Underwater Video as a Tool to Quantify Fish Density in Complex Coastal Habitats

Habitat loss is a serious issue threatening biodiversity across the planet, including coastal habitats that support important fish populations. Many coastal areas have been extensively modified by the construction of infrastructure such as ports, seawalls, docks, and armored shorelines. In addition, habitat restoration and enhancement projects often include constructed breakwaters or reefs. Such infrastructure may have incidental or intended habitat values for fish, yet their physical complexity makes quantitatively sampling these habitats with traditional gears challenging. We used a fleet of unbaited underwater video cameras to quantify fish communities across a variety of constructed and natural habitats in Perdido and Pensacola Bays in the central northern Gulf of Mexico. Between 2019 and 2021, we collected almost 350 replicate 10 min point census videos from rock jetty, seawall, commercial, public, and private docks, artificial reef, restored oyster reef, seagrass, and shallow sandy habitats. We extracted standard metrics of Frequency of Occurrence and MaxN, as well as more recently developed MeanCount for each taxon observed. Using a simple method to measure the visibility range at each sampling site, we calculated the area of the field of view to convert MeanCount to density estimates. Our data revealed abundant fish assemblages on constructed habitats, dominated by important fisheries species, including grey snapper Lutjanus griseus and sheepshead Archosargus probatocephalus. Our analyses suggest that density estimates may be obtained for larger fisheries species under suitable conditions. Although video is limited in more turbid estuarine areas, where conditions allow, it offers a tool to quantify fish communities in structurally complex habitats inaccessible to other quantitative gears.

Density Estimates as Representations of Agricultural Fields for Remote Sensing-Based Monitoring of Tillage and Vegetation Cover

We consider the use of remote sensing for large-scale monitoring of agricultural land use, focusing on classification of tillage and vegetation cover for individual field parcels across large spatial areas. From the perspective of remote sensing and modelling, field parcels are challenging as objects of interest due to highly varying shape and size but relatively uniform pixel content and texture. To model such areas we need representations that can be reliably estimated already for small parcels and that are invariant to the size of the parcel. We propose representing the parcels using density estimates of remote imaging pixels and provide a computational pipeline that combines the representation with arbitrary supervised learning algorithms, while allowing easy integration of multiple imaging sources. We demonstrate the method in the task of the automatic monitoring of autumn tillage method and vegetation cover of Finnish crop fields, based on the integrated analysis of intensity of Synthetic Aperture Radar (SAR) polarity bands of the Sentinel-1 satellite and spectral indices calculated from Sentinel-2 multispectral image data. We use a collection of 127,757 field parcels monitored in April 2018 and annotated to six tillage method and vegetation cover classes, reaching 70% classification accuracy for test parcels when using both SAR and multispectral data. Besides this task, the method could also directly be applied for other agricultural monitoring tasks, such as crop yield prediction.

ESTIMATES OF DERIVATIVES OF (LOG) DENSITIES AND RELATED OBJECTS

We estimate the density and its derivatives using a local polynomial approximation to the logarithm of an unknown density function f. The estimator is guaranteed to be non-negative and achieves the same optimal rate of convergence in the interior as on the boundary of the support of f. The estimator is therefore well-suited to applications in which non-negative density estimates are required, such as in semiparametric maximum likelihood estimation. In addition, we show that our estimator compares favorably with other kernel-based methods, both in terms of asymptotic performance and computational ease. Simulation results confirm that our method can perform similarly or better in finite samples compared to these alternative methods when they are used with optimal inputs, that is, an Epanechnikov kernel and optimally chosen bandwidth sequence. We provide code in several languages.

Relating Profile Wall Root-Length Density Estimates to Monolith Root-Length Density Measurements of Cover Crops

Different methods have been proposed for in situ root-length density (RLD) measurement. One widely employed is the time-consuming sampling of soil cores or monoliths (MO). The profile wall (PW) method is a less precise, but faster and less laborious alternative. However, depth-differentiated functions to convert PW RLD estimates to MO RLD measurements have not yet been reported. In this study, we perform a regression analysis to relate PW results to MO results and determine whether calibration is possible for distinct crop groups (grasses, brassicas and legumes) consisting of pure and mixed stands, and whether soil depth affects this calibration. The methods were applied over two years to all crop groups and their absolute and cumulative RLD were compared using a linear (LR) and multiple linear (MLR) regression. PW RLD was found to highly underestimate MO RLD in absolute values and in highly rooted areas. However, a close agreement between both methods was found for cumulative root-length (RL) when applying MLR, highlighting the influence of soil depth. The level of agreement between methods varied strongly with depth. Therefore, the application of PW as the main RLD estimation method can provide reliable estimates of cumulative root distribution traits of cover crops.

