DOI: 10.5061/dryad.h44j0zpq3
title: Estimating interaction strengths for diverse horizontal systems using performance data

description: 1. Network theory allows us to understand complex systems by evaluating
 how their constituent elements interact with one another. Such networks
 are built from matrices that describe the effect of each element on all
 others. Quantifying the strength of these interactions from empirical data
 can be difficult, however, because the number of potential interactions
 increases non-linearly as more elements are included in the system, and
 not all interactions may be empirically observable when some elements are
 rare. 2. We present a novel modelling framework that uses measures of
 species performance in the presence of varying densities of their
 potential interaction partners to estimate the strength of pairwise
 interactions in diverse horizontal systems. 3. Our method allows us to
 directly estimate pairwise effects when they are statistically
 identifiable and to approximate pairwise effects when they would otherwise
 be statistically unidentifiable. The resulting interaction matrices can
 include positive and negative effects, the effect of a species on itself,
 and allows for non-symmetrical interactions. 4. We show how to link the
 parameters inferred by our framework to a population dynamics model to
 make inferences about the effect of interactions on community dynamics and
 diversity. 5. The advantages of these features are illustrated with a case
 study on an annual wildflower community of 22 focal and 52 neighbouring
 species, and a discussion of potential applications of this framework
 extending well beyond plant community ecology.
description: This dataset comes from an annual wildflower community in Western
 Australia. This system is a diverse and well-studied community of annual
 plants which germinate, grow, set seed and die within approximately 4
 months every year. Individual fecundity data were collected in 2016 when
 100 50 x 50 cm plots established in the understory of West Perenjori
 Reserve were monitored over the length of the full field season. The
 resulting dataset includes between 29 to over 1,000 counts of individual
 plant seed production from 22 different focal species (with a median of
 108 observations per species), in addition to the identity and densities
 of all neighbouring individuals within the interaction neighbourhood of
 each focal plant. Interaction neighbourhoods varied in radius from 3 to 5
 cm depending on the size of the focal species. Total neighbourhood
 diversity was 71 wildflower species, 19 of which were recorded fewer than
 10 times across the whole dataset. The species-specific effects of this
 latter group of species on focals were deemed negligible due to their
 extremely low density; they were thus grouped into an 'other'
 category and their effects on focals averaged. This resulted in 53
 potential neighbour identities. Plots were randomly positioned across the
 reserve to capture natural environmental variation in the system. Major
 factors known to impact plant composition and within species abundances
 are soil P concentrations, shade, and the presence of woody debris.
 Natural levels of soil P are very low in this system with elevated P
 concentrations occurring predominantly on the edge of the reserve near
 agricultural fields that use P fertiliser. All study plots were placed far
 from reserve edges to avoid artificially elevated levels of P, which are
 easy to detect due to an association between high P levels and extensive
 exotic grass abundances, which are largely absent from the core reserve
 where this study was conducted. Thus, environmental variation captured by
 this dataset reflects natural variation in tree cover, soil nutrients and
 woody debris. To account for confounding effects between plot location and
 plant density, half of all plots were thinned (a quarter to 60% abundance
 and a quarter to 30%). Thinning did not target any particular species.
 This dataset also contains seed germination rates and seed survival rates
 for the focal species collected from a set of field experiments conducted
 by T. Martyn, M. Raymundo and I. Towers at Perenjori reserve between 2015
 and 2019. Further details on the collection of this
 data are available in the Methods sections of the associated manuscript,
 'Estimating interaction strengths for diverse horizontal systems
 using performance data' (Bimler et al. 2023, Methods in Ecology and
 Evolution).
description: Files are intended to be opened and used with R. Associated
 scripts and functions are available at https://github.com/malbion/JointModelFramework/.