Issue 8.8

Issue 8.10 is now online!

The October issue of Methods is now online!

This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

 Phylogenetic TreesThe fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.

 Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.

 Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

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Issue 8.5

Issue 8.5 is now online!

The May issue of Methods is now online!

This issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

MatlabHTK: A software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing.

 PrimerMiner: The R package PrimerMiner batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units to reduce biases introduced by the different number of available sequences per species.

 BarcodingR: 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.

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The Field Guide to Sequence-Based Identification of Biodiversity: An Interview with Simon Creer

In a new Methods in Ecology and Evolution podcast, Georgina Brennan (Bangor University) interviews Simon Creer (Bangor University) about his article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘. They talk about about where the idea for the paper came from, what it’s aim are and who will benefit from it. We hear how new sequences can improve and enhance current biomonitoring programmes (and make them quicker and cheaper).

To find out more about Sequence-based Identification of Biodiversity, read the Open Access Methods in Ecology and Evolution article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘.

 

Issue 8.3

Issue 8.3 is now online!

The March issue of Methods is now online!

This issue contains two Applications articles and one Open Access article. These three papers are freely available to everyone, no subscription required.

 Solo: Solo audio recorders are inexpensive, easy to construct and record audible sound continuously for around 40 days. The paper also has a video tutorial explaining how to assemble the required hardware and comes with a companion website with more information.

 The third dimension: A novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140m. The set-up consists of two synchronised 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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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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