iEcology identifies extent of synthetic polymer habitats

22 01 2025

The internet has become an informational telescope to study what happens nearly everywhere the planet. Using internet observations, it has been recently documented that terrestrial hermit crabs use plastic waste as shelter along tropical coasts.

Before the internet irrupted, I was living in Spain and frequently travelled from my hometown to universities in Valencia and Barcelona to access scientific journals. Back then, these journals were only available in print or on compact discs. Today, I can do the same thing from home with an internet connection.

 The emergence of public internet since the 1990s has globalised information and represents a data source for many areas of science (1, 2). When applied to nature, the term iEcology (internet Ecology) refers to the use of online documentation to study the natural history of plants and animals, their distributions, and the effects of humans on them (3). In fact, the internet highlights and promotes certain research topics. For example, bird species that are more frequently mentioned on social networks tend to be described taxonomically earlier, and are also the ones that interact most (positively or negatively) with human activity (4).

In search of the phenomenon

By exploring internet platforms Alamy, Flickr, Google, YouTube, and iNaturalist, Zuzanna Jagiello and her collaborators collected nearly 30 thousand photographs of hermit crabs to study the use of rubbish by these crustaceans (5). Hermit crabs are known for their peculiar habit of using empty snail shells to house their unprotected abdomens, carrying them around like someone travelling with their house on their back (6) — David Attenborough narrates here a funny swapping of shells among crabs of different size. The researchers aimed to assess the extent of the phenomenon of hermit crabs replacing natural shells with artificial materials as mobile homes (see video capturing the scene).

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Categories : citizen science, marine, ocean, pollution, research, science

The (new) birds and the bees

20 01 2025

‘Nuff said


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Categories : agriculture, algae, anthropocene, biodiversity, birds, bottom-up ecology, conservation, ecology, ecosystem services, extinction, pollination

Add a voice update to your loops in R

15 01 2025

If you’re like me, you use a lot of loops in R. I do not profess to be the most efficient coder, but loops make sense to me and I’m generally not concerned about make the fastest simulations.

But sometimes my loops take some time to finish, so I often add a rolling text update during the simulation to know how far it has progressed. But of course, I have to look at the R console to see how far things have come. Being a bit away from the central tendency of the spectrum, I can get absorbed in doing other things, so I often miss when the simulation is complete.

In a fit of excess geekiness, I’ve recently discovered voice prompts in MacOS that I can now code directly into my R simulations to give verbal updates on their progress. I find these immensely useful. I’ve therefore decided to share the basic code, because I know some other geeks out there might also appreciate the tool. Apologies — I haven’t investigated how to do this in a PC environment, so the following examples are MacOS-specific.

First, go to your Accessibility settings in System Settings in your Mac. Click on System Voice to see what voices you have access to, and which voices you wish to download to your machine. There are many languages supported.

When you construct a loop in R, add the following code within and before the loop content (this example is in English):

iter <- 1000 # number of iterations
itdiv <- iter/100 # iteration divisor 1
itdiv2 <- iter/10 # iteration divisor 2
st.time <- Sys.time() # time at start of simulation

# loop from 1 to iter
for (i in 1:iter) {
    
    # pause execution for 0.05 seconds (this would normally be the guts of your loop functions)
    Sys.sleep(0.05)
    
    # loop updaters with voice (English)
    if (i %% itdiv==0) print(paste("iter = ", i, sep=""))
    
    if (i %% itdiv2==0 & i < iter) system2("say", c("-v", "Fiona", paste(round(100*(i/iter), 0), 
                                            "per cent complete"))) # updates every 10% complete
    if (i == 0.95*iter) system2("say", c("-v", "Fiona", paste(round(100*(i/iter), 0), 
                                 "per cent complete"))) # announce at 95% complete
    if (i == 0.99*iter) system2("say", c("-v", "Fiona", paste(round(100*(i/iter), 0),
                                 "per cent complete"))) # announce at 99% complete
      
    if (i == iter) system2("say", c("-v", "Lee", "simulation complete"))
    if (i == iter) system2("say", c("-v", "Lee", paste(round(as.numeric(Sys.time() - st.time,
                            units = "mins"), 2), "minutes elapsed")))
}

Here I’ve used the female Scottish voice ‘Fiona’ and the male Australian voice ‘Lee’.

Here’s an example in French:

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Categories : conservation