Search bioRxivSearch

Biology subjects

Rocchini, D.

Publications and source records attributed to Rocchini, D..

4 recordsLinked to original sources

rasterdiv - an Information Theory tailored R package for measuring ecosystem heterogeneity from space: to the origin and back

O_LIEcosystem heterogeneity has been widely recognized as a key ecological feature, influencing several ecological functions, since it is strictly related to several ecological functions like diversity patterns and change, metapopulation dynamics, population connectivity, or gene flow. C_LIO_LIIn this paper, we present a new R package - rasterdiv - to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns. C_LIO_LIThe rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open source algorithms. C_LI

ecology

From zero to infinity: minimum to maximum diversity of the planet by spatio-parametric Rao's quadratic entropy

AimThe majority of work done to gather information on Earth diversity has been carried out by in-situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs), among others. An alternative way to gather information about spatial ecosystem variability is the use of satellite remote sensing. It works as a powerful tool for attaining rapid and standardized information. Several metrics used to calculate remotely sensed diversity of ecosystems are based on Shannons Information Theory, namely on the differences in relative abundance of pixel reflectances in a certain area. Additional metrics like the Raos quadratic entropy allow the use of spectral distance beside abundance, but they are point descriptors of diversity, namely they can account only for a part of the whole diversity continuum. The aim of this paper is thus to generalize the Raos quadratic entropy by proposing its parameterization for the first time. InnovationThe parametric Raos quadratic entropy, coded in R, i) allows to represent the whole continuum of potential diversity indices in one formula, and ii) starting from the Raos quadratic entropy, allows to explicitly make use of distances among pixel reflectance values, together with relative abundances. Main conclusionsThe proposed unifying measure is an integration between abundance- and distance-based algorithms to map the continuum of diversity given a satellite image at any spatial scale.

ecology

Measuring diversity from space: a global view of the free and open source rasterdiv R package under a coding perspective

The variation of species diversity over space and time has been widely recognised as a key challenge in ecology. However, measuring species diversity over large areas might be difficult for logistic reasons related to both time and cost savings for sampling, as well as accessibility of remote ecosystems. In this paper, we present a new R package - rasterdiv - to calculate diversity indices based on remotely sensed data, by discussing the theory beyond the developed algorithms. Obviously, measures of diversity from space should not be viewed as a replacement of in-situ data on biological diversity, but they are rather complementary to existing data and approaches. In practice, they integrate available information of Earth surface properties, including aspects of functional (structural, biophysical and bio-chemical), taxonomic, phylogenetic and genetic diversity. Making use of the rasterdiv package can result useful in making multiple calculations based on reproducible open source algorithms, robustly rooted in Information Theory.

ecology

From local spectral species to global spectral communities: a benchmark for ecosystem diversity estimate by remote sensing

In the light of unprecedented change in global biodiversity, real-time and accurate ecosystem and biodiversity assessments are becoming increasingly essential. Nevertheless, estimation of biodiversity using ecological field data can be difficult for several reasons. For instance, for very large areas, it is challenging to collect data that provide reliable information. Some of these restrictions in Earth observation can be avoided through the use of remote sensing approaches. Various studies have estimated biodiversity on the basis of the Spectral Variation Hypothesis (SVH). According to this hypothesis, spectral heterogeneity over the different pixel units of a spatial grid reflects a higher niche heterogeneity, allowing more organisms to coexist. Recently, the spectral species concept has been derived, following the consideration that spectral heterogeneity at a landscape scale corresponds to a combination of subspaces sharing a similar spectral signature. With the use of high resolution remote sensing data, on a local scale, these subspaces can be identified as separate spectral entities, the so called "spectral species". Our approach extends this concept over wide spatial extents and to a higher level of biological organization. We applied this method to MODIS imagery data across Europe. Obviously, in this case, a spectral species identified by MODIS is not associated to a single plant species in the field but rather to a species assemblage, habitat, or ecosystem. Based on such spectral information, we propose a straightforward method to derive - (local relative abundance and richness of spectral species) and {beta}-diversity (turnover of spectral species) maps over wide geographical areas.

ecology