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  1. Article: LiDAR GEDI derived tree canopy height heterogeneity reveals patterns of biodiversity in forest ecosystems.

    Torresani, Michele / Rocchini, Duccio / Alberti, Alessandro / Moudrý, Vítězslav / Heym, Michael / Thouverai, Elisa / Kacic, Patrick / Tomelleri, Enrico

    Ecological informatics

    2023  Volume 76, Page(s) 102082

    Abstract: The "Height Variation Hypothesis" is an indirect approach used to estimate forest biodiversity through remote sensing data, stating that greater tree height heterogeneity (HH) measured by CHM LiDAR data indicates higher forest structure complexity and ... ...

    Abstract The "Height Variation Hypothesis" is an indirect approach used to estimate forest biodiversity through remote sensing data, stating that greater tree height heterogeneity (HH) measured by CHM LiDAR data indicates higher forest structure complexity and tree species diversity. This approach has traditionally been analyzed using only airborne LiDAR data, which limits its application to the availability of the dedicated flight campaigns. In this study we analyzed the relationship between tree species diversity and HH, calculated with four different heterogeneity indices using two freely available CHMs derived from the new space-borne GEDI LiDAR data. The first, with a spatial resolution of 30 m, was produced through a regression tree machine learning algorithm integrating GEDI LiDAR data and Landsat optical information. The second, with a spatial resolution of 10 m, was created using Sentinel-2 images and a deep learning convolutional neural network. We tested this approach separately in 30 forest plots situated in the northern Italian Alps, in 100 plots in the forested area of Traunstein (Germany) and successively in all the 130 plots through a cross-validation analysis. Forest density information was also included as influencing factor in a multiple regression analysis. Our results show that the GEDI CHMs can be used to assess biodiversity patterns in forest ecosystems through the estimation of the HH that is correlated to the tree species diversity. However, the results also indicate that this method is influenced by different factors including the GEDI CHMs dataset of choice and their related spatial resolution, the heterogeneity indices used to calculate the HH and the forest density. Our finding suggest that GEDI LIDAR data can be a valuable tool in the estimation of forest tree heterogeneity and related tree species diversity in forest ecosystems, which can aid in global biodiversity estimation.
    Language English
    Publishing date 2023-09-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2212016-6
    ISSN 1878-0512 ; 1574-9541
    ISSN (online) 1878-0512
    ISSN 1574-9541
    DOI 10.1016/j.ecoinf.2023.102082
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Scientific maps should reach everyone: The cblindplot R package to let colour blind people visualise spatial patterns

    Rocchini, Duccio / Nowosad, Jakub / D'Introno, Rossella / Chieffallo, Ludovico / Bacaro, Giovanni / Cazzolla Gatti, Roberto / Foody, Giles M. / Furrer, R. / Gábor, Lukáš / Malavasi, Marco / Marcantonio, Matteo / Marchetto, Elisa / Moudrý, Vítězslav / Ricotta, Carlo / Šimová, Petra / Torresani, Michele / Thouverai, Elisa

    Ecological Informatics. 2023 Mar. 03, p.102045-

    2023  , Page(s) 102045–

    Abstract: Maps represent powerful tools to show the spatial variation of a variable in a straightforward manner. A crucial aspect in map rendering for its interpretation by users is the gamut of colours used for displaying data. One part of this problem is linked ... ...

