Meta-Analysis: How to Increase the Reach of Your Research and Make it Longer Lasting

Post provided by Katharina Gerstner

Like each coral, every single primary research study contributes to the larger picture.  © Wise Hok Wai Lum

Like each coral, every single primary research study contributes to the larger picture. © Wise Hok Wai Lum

Quantitative syntheses of primary research studies (meta-analysis) are being used more and more in ecological and evolutionary research. So knowing the basics of how meta-analysis works is important for every researcher. Meta-analytical thinking also encourages us scientists to see each single primary research study as a substantial contribution to a larger picture.

To be included in a meta-analysis, relevant primary research studies must be easy to find and basic information about the methods and results must be thoroughly, clearly and transparently reported. Moreover, papers with accessible data are the most useful for meta-analyses. Many published papers provide this information, but it’s not unusual for essential data to be omitted. Studies that are missing these details can’t be used in meta-analyses, which limits their reach. Continue reading


Issue 9.1: Qualitative Methods for Eliciting Judgements for Decision Making

Issue 9.1 is now online!

Our first issue of 2018, which includes our latest Special Feature – “Qualitative methods for eliciting judgements for decision making” – is now online!

This new Special Feature is a collection of five articles (plus an Editorial from Guest Editors Bill Sutherland, Lynn Dicks, Mark Everard and Davide Geneletti) brings together authors from a range of disciplines (including ecology, human geography, political science, land economy and management) to examine a set of qualitative techniques used in conservation research. They highlight a worrying extent of poor justification and inadequate reporting of qualitative methods in the conservation literature.

As stated by the Guest Editors in their Editorial “these articles constitute a useful resource to facilitate selection and use of some common qualitative methods in conservation science. They provide a guide for inter-disciplinary researchers to gauge the suitability of each technique to their research questions, and serve as a series of checklists for journal editors and reviewers to determine appropriate reporting.”

All of the articles in the ‘Qualitative methods for eliciting judgements for decision making‘  Special Feature are all freely available.
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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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