DOI: 10.5061/dryad.ksn02v78d
title: Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data

description: 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 completeness of networks, (ii) asymptotic analysis via estimating
 the true network diversity, (iii) non-asymptotic analysis based on
 standardizing sample completeness via rarefaction and extrapolation with
 network diversity, and (iv) estimation of the degree of unevenness or
 specialization in networks based on standardized diversity. Interaction
 data between European trees and saproxylic beetles are used for
 illustrating the proposed procedures. The software iNEXT.link is developed
 to facilitate all computations and graphics.
description: 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
 (<em>Abies alba, Carpinus betulus, Fagus sylvatica, Pinus
 sylvestris, Populus tremula</em> and <em>Quercus</em>
 <em>petraea</em>) were exposed on each subplot. Deadwood objects were sampled for saproxylic
 beetles using stem emergence traps. With this sampling technique, it is
 possible to collect emerging individuals, developing in deadwood, while
 excluding other occasional visitors. Traps were filled with saturated
 saline solution as sampling fluid and emptied monthly between April and
 September in 2016, 2017, 2018, and 2019. Beetles were classified as
 saproxylic according to Schmidl and Bussler
 (2004).  Within each plot and each
 habitat, data from the four years were pooled. Taxonomic data were adapted
 from Vogel et al. (2020); a summary table of statistics is provided in
 Table S3.1 of Appendix S3. The phylogeny and traits for beetle species
 were based on Hagge et al. (2021) and Seibold et al. (2015) respectively.
 All species were characterized by a set of 10 functional traits (Chao et
 al. 2019); species pairwise distances were computed from the Gower
 distance. 
description: 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) <strong>Data Files:</strong> (1a) "Data tree-beetle interaction frequency.csv" (for Figures 5 to 8 in the main text, and figures in Appendices S3 and S4): tree-beetle interaction frequencies. (1b) "Data phylo_tree.txt" (for Figures 6 and 7, and figures in Appendix S3): phylogeny tree for beetle species. (1c) "Data distance matrix.txt" (for Figures 6 and 7, and figures in Appendix S3): trait-based functional distance between any two beetle species. (2) <strong>"R code.R":</strong> Main code for plotting all figures (Figures 1, 2, 5 to 8 in the main text, and figures in Appendices S3 and S4). NOTE: <em style="color:#333333;font-family:'Helvetica Neue' , Helvetica , Arial , sans-serif;background-color:#ffffff;">Because this code runs a random bootstrapping process in the background, with default = 100 replications, to estimate standard error, the output (for s.e. and 95% confidence intervals) will vary very slightly each time you enter the same data. Also, the bootstrap procedure is very time-consuming; please change the argument nboot = 100 (default) in any function to nboot = 0 (to skip the bootstrap process) or nbbot = 20 (to roughly browse the resulting confidence intervals).    </em>