Where does Hubbell’s ‘species generator’ come from?

On page 289 onwards, Hubbell (2001) gives an algorithm for sequentially sampling individuals from the neutral metacommunity and obtaining their species identities. The algorithm makes use of a quantity he calls the ‘species generator’ \[ \frac{\theta}{\theta + j – 1} \] where \( \theta \) is the “fundamental biodiversity number” and \( j \) is the index of the individual drawn (1st, 2nd, …). In … Continue reading Where does Hubbell’s ‘species generator’ come from?

Boolean qualitative modelling on Christmas Island

Conservation managers often want us to predict how species will respond to different management options when we don’t have enough data to parameterise a dynamical model. Previously, we found that a popular Qualitative Modelling technique involving probabilistic analysis has philosophical problems and produces contradictory results. We proposed a new method, based on Boolean analysis, that remedied these problems (Kristensen et al. 2019 Meth Ecol Evol). … Continue reading Boolean qualitative modelling on Christmas Island

Extended Tea Bag Index to measure microbial- and termite-driven decomposition in the tropics

Our new paper about using the Tea Bag Index in the tropics, headed by Aloysius Teo, has just come out in Pedobiologia. The Tea Bag Index (TBI) was designed by Keuskamp et al. (2013) as a standardised and cheap method to quantify microbial-driven decomposition by measuring the mass loss of tea within tea bags. It can be used by scientists and citizen-scientists alike. However, we … Continue reading Extended Tea Bag Index to measure microbial- and termite-driven decomposition in the tropics

Example debugging mixed Python C++ in VS Code

Visual Studio Code has the ability to debug mixed Python with C++ extensions. In this blog post, I give an example of how to get it working. I’m going to do the example from scratch in five steps: Make virtual environment. Chances are that, if you’re doing this kind of thing, you’ll be wanting to use a virtual environment too. Write code. My toy example … Continue reading Example debugging mixed Python C++ in VS Code

Transient dynamics in neutral models

In their 10-year-anniversary review of neutral theory (Hubbell, 2001), Rosindell et al. (2011) note that little work has been done on the model’s transient dynamics. Transient dynamics are nonetheless interesting because they can capture important processes occurring in recently disturbed landscapes. For example, if forest is cleared such that only a small patch remains, then the number of species in that patch will continue to … Continue reading Transient dynamics in neutral models

Extinction of undiscovered butterflies + tutorial

Meryl Theng just had a new paper published in Biological Conservation, where she estimated that 46% of Singapore’s butterfly species have been extirpated since 1854. The special thing about this estimate is that it includes all species that existed, including species that went extinct before we had a chance to discover them. The trick to estimating undiscovered extinctions is the SEUX model. There is a … Continue reading Extinction of undiscovered butterflies + tutorial

New solutions for Parker sperm competition model

Parker et al. (2013) created a general model for sperm allocation under a trade-off between male investment of resources \(R\) into pre-copulatory effort (e.g. search time) \(T\) versus post-copulatory effort (e.g. ejaculate) \(U\). Their model is interesting because it encompasses a range of different scenarios of female remating and the type of competition between males. For female remating scenarios, the risk model has females mating … Continue reading New solutions for Parker sperm competition model

Playing with a new model for fugitive coexistence

I recently read a paper by Kawecki (2017), which presents a new mechanism for something analogous to fugitive coexistence. The paper has a really great literature overview, which I won’t be able to do justice here. In short, fugitive coexistence is when an inferior species persists on a patchy landscape by being a better coloniser: when a local extinction occurs, they are quicker to arrive … Continue reading Playing with a new model for fugitive coexistence