Issue 8.11

Issue 8.11 is now online!

The November issue of Methods is now online!

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

 LSCorridors: LandScape Corridors considers stochastic variation, species perception and landscape influence on organisms in the design of ecological corridors. It lets you simulate corridors for species with different requirements and considers that species perceive the surrounding landscape in different ways.

 HistMapR: HistMapR contains a number of functions that can be used to semi-automatically digitize historical land use according to a map’s colours. Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. This manuscript has a companion video and was recommended by Associate Editor Sarah Goslee.

 vortexR: An R package to automate the analysis and visualisation of outputs from the population viability modelling software Vortex. vortexR facilitates collating Vortex output files, data visualisation and basic analyses (e.g. pairwise comparisons of scenarios), as well as providing more advanced statistics.

 FLightR: Accurate reconstruction of the annual schedules and movement patterns of individual animals requires estimates of daily locations, distances between the locations and the directions of movement. The new R package FLightR meets all these requirements. It enables refined and statistically validated estimations of movement patterns of birds.

 TropFishR: The R package TropFishR is a new analysis toolbox compiling single-species stock assessment methods specifically designed for data-limited fisheries analysis using length-frequency data. It modernises traditional stock assessment methods by easing application and development and by combining it with advanced statistical approaches.

 frairThe R package frair provides tools for selecting and differentiating various forms of consumer functional response models, a consistent interface for fitting and visualising response curves, and a selection of statistically robust methods for comparing fitted parameters.

– rptR: The R package rptR allows you to estimate Intra-class correlations and repeatabilities for Gaussian, binomial and Poisson-distributed data. Uncertainty in estimators is quantified by parametric bootstrapping and significance testing is implemented by likelihood ratio tests and through permutation of residuals.

The first Open Access article in this issue – by David Warton and Francis Hui – is part of a forum debate mean-variance ratios. ‘Distance, dissimilarity, and mean–variance ratios in ordination‘ by David Roberts is the first article in the debate. Roberts re-evaluates previous work on the importance of aligning distance- or dissimilarity-based methods with the mean–variance ratios of underlying data and extends the analyses to additional simulated data designed to test the specific assertions of model-based advocates with respect to ordination analysis.

In ‘The central role of mean-variance relationships in the analysis of multivariate abundance data: a response to Roberts (2017)‘, Warton and Hui use simulations to show that mean-variance relationships are important in understanding properties of distance-based analyses, and that row standardisation does not fix the problem of apparent location-dispersion confounding.

Casalegno et al. provide the second Open Access article in our Novemberber issue: ‘Improving models of urban greenspace: from vegetation surface cover to volumetric survey, using waveform laser scanning‘. The authors explain that waveform lidar has a key role to play in estimating important quantitative metrics of urban green infrastructure, which is important because urban greenspace is highly fragmented and shows high levels of spatial and volumetric heterogeneity.

The final Open Access article in this issue is ‘A general sampling formula for community structure data‘ by Haegeman and Etienne. In this article, the authors argue that many of the technical problems with neutral community theory can be overcome by replacing the assumption of constant community size (the zero-sum constraint) by the assumption of independent species abundances.

Our November issue also features articles on Conservation, Movement Ecology, Community Ecology, Population Ecology, Measurement and more.

This month’s cover image shows the topography of both scales and fi n rays on the surface of the pectoral fin of a polypertus (warm colours are higher, cool colours are lower). In general, capturing surface topography is difficult in biology because most methods require specimen preparation or work best on areas that are too small. To capture this image, Wainwright et al. used an existing technique called gel-based profilometry that shows great promise for biology because it allows for rapid imaging of surface topography without the need for preparation. Also, it can image at biologically relevant sizes (square centimetres to square millimetres) with high spatial resolution (over 18 million 3D points per image).

In ‘Imaging biological surface topography in situ and in vivo’ the authors use fish scales to demonstrate the utility of this method, and we show how gel-based profilometry is able to capture surface topography of shiny, wet, and clear surfaces as well as surfaces of live fish with mucus coats intact. They also demonstrate this technique’s ability to reconstruct surface topography from a variety of biological samples, ranging from bat wings and squid suckers to fossilised trilobites.

Photo: © Dylan Wainwright

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

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