A brief history about the R package ‘metan’

Post provided by Tiago Olivoto

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In our recent paper in Methods in Ecology and Evolution, Alessandro Lúcio and I describe a new R package, metan, for multi-environment trial analysis. Multi-environment trials are a kind of trial in plant breeding programs where several genotypes are evaluated in a set of environments. Analyzing such data requires the combination of several approaches including data manipulation, visualization and modelling. The latest stable version of metan (v1.5.1) is now on CRAN. So, I want to share the history about my first foray into using R, creating an R package, and submitting a paper to a journal that I’ve never had submitted before.

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Uma breve história sobre o pacote R ‘metan’

Post ESCRITO POR Tiago Olivoto

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Em nosso recente artigo na Methods in Ecology and Evolution, Alessandro D. Lúcio e eu descrevemos um novo pacote R para análise de ensaios multi-ambientes chamado metan. Ensaios multi-ambientes são um tipo de ensaio em programas de melhoramento de plantas, onde vários genótipos são avaliados em um conjunto de ambientes. A análise desses dados requer a combinação de várias abordagens, incluindo manipulação, visualização e modelagem de dados. A versão estável mais recente do metan (v1.5.1) está disponível agora no repositório CRAN. Então, pensei em compartilhar a história da minha primeira incursão no uso do R criando um pacote e submetendo um artigo para uma revista que nunca havia submetido antes.

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An interview with the editors of “Population Ecology in Practice”: Part I

Post provided by Daniel Caetano

Today we bring the first part of an interview with Dennis Murray and Brett Sandercock about their brand new book in population ecology methods: “Population Ecology in Practice.” The editors were kind enough to share some interesting backstage information with us.

Snowshoe hare in winter

Population Ecology in Practice introduces a synthesis of analytical and modelling approaches currently used in demographic, genetic, and spatial analyses. Chapters provide examples based on real datasets together with a companion website with study cases and exercises implemented in the R statistical programming language.

Stay tuned for the second part of this interview, where we talk about some of the challenges of editing a large book and the editors share essential advice for anyone looking into leading such a project!

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10th Anniversary Volume 1: The Art of Modelling Range-Shifting Species

Post provided by Jane Elith, Mike Kearney and Steven Phillips  

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 1, we have selected ‘The art of modelling range-shifting species’ by Elith et al. (2010).  In this post, first author, Professor Jane Elith, discusses the background and key concepts of the article, and how things have changed since the paper was published.

Illustration of the idea that model settings affect prediction.

We started work on this manuscript around 2008, prompted by increasing use of species distribution models for climate change and invasive species problems. At that stage there was growing recognition of the problems in these applications (e.g. see a recent MEE review on transferability) but relatively few tools for dealing with them. In our view, if correlative models are to be used for such purposes, the data and models require special attention.

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Reconnecting the Web of Life: Rewiring and Network Robustness


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Species Loss and Cascading Effects

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Minimising the effects the ongoing Anthropocene mass extinction has become one of the main challenges of our era. The data suggest that the current rate of species loss is 100–1,000 greater than the background rates seen in the geological record. “But does it really matter if species are lost?” This question has permeated social and political debates. It’s usually used to demean conservation efforts. But it has also intrigued conservation scientists.

We know that species don’t occur alone in their environment. They’re entangled by their interactions, forming complex networks. In these networks the loss of one species may result in the loss of other species that depend on it. This process is known as co-extinction. Estimates of the magnitude of past and future extinction rates have often failed to account for the interdependence among species and the consequences of primary species loss on other species though. Continue reading

Religando a rede da vida: Reconexões de interações e a robustez de redes ecológicas


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Perda de espécies e efeitos em cascata

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Rabo-branco-de-garganta-rajada (Phaethornis eurynome). ©Pedro Lorenzo.

Minimizar os efeitos do atual processo de extinção em massa do Antropoceno se tornou um dos principais desafios da nossa era. Os dados sugerem que a taxa atual de perda de espécies é 100-1.000 vezes maior do que as taxas de fundo observadas no registro geológico. “Mas realmente importa se uma espécie é perdida?” Essa questão que permeia os debates sociais e políticos, geralmente para desqualificar os esforços de conservação, também tem intrigado os cientistas da conservação.

Sabemos que as espécies não ocorrem sozinhas em seu ambiente. Elas estão  interligadas por suas interações ecológicas, formando redes complexas. Nessas redes, a perda de uma espécie pode resultar em um efeito dominó, culminando na perda secundária de outras espécies. Esse processo é conhecido como co-extinção. As estimativas da magnitude das taxas de extinção passadas e futuras muitas vezes falharam em explicar a interdependência entre as espécies e as conseqüências da perda primaria de espécies. Continue reading

What method has transformed your field the most, during your career?

In the 4th and final installment of Barb Anderson’s INTECOL 2013 podcasts, she asks a number of delegates: What method has transformed your field the most, during your career?

The answers in this podcast are given by the following people:

  1. Steve Hubbell, University of California, Los Angeles, USA (00.21)
  2. Georgina Mace, University College London, UK (00.44)
  3. Carsten Dormann, University of Freiburg, Germany (01.07)
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What are the newest methods being used?

At INTECOL 2013, Methods’ Associate Editor, Barb Anderson, interviewed a number of delegates and asked them: What is the newest method that you currently use?

The answers in this podcast are given by the following people:

  1. Bill Sutherland, University of Cambridge, UK (00.18)
  2. Georgina Mace, University College London, UK (01.04)
  3. Simon Leather, Harper Adams University, UK (01.12) Continue reading