphylopars provides expanded capabilities over the original PhyloPars interface including a fast linear-time algorithm, thus allowing for extremely large data sets (which were previously computationally infeasible) to be analysed in seconds or minutes rather than hours.

– ggtree: An R package that provides programmable visualisation and annotation of phylogenetic trees. ggtree can read more tree file formats than other software and allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.

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Issue 7.12

Issue 7.12 is now online!

The final 2016 issue of Methods is now online!

This month’s issue contains four Applications articles and two Open Access articles, all of which are freely available.

– iNEXT: The R package iNEXT (iNterpolation/EXTrapolation) 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).

– camtrapR: A new toolbox for flexible and efficient management of data generated in camera trap-based wildlife studies. The package implements a complete workflow for processing camera trapping data.

– rotl: An R package to 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.

– Fluctuating-temperature chamber: A design for economical, programmable fluctuating-temperature chambers based on a relatively small commercially manufactured constant temperature chamber modified with a customized, user-friendly microcontroller.

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Issue 7.11

Issue 7.11 is now online!

The November issue of Methods is now online!

This month’s issue contains four Applications articles and two Open Access articles, all of which are freely available.

– moveHMM: This R package 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, in particular, for the incorporation of environmental covariates.

– BORIS: An open-source and multiplatform standalone program that allows a user-specific coding environment to be set for a computer-based review of previously recorded videos or live observations. Being open to user-specific settings, the program allows a project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified.

– inbreedR: An R package that provides functions to measure variance in inbreeding – through the strength of correlation in heterozygosity across marker loci – based on microsatellite and SNP markers with associated P-values and confidence intervals. Within the framework of Heterozygosity–fitness correlation theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness.

– Terrestrial Precipitation Analysis: This package is comprised of the 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.

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Issue 7.8

Issue 7.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

Plant-O-Matic: A free iOS application that combines the species distribution models with the location services built into a mobile device to provide 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.

RClone: An R package built upon genclone software which includes functions to handle clonal data sets, allowing:

  • Checking for data set reliability to discriminate multilocus genotypes (MLGs)
  • Ascertainment of MLG and semi-automatic determination of clonal lineages (MLL)
  • Genotypic richness and evenness indices calculation based on MLGs or MLLs
  • Describing several spatial components of clonality

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State-and-Transition Models: An Interview with Marie-Josee Fortin

David Warton (University of New South Wales) interviews Marie-Josee Fortin (University of Toronto) about a recent article on state-and-transition models from her group in Methods in Ecology and Evolution. David and Marie-Josee also discuss what motivated her career to date in spatial ecology, and what she sees as the main advances in this area and current challenges in the field.

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Issue 7.7

Issue 7.7 is now online!

The July issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.

– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..

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Issue 7.6: Methods in Ecology and Evolution 5th Anniversary Special Feature

Issue 7.6 is now online!

The June issue of Methods, which includes our latest Special Feature – “5th Anniversary of Methods in Ecology and Evolution” – is now online!

Our 5th Anniversary Special Feature is a collection of six articles (plus an Editorial from Executive Editor Rob Freckleton) that highlights the breadth and depth of topics covered by the journal so far. It grew out of our 5th Anniversary Symposium – a joint event held in London, UK and Calgary, Canada and live-streamed around the world in April 2015 – and contains papers by Associate Editors, a former Robert May prize winner and regular contributors to the journal.

The six articles are based on talks given at last May’s Symposium. They focus on:

In his Editorial for the Special Feature, Rob Freckleton looks to the future. In his words: “we hope to continue to publish a wide range of papers on as diverse a range of topics as possible, exemplified by the diversity of the papers in this feature”.

All of the articles in the Special Feature will be freely available for a limited time. In addition to this, two of the articles (Shedding light on the ‘dark side’ of phylogenetic comparative methods and Perturbation analysis of transient population dynamics using matrix projection models) are Open Access.
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Issue 7.4

Issue 7.4 is now online!

The April issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

CPW Photo Warehouse: freely available software that has been customized to identify, archive, and transform photographs 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, import photos and store data. Images are seamlessly incorporated into the database windows, but are stored separately.

SIMR: An R package that 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 (i) running a power analysis for a given model and design; and (ii) calculating power curves to assess trade-offs between power and sample size.

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Issue 7.3

Issue 7.3 is now online!

The March issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

METAGEAR: A comprehensive, multifunctional toolbox with capabilities aimed to cover much of the research synthesis taxonomy: 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.

Universal FQA Calculator: A free, open-source web-based Floristic Quality Assessment (FQA) Calculator. The calculator offers 30 FQA data bases (with more being added regularly) from across the United States and Canada and has been used to calculate thousands of assessments. Its growing repository for site inventory and transect data is accessible via a REST API and represents a valuable resource for data on the occurrence and abundance of plant species. Continue reading