DOI: 10.5061/dryad.3bk3j9kww
title: Data from: Drivers of viral prevalence in landscape-scale pollinator networks across Europe: Honey bee viral density, niche overlap with this reservoir host and network architecture

description: We looked at 144 plant-pollinator networks from 48 sites divided over 4
 countries along an urbanization and agricultural intensification gradient
 to assess how landscape, honey bees, and plant-pollinator network
 structure affect the prevalence and load of three honeybee RNA viruses
 (DWV-A, DWV-B, and BQCV) in wild bees and hoverflies. We provide
 information on plant-pollinator interactions, land use in the study
 landscapes, plant-pollinator network structure, niche overlap between wild
 bees and honeybees, and data on prevalence and load of analyzed honeybees
 and wild pollinators. The R code used for statistical analysis and
 creation of figures in the accompanying paper is also provided.
description: # Data from: Drivers of viral prevalence in landscape-scale pollinator
 networks across Europe: Honey bee viral density, niche overlap with this
 reservoir host and network architecture We analysed plant-pollinator
 networks in 48 landscapes over 4 countries (France, Germany, Poland,
 Switzerland), during three sampling rounds (144 visits in total), and
 looked at plant-pollinator network structure and how this affected the
 presence of three types of RNA virus in wild pollinators (DWV-A, DWV-B,
 and BQCV). We analyzed plant-pollinator network structure, the presence of
 viruses, landscape composition, and vegetation. The dataset does not
 contain any threatened species. All missing data represented as NA. ####
 Description of the data and file structure This dataset contains
 information on raw landscape composition, plant-pollinator interactions,
 vegetation composition and viral analysis of pollinators. All data is
 contained in the zipped folder "Raw_data_Proesmans_ea_EL_v2.zip"
 (Raw_data_Proesmans_ea_EL.zip contains an older, less well-annotated
 version of the data, lacks two scripts on nectar caclulation and has the
 floral data divided in 4 different files each representing one of the four
 sampled countries, but is otherwise identical). Contains following
 datasets (each with associated .xlsx metadata file): *
 Landscape_centroids.csv: File with the GPS coordinates of all site
 centroids. Used to account for spatial autocorrelation. *
 Pollinator_masterfile.csv: File with all plant-pollinator interactions
 observed in all landscapes - Landscape_composition.csv: File containing
 the landscape composition (EUNIS level 3) within a 1 km radius from the
 landscape centroids * Flower_data.csv: File containing raw vegetation data
 from 0.5 x 2 m plots in each landscape, during each sampling roun -
 Connectancelist.csv: File containing connectance values for each
 plant-pollinator network * Niche_overlap.csv: File containing for each
 individual network the niche overlap (Horn-Morisita) of all pollinator
 species with honeybee (Apis mellifera). If honeybees are absent from
 networks, Niche overlap is given as NA. - European_networkmetrics.csv:
 File containing metrics at the level of all plant-pollinator networks.
 This includes network structure (web asymmetry, modularity,...) but also
 nectar diversity and nectar abundance and information on viral prevalence
 in honeybees. * Viral_masterfile.csv: File containing information on the
 presence and concentration of the analyzed viruses in honeybees and wild
 pollinators. Furthermore, following R scripts were used in the analysis:
 (each of them is annotated, so no further dedicated metadata). 
 
 * Nectar_per_site_script_v1.1.R: This script calculates the amount of
 nectar in mg of sugar per m² at the site-visit level. Not necessary to run
 before the overarching analysis as the European_networkmetrics.csv file
 already contains this information. * Calculate_nectar_diversity_v1.1.R:
 This script calculates the mean plot-level Shannon nectar diversity at the
 site-visit level. Not necessary to run before the overarching analysis as
 the European_networkmetrics.csv file already contains this information *
 Calculate_networkmetrics_v1.2..1R: This script calculates connectance,
 modularity and niche overlap with honeybees. Not necessary to run this
 before the other script, as the csv files already contain this data.
 Script is purely informative and added for transparency concerning
 calculation of these metrics. - Overarching_analysis_v1.8.1.R: This script
 runs the complete analysis, from compiling the final dataset to running
 models and creating figures. If all files are available, it will run just
 by copy-pasting the full script, although some models take several hours
 to run. Requires installation of Stan to run MCMC and the library
 rethinking, which can be a bit of a pain to install. **Sharing/Access
 information** This dataset is provided under a CC0 1.0 Universal (CC0 1.0)
 Public Domain Dedication **Code/Software** The data was analysed in R. See
 above for a further explanation on the different scripts used. The scripts
 are extensively annotated.