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.

Gregory Roth and Hal Caswell provide this month’s first open access article: ‘Hyperstate matrix models: extending demographic state spaces to higher dimensions‘. In their article the authors present a framework, called hyperstate matrix model, in which individuals may be classified by any number of characteristics, using the generalisation of the vec-permutation approach to hypermatrices. They apply this approach to a three-dimensional example in which individuals are classified by developmental stage, age and heterogeneity classes. The analysis of this model provides insights into how the heritability of the heterogeneity classes affects the long-term growth rate of the population.

How to manipulate landscapes to improve the potential for range expansion‘ by Jenny Hodgson et al. is our second Open Access article in this issue. The authors propose and test two methods that can help to optimise the spatial arrangement of habitat for range expansion. This article lays the foundation for a new genre of systematic conservation planning, which efficiently proposes restoration while minimising loss. You can find out more about this article in the blog post ‘Planning Habitat for Very Long-Distance Connectivity under Climate Change‘ by Jenny Hodgson.

Our December issue also features articles on Population Ecology, Evolutionary Biology, Monitoring, Statistical Ecology and much more.

This month’s cover image shows a beautiful, brilliantly coloured fairy pitta (Pitta nympha) perched on a bamboo branch. The migratory fairy pitta breeds in Northeast Asia (Japan, South Korea, east China and Taiwan) from late April to September and winters mainly in Borneo from October to March. In Taiwan, the fairy pitta is also called the “eight coloured bird” (as there are eight colours in its plumage: beige, yellow, green, brown, black, white, red on the vent area, and shiny blue on its wings) or the “little forest fairy” (as its body length is around 16–19 cm). The fairy pitta is rare and elusive, and is classified as Vulnerable on the IUCN Red List, mainly due to the destruction of its primary habitats.
The majestic beauty of this fairy has provided the authors of ‘iNEXT: An R package for rarefaction and extrapolation of species diversity (Hill numbers)’ with a wealth of inspiration in formulating their methodology and relevant software to compute and plot the seamless sample-size- and sample-coverage-based rarefaction and extrapolation sampling curves for species diversity. Hsieh, Ma and Chao developed the iNEXT (iNterpolation and EXTrapolation) R package, which features an easy-to-use interface and effi ciently uses all data to not only make robust and detailed inferences about the sampled assemblages, but also to make objective comparisons of species diversity among multiple assemblages.

Photo © Jia Hong Chen

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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