Kernel density smoothing of composite spatial data on administrative area level

Composite spatial data on administrative area level are often presented by maps. The aim is to detect regional differences in the concentration of subpopulations, like elderly persons, ethnic minorities, low-educated persons, voters of a political party or persons with a certain disease. Thematic collections of such maps are presented in different atlases. The standard presentation is by Choropleth maps where each administrative unit is represented by a single value. These maps can be criticized under three aspects: the implicit assumption of a uniform distribution within the area, the instability of the resulting map with respect to a change of the reference area and the discontinuities of the maps at the borderlines of the reference areas which inhibit the detection of regional clusters.In order to address these problems we use a density approach in the construction of maps. This approach does not enforce a local uniform distribution. It does not depend on a specific choice of area reference system and there are no discontinuities in the displayed maps. A standard estimation procedure of densities are Kernel density estimates. However, these estimates need the geo-coordinates of the single units which are not at disposal as we have only access to the aggregates of some area system. To overcome this hurdle, we use a statistical simulation concept. This can be interpreted as a Simulated Expectation Maximisation (SEM) algorithm of Celeux et al (1996). We simulate observations from the current density estimates which are consistent with the aggregation information (S-step). Then we apply the Kernel density estimator to the simulated sample which gives the next density estimate (E-Step).This concept has been first applied for grid data with rectangular areas, see Groß et al (2017), for the display of ethnic minorities. In a second application we demonstrated the use of this approach for the so-called “change of support” (Bradley et al 2016) problem. Here Groß et al (2020) used the SEM algorithm to recalculate case numbers between non-hierarchical administrative area systems. Recently Rendtel et al (2021) applied the SEM algorithm to display spatial-temporal clusters of Corona infections in Germany.Here we present three modifications of the basic SEM algorithm: 1) We introduce a boundary correction which removes the underestimation of kernel density estimates at the borders of the population area. 2) We recognize unsettled areas, like lakes, parks and industrial areas, in the computation of the kernel density. 3) We adapt the SEM algorithm for the computation of local percentages which are important especially in voting analysis.We evaluate our approach against several standard maps by means of the local voting register with known addresses. In the empirical part we apply our approach for the display of voting results for the 2016 election of the Berlin parliament. We contrast our results against Choropleth maps and show new possibilities for reporting spatial voting results.

Density Estimates of Unmarked Large Mammals at Camera Traps Vary among Models, Species, and Years, Signalling Importance of Model Assumptions

Density estimation is a key goal in ecology but accurate estimates remain elusive, especially for unmarked animals. Data from camera-trap networks combined with new density estimation models can bridge this gap but recent research has shown marked variability in accuracy, precision, and concordance among estimators. We extend this work by comparing estimates from two different classes of models: unmarked spatial capture-recapture (spatial count, SC) models, and Time In Front of Camera (TIFC) models, a class of random encounter model. We estimated density for four large mammal species with different movement rates, behaviours, and sociality, as these traits directly relate to model assumptions. TIFC density estimates were typically higher than SC model estimates for all species. Black bear TIFC estimates were ~ 10-fold greater than SC estimates. Caribou TIFC estimates were 2-10 fold greater than SC estimates. White-tailed deer TIFC estimates were up to 100-fold greater than SC estimates. Differences of 2-5 fold were common for other species in other years. SC estimates were annually stable except for one social species; TIFC estimates were highly annually variable in some cases and consistent in others. Tests against densities obtained from DNA surveys and aerial surveys also showed variable concordance and divergence. For gregarious animals TIFC may outperform SC due to the latter model’s assumption of independent activity centres. For curious animals likely to investigate camera traps, SC may outperform TIFC, which assumes animal behavior is unaffected by cameras. Unmarked models offer great possibilities, but a pragmatic approach employs multiple estimators where possible, considers the ecological plausibility of assumptions, and uses an informed multi-inference approach to seek estimates from models with assumptions best fitting a species’ biology.

Pilot Study and Early Results of the Cosmic Filaments and Magnetism Survey with Nenufar: The Coma Cluster Field

NenuFAR, the New Extension in Nancay Upgrading LOFAR, is currently in its early science phase. It is in this context that the Cosmic Filaments and Magnetism Pilot Survey is observing sources with the array as it is still under construction—with 57 (56 core, 1 distant) out of a total planned 102 (96 core, 6 distant) mini-arrays online at the time of observation—to get a first look at the low-frequency sky with NenuFAR. One of its targets is the Coma galaxy cluster: a well-known object, host of the prototype radio halo. It also hosts other features of scientific import, including a radio relic, along with a bridge of emission connecting it with the halo. It is thus a well-studied object.In this paper, we show the first confirmed NenuFAR detection of the radio halo and radio relic of the Coma cluster at 34.4 MHz, with associated intrinsic flux density estimates: we find an integrated flux value of 106.3 ± 3.5 Jy for the radio halo, and 102.0 ± 7.4 Jy for the radio relic. These are upper bound values, as they do not include point-source subtraction. We also give an explanation of the technical difficulties encountered in reducing the data, along with steps taken to resolve them. This will be helpful for other scientific projects which will aim to make use of standalone NenuFAR imaging observations in the future.