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Ecological processes are often spatially and temporally structured, potentially leading to autocorrelation either in environmental variables or species distribution data. Because of that, spatially-biased in-situ samples or predictors might affect the outcomes of ecological models used to infer the geographic distribution of species and diversity. There is a vast heterogeneity of methods and approaches to assess and measure spatial bias; this paper aims at addressing the spatial component of data-driven biases in species distribution modelling, and to propose potential solutions to explicitly test and account for them. Our major goal is not to propose methods to remove spatial bias from the modelling procedure, which would be impossible without proper knowledge of all the processes generating it, but rather to propose alternatives to explore and handle it. In particular, we propose and describe three main strategies that may provide a fair account of spatial bias, namely: (i) how to represent spatial bias; (ii) how to simulate null models based on virtual species for testing biogeographical and species distribution hypotheses; and (iii) how to make use of spatial bias - in particular related to sampling effort - as a leverage instead of a hindrance in species distribution modelling. We link these strategies with good practice in accounting for spatial bias in species distribution modelling. more...

Ecological processes are often spatially and temporally structured, potentially leading to autocorrelation either in environmental variables or species distribution data. Because of that, spatially-biased in-situ samples or predictors might affect the outcomes of ecological models used to infer the geographic distribution of species and diversity. There is a vast heterogeneity of methods and approaches to assess and measure spatial bias; this paper aims at addressing the spatial component of data-driven biases in species distribution modelling, and to propose potential solutions to explicitly test and account for them. Our major goal is not to propose methods to remove spatial bias from the modelling procedure, which would be impossible without proper knowledge of all the processes generating it, but rather to propose alternatives to explore and handle it. In particular, we propose and describe three main strategies that may provide a fair account of spatial bias, namely: (i) how to represent spatial bias; (ii) how to simulate null models based on virtual species for testing biogeographical and species distribution hypotheses; and (iii) how to make use of spatial bias - in particular related to sampling effort - as a leverage instead of a hindrance in species distribution modelling. We link these strategies with good practice in accounting for spatial bias in species distribution modelling. more...

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. more...

Superpixels are a promising group of techniques allowing for generalization of spatial information. Among this group, the Simple Linear Iterative Clustering (SLIC) superpixels algorithm proved to be first-rate, both in terms of the quality of the output and the performance. SLIC, however, is limited to detecting homogeneous areas and uses the Euclidean distance only. Here, we propose an extension of SLIC allowing to use any specified distance measure for single or multi-layered spatial raster data. To present our idea, we use the extension to create an over-segmentation of areas with similar proportions of different land cover categories in Ohio. Given a proper distance measure, the proposed extension can also be used for other scenarios, including creating regions of similar temporal patterns or similarly ranked areas. Depending on the use case, the resulting superpixels could be either the result of the analysis or the input for further classification or clustering. more...

Superpixels are a promising group of techniques allowing for generalization of spatial information. Among this group, the Simple Linear Iterative Clustering (SLIC) superpixels algorithm proved to be first-rate, both in terms of the quality of the output and the performance. SLIC, however, is limited to detecting homogeneous areas and uses the Euclidean distance only. Here, we propose an extension of SLIC allowing to use any specified distance measure for single or multi-layered spatial raster data. To present our idea, we use the extension to create an over-segmentation of areas with similar proportions of different land cover categories in Ohio. Given a proper distance measure, the proposed extension can also be used for other scenarios, including creating regions of similar temporal patterns or similarly ranked areas. Depending on the use case, the resulting superpixels could be either the result of the analysis or the input for further classification or clustering. more...

Superpixels are a promising group of techniques allowing for generalization of spatial information. Among this group, the Simple Linear Iterative Clustering (SLIC) superpixels algorithm proved to be first-rate, both in terms of the quality of the output and the performance. SLIC, however, is limited to detecting homogeneous areas and uses the Euclidean distance only. Here, we propose an extension of SLIC allowing to use any specified distance measure for single or multi-layered spatial raster data. To present our idea, we use the extension to create an over-segmentation of areas with similar proportions of different land cover categories in Ohio. Given a proper distance measure, the proposed extension can also be used for other scenarios, including creating regions of similar temporal patterns or similarly ranked areas. Depending on the use case, the resulting superpixels could be either the result of the analysis or the input for further classification or clustering. more...

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 a function in R - \texttt{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 colur blind friendly ramp palette. The function described in this paper (\ttt{cblind.plot}), 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. more...

Racial geography in US urban areas is extensively studied with the emphasis on assessing the extent of racial segregation. However, the used methodology has not changed for at least two decades; it relies on calculating ratios of population counts in the entire city and its subdivisions – census aggregation areas. This has a number of limitations; the two most important are: assessment of segregation depends on the subdivisions used, segregation can only be calculated for regions with census subdivisions. Here we present a different conceptualization of racial geography, which leads to a new method called racial landscape (RL). We use block-level census data to construct a high-resolution grid where each cell represents single race inhabitants. The result is a spatial, racial pattern; a degree of spatial autocorrelation of this pattern is a measure of segregation that does not require using subdivisions. We shortly describe the RL method and its application to Cook County, IL. We also describe here its implementation in the R computational environment. more...

