scholarly journals Using Spatial Validity and Uncertainty Metrics to Determine the Relative Suitability of Alternative Suites of Oceanographic Data for Seabed Biotope Prediction. A Case Study from the Barents Sea, Norway

Geosciences ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 48
Author(s):  
Margaret F.J. Dolan ◽  
Rebecca E. Ross ◽  
Jon Albretsen ◽  
Jofrid Skarðhamar ◽  
Genoveva Gonzalez-Mirelis ◽  
...  
Keyword(s):  
Barents Sea ◽  
Predictor Variable ◽  
Environmental Data ◽  
Spatial Uncertainty ◽  
Benthic Habitat ◽  
Habitat Distribution ◽  
Distribution Models ◽  
Entire Study ◽  
Oceanographic Data ◽  
Uncertainty Analyses

The use of habitat distribution models (HDMs) has become common in benthic habitat mapping for combining limited seabed observations with full-coverage environmental data to produce classified maps showing predicted habitat distribution for an entire study area. However, relatively few HDMs include oceanographic predictors, or present spatial validity or uncertainty analyses to support the classified predictions. Without reference studies it can be challenging to assess which type of oceanographic model data should be used, or developed, for this purpose. In this study, we compare biotope maps built using predictor variable suites from three different oceanographic models with differing levels of detail on near-bottom conditions. These results are compared with a baseline model without oceanographic predictors. We use associated spatial validity and uncertainty analyses to assess which oceanographic data may be best suited to biotope mapping. Our results show how spatial validity and uncertainty metrics capture differences between HDM outputs which are otherwise not apparent from standard non-spatial accuracy assessments or the classified maps themselves. We conclude that biotope HDMs incorporating high-resolution, preferably bottom-optimised, oceanography data can best minimise spatial uncertainty and maximise spatial validity. Furthermore, our results suggest that incorporating coarser oceanographic data may lead to more uncertainty than omitting such data.

scholarly journals A Robust Prediction Model for Species Distribution Using Bagging Ensembles with Deep Neural Networks

2021 ◽  
Vol 13 (8) ◽  
pp. 1495
Author(s):  
Jehyeok Rew ◽  
Yongjang Cho ◽  
Eenjun Hwang
Keyword(s):  
Neural Networks ◽  
Species Distribution ◽  
Best Practice ◽  
Deep Neural Networks ◽  
Species Distribution Models ◽  
Species Distribution Model ◽  
Environmental Data ◽  
Distribution Model ◽  
Distribution Models ◽  
Robust Prediction

Species distribution models have been used for various purposes, such as conserving species, discovering potential habitats, and obtaining evolutionary insights by predicting species occurrence. Many statistical and machine-learning-based approaches have been proposed to construct effective species distribution models, but with limited success due to spatial biases in presences and imbalanced presence-absences. We propose a novel species distribution model to address these problems based on bootstrap aggregating (bagging) ensembles of deep neural networks (DNNs). We first generate bootstraps considering presence-absence data on spatial balance to alleviate the bias problem. Then we construct DNNs using environmental data from presence and absence locations, and finally combine these into an ensemble model using three voting methods to improve prediction accuracy. Extensive experiments verified the proposed model’s effectiveness for species in South Korea using crowdsourced observations that have spatial biases. The proposed model achieved more accurate and robust prediction results than the current best practice models.

Very high resolution environmental predictors in species distribution models

2013 ◽  
Vol 38 (1) ◽  
pp. 79-96 ◽  
Author(s):  
Jean-Nicolas Pradervand ◽  
Anne Dubuis ◽  
Loïc Pellissier ◽  
Antoine Guisan ◽  
Christophe Randin
Keyword(s):  
High Resolution ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Environmental Data ◽  
Swiss Alps ◽  
Fine Scale ◽  
Distribution Models ◽  
Model Quality ◽  
Vegetation Height ◽  
Very High

