DOI: 10.5061/dryad.34tmpg4s0
title: Integrating data from different taxonomic resolutions to better estimate community alpha diversity

description: Integrated distribution models (IDMs), in which datasets with different
 properties are analysed together, are becoming widely used to model
 species distributions and abundance in space and time. To date, the IDM
 literature has focused on technical and statistical issues, such as the
 precision of parameter estimates and mitigation of biases arising from
 unstructured data sources. However, IDMs have an unrealised potential to
 estimate ecological properties that could not be properly derived from the
 source datasets if analysed separately. We present a model that estimates
 community alpha diversity metrics by integrating one species-level dataset
 of presence-absence records with a co-located dataset of group-level
 counts (i.e. lacking information about species identity). We illustrate
 the ability of community IDMs to capture the true alpha diversity through
 simulation studies and apply the model to data from the UK Pollinator
 Monitoring Scheme, to describe spatial variation in the diversity of
 solitary bees, bumblebees and hoverflies. The simulation and case studies
 showed that the proposed IDM produced more precise estimates of the
 community diversity than the single models, and the analysis of the real
 dataset further showed that the alpha diversity estimates from the IDM
 were averages of the single models. Our findings also revealed that IDMs
 had a higher prediction accuracy for all the insect groups in most cases,
 with this performance linked to the information provided by a data source
 into the IDM.
description: # Integrating data from different taxonomic resolutions to better estimate
 community alpha diversity This repository hosts the dataset used for the
 paper "Integrating data from different taxonomic resolutions to
 better estimate community alpha diversity". The scripts for the
 analysis can be accessed with
 ()](). This data is a subset of the UK Pollinator Monitoring Scheme (PoMS). Check section 2.1 of the main paper for details of the PoMS survey. ## Dataset ### FIT\_counts\_with\_effort.csv This file contains data on the Flower-Insect Transects (FIT) survey. The data contains information on the site identification (site ID), observation date (date), counts for each insect group (counts) and the number of surveys which is a measure of the effort (n_surveys). ### pantraps.csv This file contains data on the pantrap survey. The data is collected from five pan traps. The file contains information on the site identification (site ID), observation date (date), the taxonomic group of the species identification (taxon_group), species identification (taxon_aggregated), number of traps with the species present in them (n_traps_present) and the number of traps used in the survey at the particular site (n_traps) ### gr\_ref.csv This file contains the coordinate reference for the site identification (Site ID) in the *FIT_counts_with_effort.csv* and *pantraps.csv*. It contains information on the coordinates (EASTING and NORTHING) and region of the sites (region). ### all\_surveys.csv By the design of the POMS survey, both pantrap and 10-minute FIT count survey should be conducted by the same observer on the same sampling visit. However, due to some challenges during the sampling visits, some visits did not have both surveys. This file contains information of each site (with identification Site ID), sampling date (date) and an indication of whether pan trap and FIT count surveys (with NA indicating situations where no survey was conducted). ### species\_lookup.csv The file contains the species list for each insect group.