DOI: 10.5061/dryad.4tmpg4f8g
title: Data from: A review of seascape complexity indices and their performance in coral and rocky reefs

description: Seascape complexity is an important driver of ecological processes in
 marine systems. Today, high resolution, multiscale bathymetric data is
 being collected due to rapid advances in marine technologies and image
 processing, drastically improving the detailed mapping of the physical
 structure of the seascape. However, these data are rarely synthesized to
 create comprehensive complexity estimates, and complexity is still mostly
 measured using a small set of simple indices. The aims of this study are
 to: (1) review existing seascape complexity indices and propose innovative
 indices designed to capture the marine organism perspective, (2) quantify
 the interrelationships among these complexity indices; (3) test the
 performance of these indices in explaining fish assemblage structure; and
 (4) provide R code to easily reproduce the indices. Seascape bottom
 topography for this study was quantified using digital depth recordings
 along transects in Mediterranean subtropical rocky reefs and Red Sea
 tropical coral reefs. These were used to generate complexity indices that
 were then compared to visually surveyed fish assemblages. We found that
 several common indices captured similar complexity facets, while an
 innovative family of structural diversity indices, representing the
 diversity of physical elements, captured distinct complexity facets not
 represented by existing indices. No single index was consistently
 superior; however, vertical relief was consistently included as a top
 predictor of fish assemblage structure. Interestingly, the most commonly
 used index, rugosity, was a poor predictor. We suggest a new, distinct set
 of structural diversity indices that may explain considerable variation in
 fish assemblages. The results suggest that several indices may need to be
 combined to capture the full influence of complexity on marine diversity
 and caution against the use of a single ‘universal’ index. While
 bathymetric data is increasingly being collected at high resolutions and
 increasing scales, synthesizing this data requires the use of appropriate
 complexity indices. The guidelines and recommendations presented here,
 along with the supplemental R code, will facilitate progress towards a
 more complete representation of different complexity facets.
description: Each transect was conducted by a single or two observers. For
 each transect, species richness ('max_richness'), species
 abundance ('max_abundance') and species biomass
 ('max_biomass', calculated using literature-based
 species-specific conversion factors) were calculated using the maximum
 values observed by one of the surveyors. Shannon diversity
 ('shannon') was claculated as the mean between two observers.
 Sampling sites were randomly chosen in areas with continuous hard
 substrate cover. Bottom profiles were created using a
 digital depth water level data logger (by 'Onset') (accompanied
 by visual fish censuses). From these bottom profiles 21 complexity indices
 were calculated (columns M to AH) along with the mean depth along the
 transect ('mean_depth' variable).
description: This dataset includes all the information used for analyses in
 the manuscript "A review of seascape complexity indices and their
 performance in coral and rocky reefs": 1. The file
 'data_for_publication' includes fish community structure data
 per sampling unit along with structural complexity indices calculated per
 sampling unit. The file includes data from both the Mediterranean Sea and
 the Red Sea ('coast' variable). Data from the Mediterranean were
 collected between 2015-2017 and includes 183 transects conducted in four
 locations ('location' variable), within marine reserves and in
 their surroundings ('reserve' variable). Data from the Red Sea
 were collected along the Israeli coast of the Gulf of Aqaba between
 2018-2019 and includes 60 transects conducted in five locations
 ('location variable). An identifier variable for each transect
 ('transect_id') is composed of the sampling point
 ('sampling_point'), trasect letter/number (within the Red Sea,
 due to longer protocol duration, sampling points are identical to
 transects letters), sampling site ('location'), year
 ('year'), sampling season and name of first observer and of
 second observer.  2. The file
 'copmlexity_papers' summarizes the information we used for a
 mini-review about the use of complexity indices to date. This information
 includes the author of the paper ('Author', if one or two
 authors, all are specificed, if more than two authors, the first auther is
 specified), paper title ('Paper title'), year of publication
 ('Year'). Columns D-I specify the amount of indices used in each
 publication, and which ones used the rugosity index or its
 derivatives.