Data and scripts for PCA analysis of BIOLOG Ecoplate data from soil samples taken at mixed gull colony

Raw data and scripts needed to reproduce the principal component analysis and calculate diversity counts as described in the method section and supplementary files (S2.8 and S3) of my thesis "Inter-species, spatial, and temporal variability in soil properties of a colony of lesser black-backed and European herring gulls on Texel island". Raw data consists of read-outs of BIOLOGTMEcoplates using the SPECTROstar Nano microplate reader. The measuring protocol information from the SPECTROstar Nano microplate reader is also made available. First run dbEcoplates.R to construct a usable dataframe with organised data, in order to calculate the diversity count and conduct a PCA analysis with the script PCAEcoplates.R. For a detailed description of the sampling strategy, see my thesis. Here, a short description follows, describing the numeric values for some categories that were used in the building of the ecoplates database. Sampling took place in June (month 1), August (month 2) and October (month 4), there was ecoplate analysis performed on samples from September (month 3). Nest types were limited to active nest sites of lesser black-backed gulls, (1) and European herring gulls (2), club sites of lesser black-backed gulls (3) and European herring gulls (4), control sites (5) and old nest sites (6), Locations are active nest sites (1), club sites (2), control sites (3) and old nest sites (4) Species are limited to lesser black-backed gulls (1), european herring gulls (2) and control sites, which contained no species (3) Abbreviations for axes and titles are constructed as follows: "L" in front of AN, CLS, or ON, or "LBBG" on its' own pertains to a site that belongs to the lesser black-backed gull "E" in front of AN, CLS or ON, or "EHG" on its' own pertains to a site that belongs to the European herring gull "AN" is an active nest site "CLS" is a club site "ON" is an old nest site "COS" is a control site