Quantifying and estimating ecological network diversity based on incomplete sampling data

An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic, and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species’ phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyze network sampling data. The proposed method integrates the following four inference procedures: (i) Assessment of sample..., The experiment underlying the data was conducted by Vogel and colleagues in the Steigerwald forest located in northern Bavaria, Germany (49°32' N; 10°23' E). The Steigerwald forest covers around 16,500 ha of forests from colline up to sub-montane mountain range with a mean annual temperature around 8 °C and an annual precipitation around 750 to 800 mm (forest climate station Ebrach). Temperatures higher than 10°C are reached on about 160 days per year. 
In 2015, six study sites (Plot A−F) were established. We focus on the data based on two subplots within each plot: (1) open habitat (sun-exposed on a forest meadow), and (2) closed habitat (canopy-shaded within a closed forest stand). Freshly cut logs and branch bundles of six tree species (Abies alba, Carpinus betulus, Fagus sylvatica, Pinus sylvestris, Populus tremula and Quercus petraea) were exposed on each subplot. Deadwood objects were sampled for saproxylic beetles using stem emergence traps. With this sampling technique, it is po..., In this dataset, R code and data are provided for plotting all figures in the paper \"Quantifying and estimating ecological network diversity based on incomplete sampling data\". Before using the R code, you must download the packages \"iNEXT.3D\", \"iNEXT.4steps\", \"iNEXT.beta3D\", and \"iNEXT.link\" from Anne Chao's Github at  https://github.com/AnneChao?tab=repositories
Part of the dataset is also avialable from the repository \"PTB_iNEXT.link\" on Anne Chao's Github at https://github.com/AnneChao/PTB_iNEXT.link
The data used for examples are based on tree-beetle interaction frequency data collected from 2016 to 2019 in six study sites (Plot A−F) located in the Steigerwald forest, Germany. Taxonomic data were adapted from Vogel et al. (2020); the phylogeny and trait-based functional distance for beetle species were based on Hagge et al. (2021) and Seibold et al. (2015) respectively.
This dataset includes the following files:
(1) Data Files:
(1a) \"Data tree-beetle interaction frequency.csv\" (for...