Earth Observation and Biodiversity Big Data for Forest Habitat Types Classification and Mapping

Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data

Premise

Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).

Methods and Results

The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.

Conclusions

Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.

Editorial for Special Issue: “New Insights into Ecosystem Monitoring Using Geospatial Techniques”

Recent global-scale environmental issues from climate change to biodiversity loss are generating an intense social pressure on the scientific community [...]

Airborne HySpex Hyperspectral Versus Multitemporal Sentinel-2 Images for Mountain Plant Communities Mapping

Climate change and anthropopression significantly impact plant communities by leading to the spread of expansive and alien invasive plants, thus reducing their biodiversity. Due to significant elevation gradients, high-mountain plant communities in a small area allow for the monitoring of the most important environmental changes. Additionally, being a tourist attraction, they are exposed to direct human influence (e.g., trampling). Airborne hyperspectral remote sensing is one of the best data sources for vegetation mapping, but flight campaign costs limit the repeatability of surveys. A possible alternative approach is to use satellite data from the Copernicus Earth observation program. In our study, we compared multitemporal Sentinel-2 data with HySpex airborne hyperspectral images to map the plant communities on Tatra Mountains based on open-source R programing implementation of Random Forest and Support Vector Machine classifiers. As high-mountain ecosystems are adapted to topographic conditions, the input of Digital Elevation Model (DEM) derivatives on the classification accuracy was analyzed and the effect of the number of training pixels was tested to procure practical information for field campaign planning. For 13 classes (from rock scree communities and alpine grasslands to montane conifer and deciduous forests), we achieved results in the range of 76–90% F1-score depending on the data set. Topographic features: digital terrain model (DTM), normalized digital surface model (nDSM), and aspect and slope maps improved the accuracy of HySpex spectral images, transforming their minimum noise fraction (MNF) bands and Sentinel-2 data sets by 5–15% of the F1-score. Maps obtained on the basis of HySpex imagery (2 m; 430 bands) had a high similarity to maps obtained on the basis of multitemporal Sentinel-2 data (10 m; 132 bands; 11 acquisition dates), which was less than one percentage point for classifications based on 500–1000 pixels; for sets consisting of 50–100 pixels, Random Forest (RF) offered better accuracy.

Earth Observation for Phenological Metrics (EO4PM): Temporal Discriminant to Characterize Forest Ecosystems

The study of vegetation phenology has great relevance in many fields since the importance of knowing timing and shifts in periodic plant life cycle events to face the consequences of global changes in issues such as crop production, forest management, ecosystem disturbances, and human health. The availability of high spatial resolution and dense revisit time satellite observations, such as Sentinel-2 satellites, allows high resolution phenological metrics to be estimated, able to provide key information from time series and to discriminate vegetation typologies. This paper presents an automated and transferable procedure that combines validated methodologies based on local curve fitting and local derivatives to exploit full satellite Earth observation time series to produce information about plant phenology. Multivariate statistical analysis is performed for the purpose of demonstrating the capacity of the generated smoothed vegetation curve, temporal statistics, and phenological metrics to serve as temporal discriminants to detect forest ecosystems processes responses to environmental gradients. The results show smoothed vegetation curve and temporal statistics able to highlight seasonal gradient and leaf type characteristics to discriminate forest types, with additional information about forest and leaf productivity provided by temporal statistics analysis. Furthermore, temporal, altitudinal, and latitudinal gradients are obtained from phenological metrics analysis, which also allows to associate temporal gradient with specific phenophases that support forest types distinction. This study highlights the importance of integrated data and methodologies to support the processes of vegetation recognition and monitoring activities.