    Abstract Maps represent powerful tools to show the spatial variation of a variable in a straightforward manner. A crucial aspect in map rendering for its interpretation by users is the gamut of colours used for displaying data. One part of this problem is linked to the proportion of the human population that is colour blind and, therefore, highly sensitive to colour palette selection. The aim of this paper is to present the cblindplot R package and its founding function - cblind.plot() - which enables colour blind people to just enter an image in a coding workflow, simply set their colour blind deficiency type, and immediately get as output a colour blind friendly plot. We will first describe in detail colour blind problems, and then show a step by step example of the function being proposed. While examples exist to provide colour blind people with proper colour palettes, in such cases (i) the workflow include a separate import of the image and the application of a set of colour ramp palettes and (ii) albeit being well documented, there are many steps to be done before plotting an image with a colour blind friendly ramp palette. The function described in this paper, on the contrary, allows to (i) automatically call the image inside the function without any initial import step and (ii) explicitly refer to the colour blind deficiency type being experienced, to further automatically apply the proper colour ramp palette.
    Keywords color ; human population ; imports ; people ; Colour blindness ; Computational ecology ; Ecological informatics ; Mapping ; R ; Scientific communication
    Language English
    Dates of publication 2023-0303
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 2212016-6
    ISSN 1878-0512 ; 1574-9541
    ISSN (online) 1878-0512
    ISSN 1574-9541
    DOI 10.1016/j.ecoinf.2023.102045
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Integrals of life: Tracking ecosystem spatial heterogeneity from space through the area under the curve of the parametric Rao's Q index

    Thouverai, Elisa / Marcantonio, Matteo / Lenoir, Jonathan / Galfré, Mariasole / Marchetto, Elisa / Bacaro, Giovanni / Cazzolla Gatti, Roberto / Da Re, Daniele / Di Musciano, Michele / Furrer, R. / Malavasi, Marco / Moudrý, Vítězslav / Nowosad, Jakub / Pedrotti, Franco / Pelorosso, Raffaele / Pezzi, Giovanna / Šimová, Petra / Ricotta, Carlo / Silvestri, Sonia /
    Tordoni, Enrico / Torresani, Michele / Vacchiano, Giorgio / Zannini, Piero / Rocchini, Duccio

    Ecological Complexity. 2022 Dec., v. 52 p.101029-

    2022  

    Abstract: Spatio-ecological heterogeneity is strongly linked to many ecological processes and functions such as plant species diversity patterns and change, metapopulation dynamics, and gene flow. Remote sensing is particularly useful for measuring spatial ... ...

    Abstract Spatio-ecological heterogeneity is strongly linked to many ecological processes and functions such as plant species diversity patterns and change, metapopulation dynamics, and gene flow. Remote sensing is particularly useful for measuring spatial heterogeneity of ecosystems over wide regions with repeated measurements in space and time. Besides, developing free and open source algorithms for ecological modelling from space is vital to allow to prove workflows of analysis reproducible. From this point of view, NASA developed programs like the Surface Biology and Geology (SBG) to support the development of algorithms for exploiting spaceborne remotely sensed data to provide a relatively fast but accurate estimate of ecological properties in vast areas over time. Most of the indices to measure heterogeneity from space are point descriptors : they catch only part of the whole heterogeneity spectrum. Under the SBG umbrella, in this paper we provide a new R function part of the rasterdiv R package which allows to calculate spatio-ecological heterogeneity and its variation over time by considering all its possible facets. The new function was tested on two different case studies, on multi- and hyperspectral images, proving to be an effective tool to measure heterogeneity and detect its changes over time.
    Keywords ecosystems ; gene flow ; geology ; remote sensing ; spatial variation ; species diversity ; Biodiversity ; Ecological informatics ; Modelling ; Satellite imagery
    Language English
    Dates of publication 2022-12
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 2160288-8
    ISSN 1476-945X
    ISSN 1476-945X
    DOI 10.1016/j.ecocom.2023.101029
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back.

    Rocchini, Duccio / Thouverai, Elisa / Marcantonio, Matteo / Iannacito, Martina / Da Re, Daniele / Torresani, Michele / Bacaro, Giovanni / Bazzichetto, Manuele / Bernardi, Alessandra / Foody, Giles M / Furrer, Reinhard / Kleijn, David / Larsen, Stefano / Lenoir, Jonathan / Malavasi, Marco / Marchetto, Elisa / Messori, Filippo / Montaghi, Alessandro / Moudrý, Vítězslav /
    Naimi, Babak / Ricotta, Carlo / Rossini, Micol / Santi, Francesco / Santos, Maria J / Schaepman, Michael E / Schneider, Fabian D / Schuh, Leila / Silvestri, Sonia / Ŝímová, Petra / Skidmore, Andrew K / Tattoni, Clara / Tordoni, Enrico / Vicario, Saverio / Zannini, Piero / Wegmann, Martin

    Methods in ecology and evolution

    2021  Volume 12, Issue 6, Page(s) 1093–1102

    Abstract: Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package- ... ...

