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

Abstract

Ecosystem 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. In 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. The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open source algorithms.

Scientific maps should reach everyone: a straightforward approach to let colour blind people visualise spatial patterns

“…In order to test the function we decided to directly get in the game by making use of a (wrong) plot that we published in Rocchini et al (2021), where a rainbow colour palette was used to show the variability in space of the Similaun Glacier (Italy, Figure 2). In that case, a rainbow colour ramp palette was used passing from: (i) low spatial variability, represented by blue and green, related to a small lake at north-east and snow at north-west, respectively; (ii) medium variability (yellow) related to woodlands and high elevation grasslands; and (iii) high variability (red), related to crevasses and cracks of the calcareous rock composing the glacier.…”

“…It has an autosomal dominant genetic inheritance, therefore independent of sex. Rocchini et al (2021). Low spatial variability is represented in blue and green (lake), while medium variability is in yellow (woodlands), high variability is in red (crevasses and cracks).…”

“…This leads to the impossibility of recognizing some types of colour ramps in which there is a gradient from blue to green/yellow to red. For instance, this is the case of frequently (mis)used rainbow colour palettes (Golebiowska & Coltekin, 2020;Stoelzle et al, 2021), which are part of a bunch of papers in the scientific literature (e.g., Mesgaran et al, 2014;Gardner et al, 2019;Ellis-Soto et al, 2021;Feilhauer et al, 2021;Rocchini et al, 2021).…”

“…Figure2: The variability in space of the Similaun Glacier shown by a rainbow colour ramp palette (a) as inRocchini et al (2021). Low spatial variability is represented in blue and green (lake), while medium variability is in yellow (woodlands), high variability is in red (crevasses and cracks).…”

comspat: an R package to analyze within‐community spatial organization using species combinations

“…The R environment is rich in contributed packages (ca 20 000 current packages, <https://www.r-project.org>), and several exist which analyze biodiversity with information theory. entropy (Hausser and Strimmer 2009), entropart (Marcon and Hérault 2015) and EntropyEstimation (Cao and Grabchak 2015) are perhaps most widely known, while recent contributions of rasterdiv (Rocchini et al 2021) and SpatEntropy (Altieri et al 2021) will undoubtedly gain popularity (see the total downloads in the Supporting information); all calculate the Shannon's diversity index (Shannon 1948). Although colloquially described as a measure of diversity, the Shannon index is not a measure of diversity; instead, it is an entropy estimation, giving uncertainty in the outcome of a sampling process (Jost 2006).…”