The June issue of Methods is now online!
This month’s issue features articles on designing camera trap studies, measuring coral growth rates, quantifying carbon assimilation by marine calcifiers and much more.
Senior Editor Rob Freckleton has selected six featured articles this month – find out about them below. We’ve also got three Applications and a Practical Tools article which are freely available to everyone – no subscription required!
Camera trap study design:
Camera traps are a well-established survey tool for wildlife, but there has been little evaluation of study design parameters. This analysis of mammal camera trap data, from 41 study areas around the world, helps answer the questions – ‘How many sites do I need? How long should I run them? And when?’
Portable heaters (Practical Tools) free access: Field heating experiments are essential to test how global warming will change species interactions, but pose many logistical challenges. To facilitate these experiments, Baer et al. developed and tested portable active heaters suitable for heating microhabitats and sites of species interactions. Their adjustability and portability mean that studies can be run in many environments, particularly in remote and less developed areas.
EasieRR (Application) free access: EasieRR is an open-source stand-alone software for the analysis of heart rate variability in the time and non-linear domain. Special attention was placed on easy handling of the software, simplification of the artefact detection process and a transparent correction process. This was achieved by simultaneously displaying electrocardiogram, tachogram and Poincaré plots in the graphical user interface.
Lipid‐correction models: Lipid‐rich animal tissues have low δ13C values, and chemical lipid extraction can alter δ15N values, which can lead to inaccurate ecological inferences. Cloyed et al. studied the effects of lipid extraction on δ13C and δ15N values across taxa, tissues and trophic groups, and fit lipid‐correction models to these groups.
SuperCRUNCH: Constructing up‐to‐date supermatrices of phylogenetic data can be challenging, especially as new sequences may become available almost constantly. Here the authors present SuperCRUNCH, a versatile Python toolkit for creating large phylogenetic datasets from GenBank and local sequence data. It allows rapid construction of supermatrices, simplifying the process of updating large phylogenies with new data.
metan (Application) free access: Multi‐environment trials (MET) are crucial in plant breeding programs that aim at increasing crop productivity to ensure global food security. The analysis of MET data requires the combination of several approaches including data manipulation, visualization and modelling, and doing this correctly and completely remains a challenge. Here the authors present metan, a workflow-based R package for data manipulation and analysis of yield trials using parametric and non-parametric methods.
Applications and Practical Tools
We’ve also got three Applications articles and a Practical Tools article in this issue. Three of them have been covered in our featured articles above, so here is number four.
viewshed3d (Application) free access: The ability to visually assess the surrounding environment influences animal behaviour and ecology, but there is a lack of methods to quantify visibility in three-dimensional environments. Rachlow et al. developed the viewshed3d R package to quantify the visual environment from a single location or a cumulation of viewpoints, based on 3D point clouds acquired with Terrestrial Laser Scanning.
Other open access articles
Coral growth: Coral growth rates are essential metrics to quantify functional consequences of ongoing community changes on coral reefs. Emerging approaches, using underwater photogrammetry to create digital models of colonies, are providing novel and non‐invasive ways to address existing knowledge gaps. Lange & Perry have developed an easy‐to‐follow workflow to construct 3D models from overlapping photographs and to measure linear, radial and vertical extension rates of branching, massive and encrusting corals.
The Goat on the Cover
This issue’s cover shows a dairy goat (Capra aegagrus hircus) at the Leibniz Institute for Farm Animal Biology in Germany. The goat was participating in a project that assessed the physiological stress responses of goats towards stressors such as isolation and novelty.
Heart rate variability analysis has been established as a non-invasive approach to study the influence of the nervous system on the heartbeat cycle in humans and other animals. A low heart rate variability is caused by low influence of the parasympathetic nervous system and/or a high influence of the sympathetic nervous system, which can indicate a high level of stress.
Unfortunately, parameters of heart rate variability are highly sensitive to artefacts that arise from extra-cardiac muscle activity or bad contact between skin and the sensors. These issues are especially prevalent when recording heart activity in unrestrained animals. Hence, detection and correction of artefacts is essential for valid analysis.
However, analysis software is often expensive, difficult to use, and the process of artefact correction not transparent. This was the impetus for Rasmussen et al. to develop EasieRR – an open-access software for non-invasive heart rate variability assessment. This software has been optimised to assist in the processing of ECG data of non-restrained animals, also easing the analysis of time-domain and non-linear estimates of heart rate variability. Photo credit: ©Yves Wiesmann.
To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be showing up in issues later this year.