Racial geography in US urban areas is extensively studied with the emphasis on assessing the extent of racial segregation. However, the used methodology has not changed for at least two decades; it relies on calculating ratios of population counts in the entire city and its subdivisions – census aggregation areas. This has a number of limitations; the two most important are: assessment of segregation depends on the subdivisions used, segregation can only be calculated for regions with census subdivisions. Here we present a different conceptualization of racial geography, which leads to a new method called racial landscape (RL). We use block-level census data to construct a high-resolution grid where each cell represents single race inhabitants. The result is a spatial, racial pattern; a degree of spatial autocorrelation of this pattern is a measure of segregation that does not require using subdivisions. We shortly describe the RL method and its application to Cook County, IL. We also describe here its implementation in the R computational environment. more...

Racial geography in US urban areas is extensively studied with the emphasis on assessing the extent of racial segregation. However, the used methodology has not changed for at least two decades; it relies on calculating ratios of population counts in the entire city and its subdivisions – census aggregation areas. This has a number of limitations; the two most important are: assessment of segregation depends on the subdivisions used, segregation can only be calculated for regions with census subdivisions. Here we present a different conceptualization of racial geography, which leads to a new method called racial landscape (RL). We use block-level census data to construct a high-resolution grid where each cell represents single race inhabitants. The result is a spatial, racial pattern; a degree of spatial autocorrelation of this pattern is a measure of segregation that does not require using subdivisions. We shortly describe the RL method and its application to Cook County, IL. We also describe here its implementation in the R computational environment. more...

This article focuses on mapping tropical deforestation using time series and machine learning algorithms. Before detecting changes in the time series, we reduced seasonality using Photosynthetic Vegetation (PV) index fractions obtained from Landsat images. Single and multi-temporal filters were used to reduce speckle noise from Synthetic Aperture Radar (SAR) images (i.e., ALOS PALSAR and Sentinel-1B) before fusing them with optical images through Principal Component Analysis (PCA). We detected only one change in the two PV series using a non-seasonal detection approach, as well as in the fused images through five machine learning algorithms that were calibrated with Cross-Validation (CV) and Monte Carlo Cross-Validation (MCCV). In total, four categories were obtained: forest, cropland, bare soil, and water. We then compared the change map obtained with time series and that obtained with the classification algorithms with the best calibration performance, revealing an overall accuracy of 92.91% and 91.82%, respectively. For statistical comparisons, we used deforestation reference data. Finally, we conclude with some discussions and reflections on the advantages and disadvantages of the detections made with time series and machine learning algorithms, as well as the contribution of SAR images to the classifications, among other aspects., Cet article porte sur la cartographie de la déforestation tropicale à l’aide de séries chronologiques et d’algorithmes d’apprentissage automatique. Avant de détecter les changements dans les séries temporelles, nous avons réduit la saisonnalité en utilisant les fractions de l’indice de végétation photosynthétique (PV) obtenues à partir des images Landsat. Des filtres mono et multitemporels ont été appliqués pour réduire le bruit de chatoiement des images RSO (Radar à synthèse d’ouverture) (c’est-à-dire ALOS PALSAR et Sentinel-1B) avant de les fusionner avec les images optiques par le biais de l’analyze en composantes principales (ACP). Nous avons détecté un seul changement à la fois dans les séries de PV en utilisant une approche de détection non saisonnière, ainsi que dans les images fusionnées, grâce à cinq algorithmes d’apprentissage automatique qui ont été calibrés par validation croisée (CV) et validation croisée de Monte-Carlo (MCCV). Au total, quatre catégories ont été obtenues: forêt, terres cultivées, sol nu et eau. Ensuite, nous avons comparé la carte des changements obtenue avec les séries temporelles et celle obtenue avec les algorithmes de classification les plus performants en matière de calibration, révélant une précision globale de 92.91% et 91.82% respectivement. Pour les comparaisons statistiques, nous avons utilisé des données de référence sur la déforestation. Enfin, nous concluons par des discussions et des réflexions sur les avantages et les inconvénients des détections effectuées avec les séries temporelles et les algorithmes d’apprentissage automatique, ainsi que sur la contribution des images RSO dans les classifications., The work of Yonatan Tarazona Coronel has been partially funded by American Program in GIS and Remote Sensing and National Program of Scholarships and Educational Credit (PRONABEC–Peru) through RJ: Nº 4276-2018- MINEDU/VMGI-PRONABEC-OBE and RJ: Nº 942-2019- MINEDU/VMGI-PRONABEC-OBE. Xavier Pons is the recipient of an ICREA Academia Excellence in Research Grant. The GRUMETS Research Group is partially supported by the Catalan Government under Grant SGR2017- 1690. This work has also been supported by the Spanish MCIU Ministry through the NEWFORLAND project (RTI2018-099397-B-C21 (MCIU/AEI/ERDF, EU))., Peer Reviewed, Postprint (published version) more...