These analysis were done in the context of my Ph.D. at the University of Auckland. The primary goal was to identify any effect of fine-scale oceanic features (namely chlorophyll fronts), on the diversity of the planktonic community.

The analysis was done exclusively on R 4.0.1, using a code similar to the one available on my github. Information on the EcoTaxa project 11231 is also available here.

While the draft images where done on R using ggplot2, the figures used in the resulting article were edited by David Pierre Milesi-Gaches using Inkscape. This significantly improved their readability.

Pre-processing of the data

Considering the data was acquiered using two methods accross the three size classes selected (20-200 μm, 200-500 μm, 500+ μm), quite a bit of cleaning was requiered to obtain one global dataset that R could utilise properly.

Sampling

The sampling was done accross four dates, time 16 samples, covering two seasons (summer and autumn).

Sampling map with bathymetry as background. Samplings blue and orange done in Summer, teal and green done in Autumn. Credit David Pierre Milesi-Gaches

Species composition & Species diversity (α, β, and γ)

Basic species composition barplots were obtained using ggplot2, and later edited on Inkscape. Getting the α diversity was the easiest, followed by the γ diversity, which I decided to separate based on the sampling dates. The β diversity was used using the generalised Sørensen dissimilarity index presented by Baselga (2010), and all indexes were plotted together. The overall result indicate a shift in species caused by the presence of chlorophyll fronts.

Species composition barplots and diversity indexes lines. Credit David Pierre Milesi-Gaches

For more information on the methods and results, please go to the article. For the code, please go to the github project.