DOI: 10.5061/dryad.wdbrv15xs
title: Data from: Estimated missing interactions change the structure and alter species roles in one of the world’s largest seed-dispersal networks

description: Ecological interactions between species can affect the performance of
 individuals, influence ecological and evolutionary dynamics of
 populations, and ultimately shape community structure. 
 Therefore, documenting and studying interactions is necessary for a better
 comprehension of ecological patterns.  Yet, sampling interactions
 in the field is challenging. Even with extensive sampling efforts we can
 hardly obtain a comprehensive picture of which species interact with each
 other. Such missing interactions can produce important gaps that affect
 how we perceive and interpret the network formed by species interactions
 and the roles of individual species within those networks. In this study
 we propose two methods that combine data on species interactions with
 information on species traits and phylogenies to estimate potentially
 missing interactions. We use one of the largest datasets on
 plant-frugivore interactions, depicting thousands of interactions between
 birds and plants in the Atlantic Forest hotspot, to test those methods.
 Then, we analyze how adding newly estimated interactions change the
 network’s overall structure and the topological importance of each species
 within the seed dispersal network. We show that estimated missing
 interactions more than tripled the number of interactions in the network
 and impact the general topological properties of the network increasing
 nestedness and reducing modularity. Both methods generated networks with a
 similar structure and were effective in estimating new interactions,
 accurately predicting known interactions without overestimating
 interactions in place of true absences. More importantly, added
 interactions changed our perception on the topological role of species,
 with several undersampled species earning novel interactions and becoming
 more central to network structure. This shows that estimating interactions
 can be helpful to get a more complete idea of how a network may look like,
 besides helping to inform which interactions should be the focus of
 further sampling efforts.
description: # Data for: Estimated missing interactions change the structure and alter
 species roles in one of the world’s largest seed-dispersal networks ##
 Description of the data and file structure There are two kinds of files
 here: 1\) Two R scripts, one for each method, that detail the working of
 each the method and allow its reproduction. 2\) 5 Data files needed to run
 the above scripts. The show 3 types of data: a) The bird_phylo and
 plant_phylo are phylogenetic trees for the birds and plant species,
 respectively. b)The atlantics_info file is a table with all frugivory
 interactions recorded through the literature. The "int_s" column
 show how many studies recorded that particular interaction, while the
 "n.studies" column show how many studies recorded the two
 species, interacting or not. The "freq" column is the division
 of the "int_s" column by the "n.studies".
 "bird.gape" and "seed.size" column show the mean bird
 gape size and mean seed length (both in millimeters) for those species. c)
 The input_matrix and atlantics_matrix are both interaction matrices. The
 atlantics_matrix is a matrix with the "freq" values (described
 above). This file is not needed to run any of the scripts, but it may be
 useful for comparison of the results of those methods. The input_matrix is
 a sub-set of the atlantics matrix with just the selected species used as
 baseline values for both models. Both matrices have the plants species on
 their rows and the bird species on their columns. ## Code/Software The
 files containing the two methods are R scripts. Both scripts are commented
 to facilitate their use. For version of the packages used, please check
 the article methods session.