Recent advances in remote sensing technologies have facilitated the generation of very high resolution (VHR) environmental data. Exploratory studies suggested that, if used in species distribution models (SDMs), these data should enable modelling species’ micro-habitats and allow improving predictions for fine-scale biodiversity management. In the present study, we tested the influence, in SDMs, of predictors derived from a VHR digital elevation model (DEM) by comparing the predictive power of models for 239 plant species and their assemblages fitted at six different resolutions in the Swiss Alps. We also tested whether changes of the model quality for a species is related to its functional and ecological characteristics. Refining the resolution only contributed to slight improvement of the models for more than half of the examined species, with the best results obtained at 5 m, but no significant improvement was observed, on average, across all species. Contrary to our expectations, we could not consistently correlate the changes in model performance with species characteristics such as vegetation height. Temperature, the most important variable in the SDMs across the different resolutions, did not contribute any substantial improvement. Our results suggest that improving resolution of topographic data only is not sufficient to improve SDM predictions – and therefore local management – compared to previously used resolutions (here 25 and 100 m). More effort should be dedicated now to conduct finer-scale in-situ environmental measurements (e.g. for temperature, moisture, snow) to obtain improved environmental measurements for fine-scale species mapping and management.

Data Inter-Operability Driven by Oceanic Data Assimilation Needs

1999 ◽  
Vol 33 (3) ◽  
pp. 55-66 ◽  
Author(s):  
L. Charles Sun
Keyword(s):  
Data Assimilation ◽  
Data Access ◽  
Heterogeneous Data ◽  
Environmental Data ◽  
Ocean Dynamics ◽  
Data Systems ◽  
Oceanographic Data ◽  
Ease Of Access ◽  
Access To Data ◽  
Station Location

An interactive data access and retrieval system, developed at the U.S. National Oceanographic Data Genter (NODG) and available at <ext-link ext-link-type="uri" href="http://www.node.noaa.gov">http://www.node.noaa.gov</ext-link>, is presented in this paper. The purposes of this paper are: (1) to illustrate the procedures of quality control and loading oceanographic data into the NODG ocean databases and (2) to describe the development of a system to manage, visualize, and disseminate the NODG data holdings over the Internet. The objective of the system is to provide ease of access to data that will be required for data assimilation models. With advances in scientific understanding of the ocean dynamics, data assimilation models require the synthesis of data from a variety of resources. Modern intelligent data systems usually involve integrating distributed heterogeneous data and information sources. As the repository for oceanographic data, NOAA’s National Oceanographic Data Genter (NODG) is in a unique position to develop such a data system. In support of the data assimilation needs, NODG has developed a system to facilitate browsing of the oceanographic environmental data and information that is available on-line at NODG. Users may select oceanographic data based on geographic areas, time periods and measured parameters. Once the selection is complete, users may produce a station location plot, produce plots of the parameters or retrieve the data.

scholarly journals MAPPING OF THE SEAGRASS COVER ALONG THE MEDITERRANEAN COAST OF TURKEY USING LANDSAT 8 OLI IMAGES

2016 ◽  
Vol XLI-B8 ◽  
pp. 1103-1105 ◽  
Author(s):  
T. Bakirman ◽  
M. U. Gumusay ◽  
I. Tuney
Keyword(s):  
Accuracy Assessment ◽  
Mediterranean Coast ◽  
Environmental Data ◽  
Benthic Habitat ◽  
Landsat 8 ◽  
Landsat 8 Oli ◽  
Carbon Dioxide Absorption ◽  
Landsat Images ◽  
Marine Animals ◽  
Seagrass Cover

Benthic habitat is defined as ecological environment where marine animals, plants and other organisms live in. Benthic habitat mapping is defined as plotting the distribution and extent of habitats to create a map with complete coverage of the seabed showing distinct boundaries separating adjacent habitats or the use of spatially continuous environmental data sets to represent and predict biological patterns on the seafloor. Seagrass is an essential endemic marine species that prevents coast erosion and regulates carbon dioxide absorption in both undersea and atmosphere. Fishing, mining, pollution and other human activities cause serious damage to seabed ecosystems and reduce benthic biodiversity. According to the latest studies, only 5&ndash;10% of the seafloor is mapped, therefore it is not possible to manage resources effectively, protect ecologically important areas. In this study, it is aimed to map seagrass cover using Landsat 8 OLI images in the northern part of Mediterranean coast of Turkey. After pre-processing (e.g. radiometric, atmospheric, water depth correction) of Landsat images, coverage maps are produced with supervised classification using in-situ data which are underwater photos and videos. Result maps and accuracy assessment are presented and discussed.

