Dr Philipp Boersch‑Supan

Quantitative Ecologist

New paper - Bayesian inference for DEB models

A new paper with Leah Johnson on Bayesian inference in Dynamic Energy Budget models has just been published in the Journal of Sea Research: Two case studies detailing Bayesian parameter inference for dynamic energy budget models.

Our paper walks through two case studies to illustrate how the parameters for two different types of dynamic energy budget models can be inferred from data using the deBInfer R package.

An open access preprint can be found on bioRxiv and the code underlying the paper is archived on zenodo.

graphical summary

New paper - Ranavirus prevalence in free-living frogs

A new paper with the QDEC Lab and collaborators from SUNY-ESF on the prevalence of ranavirus in tadpoles of free-living frogs has just been published in EcoHealth: Environmental Drivers of Ranavirus in Free-Living Amphibians in Constructed Ponds.

Our paper uses generalised linear models fitted in a Bayesian inference framework to analyze four years of Frog virus 3 prevalence and associated environmental parameters in populations of wood frogs (Lithobates sylvaticus) and green frogs (Lithobates clamitans) in a constructed pond system. We identified important variables to measure in assessments of ranaviral infection risk in newly constructed ponds, including effects of zooplankton, which have not been previously quantified in natural settings. High prevalence was best predicted by low temperature, high host density, low zooplankton concentrations, and Gosner stages approaching metamorphosis.

graphical summary

Mapping one's academic career path

Yesterday I came across Gordon Pennycook’s tweet about moving in academia:

So given that there’s a transatlantic move coming up for me to take up my first permanent research position at the British Trust for Ornithology, I thought, why not figure this out quickly using R.

library(ggmap)# for geocoding and plotting 
library(geosphere)# for distance calculations
library(knitr)# for making a nice table

I used ggmap::geocode to look up the coordinates of each station on my academic career path:

academic_places <- geocode(c(home = "Neustadt an der Weinstrasse",
                             undergrad = "Marburg an der Lahn",
                             masters_phd = "St Andrews, Fife",
                             phd = "Oxford, Oxfordshire",
                             postdoc1 = "Cambridge, UK",
                             postdoc2a = "Tampa, FL",
                             postdoc2b = "Gainesville, FL",
                             job = "Thetford"),
                           source = "dsk")

A quick plot to sanity check the locations

#make a map
qmplot(lon, lat, data = academic_places, maptype = "watercolor", color = I("red")) + geom_path(color = "red")

I then used the geosphere package to calculate sequential distance between stations

#calculate distances
distances_m <- distGeo(as.matrix(academic_places[,2:3]))

#transform units
distances_km <- distances_m/1000
distances_mi <- distances_m/1609

And lastly, I made a table to sum up everything.

#make a table
kable(data.frame(stage = c(academic_places[-1,1], "Total"),
                 distance_km = round(c(distances_km, sum(distances_km))),
                 distance_mi = round(c(distances_mi, sum(distances_mi)))))
stage distance_km distance_mi
undergrad 172 107
masters_phd 992 617
phd 516 321
postdoc1 107 67
postdoc2a 7121 4426
postdoc2b 185 115
job 7005 4354
Total 16099 10006

New job - I am joining the British Trust for Ornithology

I’m thrilled to announce that I will be moving back to the United Kingdom this Spring to join the British Trust for Ornithology as an Ecological Statistician.


New paper - Albatross egg temperatures

graphical summary

New paper published on egg temperature ontogenies in subantarctic albatrosses:

Knowledge of thermal traits is essential for understanding and modelling physiological responses to environmental change. Egg temperatures are poorly studied in most tubenose species. Our new study Surface temperatures of albatross eggs and nests fills a part of this data gap.

We used a contactless infrared thermometer to measure egg and nest surface temperatures throughout the incubation period for four albatross species at Bird Island, South Georgia. Observed egg temperatures were lower than the egg temperatures reported for most Procellariiformes. Temperature gradients across viable eggs declined by up to 9°C during incubation, reflecting increased embryonic circulation and metabolic heat production. This suggests that bioenergetic models should not assume constant egg temperatures during embryo development. Non-viable (addled) eggs could be identified by large temperature gradients in late incubation, indicating that infrared thermometry can be used to determine whether the embryo has died or the egg is infertile in monitoring and managed breeding (e.g. translocation) programmes. Egg temperatures were correlated with ground temperatures, indicating that incubated eggs are vulnerable to environmental variability.

This study was conducted in collaboration with Leah Johnson, Richard Phillips, and Sadie Ryan.