    Abstract Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, 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.
    Language English
    Publishing date 2021-05-03
    Publishing country United States
    Document type Journal Article
    ISSN 2041-210X
    ISSN 2041-210X
    DOI 10.1111/2041-210X.13583
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: From zero to infinity

    Rocchini, Duccio / Marcantonio, Matteo / Da Re, Daniele / Bacaro, Giovanni / Feoli, Enrico / Foody, Giles M. / Furrer, Reinhard / Harrigan, Ryan J. / Kleijn, David / Iannacito, Martina / Lenoir, Jonathan / Lin, Meixi / Malavasi, Marco / Marchetto, Elisa / Meyer, Rachel S. / Moudry, Vítězslav / Schneider, Fabian D. / Šímová, Petra / Thornhill, Andrew H. /
    Thouverai, Elisa / Vicario, Saverio / Wayne, Robert K. / Ricotta, Carlo

    Global Ecology and Biogeography

    Minimum to maximum diversity of the planet by spatio-parametric Rao’s quadratic entropy

    2021  Volume 30, Issue 5

    Abstract: Aim: The majority of work done to gather information on the Earth's biodiversity has been carried out using in-situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs) ...

    Abstract Aim: The majority of work done to gather information on the Earth's biodiversity has been carried out using 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 Shannon’s information theory, namely on the differences in relative abundance of pixel reflectances in a certain area. Additional metrics like the Rao’s quadratic entropy allow the use of spectral distance beside abundance, but they are point descriptors of diversity, that is they can account only for a part of the whole diversity continuum. The aim of this paper is thus to generalize the Rao’s quadratic entropy by proposing its parameterization for the first time. Innovation: The parametric Rao’s quadratic entropy, coded in R, (a) allows the representation of the whole continuum of potential diversity indices in one formula, and (b) starting from the Rao’s quadratic entropy, allows the explicit use of distances among pixel reflectance values, together with relative abundances. Main conclusions: The 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. Being part of the rasterdiv R package, the proposed method is expected to ensure high robustness and reproducibility.
    Keywords biodiversity ; ecological informatics ; modelling ; remote sensing ; satellite imagery
    Subject code 410
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2021283-5
    ISSN 1466-8238 ; 1466-822X ; 0960-7447
    ISSN (online) 1466-8238
    ISSN 1466-822X ; 0960-7447
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: rasterdiv—An Information Theory tailored R package for measuring ecosystem heterogeneity from space

    Rocchini, Duccio / Thouverai, Elisa / Marcantonio, Matteo / Iannacito, Martina / Da Re, Daniele / Torresani, Michele / Bacaro, Giovanni / Bazzichetto, Manuele / Bernardi, Alessandra / Foody, Giles M. / Furrer, Reinhard / Kleijn, David / Larsen, Stefano / Lenoir, Jonathan / Malavasi, Marco / Marchetto, Elisa / Messori, Filippo / Montaghi, Alessandro / Moudrý, Vítězslav /
    Naimi, Babak / Ricotta, Carlo / Rossini, Micol / Santi, Francesco / Santos, Maria J. / Schaepman, Michael E. / Schneider, Fabian D. / Schuh, Leila / Silvestri, Sonia / Ŝímová, Petra / Skidmore, Andrew K. / Tattoni, Clara / Tordoni, Enrico / Vicario, Saverio / Zannini, Piero / Wegmann, Martin

    Methods in Ecology and Evolution

    To the origin and back

    2021  Volume 12, Issue 6

    Abstract: Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow. In this paper, we present a new R package— ... ...

    Abstract Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, 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.
    Keywords biodiversity ; ecological informatics ; modelling ; remote sensing ; satellite imagery
    Language English
    Publishing country nl
    Document type Article ; Online
    ISSN 2041-210X
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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