Examining Local Transferability of Predictive Species Distribution Models for Invasive Plants: An Example with Cogongrass (Imperata cylindrica)

2011 ◽  
Vol 4 (4) ◽  
pp. 390-401 ◽  
Author(s):  
Gary N. Ervin ◽  
D. Christopher Holly
Keyword(s):  
Invasive Species ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Imperata Cylindrica ◽  
Environmental Data ◽  
Training Data ◽  
Distribution Data ◽  
Strongly Correlated ◽  
Distribution Models ◽  
Tree Canopy Cover

AbstractSpecies distribution modeling is a tool that is gaining widespread use in the projection of future distributions of invasive species and has important potential as a tool for monitoring invasive species spread. However, the transferability of models from one area to another has been inadequately investigated. This study aimed to determine the degree to which species distribution models (SDMs) for cogongrass, developed with distribution data from Mississippi (USA), could be applied to a similar area in neighboring Alabama. Cogongrass distribution data collected in Mississippi were used to train an SDM that was then tested for accuracy and transferability with cogongrass distribution data collected by a forest management company in Alabama. Analyses indicated the SDM had a relatively high predictive ability within the region of the training data but had poor transferability to the Alabama data. Analysis of the Alabama data, via independent SDM development, indicated that predicted cogongrass distribution in Alabama was more strongly correlated with soil variables than was the case in Mississippi, where the SDM was most strongly correlated with tree canopy cover. Results suggest that model transferability is influenced strongly by (1) data collection methods, (2) landscape context of the survey data, and (3) variations in qualitative aspects of environmental data used in model development.

Habitat distribution models for intertidal seaweeds: responses to climatic and non-climatic drivers

2012 ◽  
Vol 39 (10) ◽  
pp. 1877-1890 ◽  
Author(s):  
Brezo Martínez ◽  
Rosa M. Viejo ◽  
Francisco Carreño ◽  
Silvia C. Aranda
Keyword(s):  
Habitat Distribution ◽  
Distribution Models ◽  
Climatic Drivers

scholarly journals West Florida Shelf pipeline serves as sea turtle benthic habitat based on in situ towed camera observations

2019 ◽  
Vol 29 ◽  
pp. 17-31 ◽  
Author(s):  
HA Broadbent ◽  
SE Grasty ◽  
RF Hardy ◽  
MM Lamont ◽  
KM Hart ◽  
...  
Keyword(s):  
Habitat Use ◽  
Sea Turtles ◽  
Sea Turtle ◽  
Environmental Data ◽  
Benthic Habitat ◽  
West Florida Shelf ◽  
Benthic Habitats ◽  
Florida Shelf ◽  
Turtle Species

The use of marine offshore benthic habitats by sea turtles is poorly characterized due to the difficulty of obtaining in situ data. Understanding benthic habitat use that is important to the species’ reproduction, foraging, and migrations is critical for guiding management decisions. A towed camera-based assessment survey system (C-BASS) equipped with environmental sensors was used to characterize and assess benthic habitats on the West Florida Shelf (WFS) from 2014 to 2018. During these cruises, sea turtles were opportunistically observed during the surveys, and critical in situ data such as spatiotemporal information, species identification, habitat use, behavior, and environmental data were collected and evaluated. In total, 79 sea turtles were observed during 97 transects of approximately 2700 km of seafloor, which was recorded on 380 h of video. Several sea turtle species were spotted within the WFS, including loggerhead Caretta caretta, Kemp’s ridley Lepidochelys kempii, and green turtles Chelonia mydas. These opportunistic sightings revealed an area of high use on the WFS, an anthropogenic structure known as the Gulfstream natural gas pipeline (GSPL). C-BASS survey results suggest that 2 sea turtle species (C. caretta and L. kempii) utilize this artificial structure primarily as a resting area. We emphasize the importance of combining habitat mapping techniques (towed underwater video and multibeam bathymetry/backscatter) with tracking technology to better understand the fine-scale habitat use of sea turtles.

scholarly journals SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4095 ◽  
Author(s):  
Jason L. Brown ◽  
Joseph R. Bennett ◽  
Connor M. French
Keyword(s):  
Species Distribution ◽  
Species Distribution Model ◽  
Species Distribution Modeling ◽  
Environmental Data ◽  
Distribution Model ◽  
Data Types ◽  
Distribution Models ◽  
Distribution Modeling ◽  
Modeling Software ◽  
Cost Paths

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

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