Find research datasets worth reusing

opencc-by-4.0Jul 2021View details →

Comparing and Combining Existing and Emerging Data Collection and Modeling Strategies in Support of Signal Control Optimization and Management (Project M2)

For decades, traffic signal management agencies have used signal timing optimization tools combined with fine-tuning of signal timing based on field observations in their updates of time-of-day signal timing plans.  These traditional signal optimization methods and tools use very limited amount of data and depend on default values in the signal timing optimization/simulation tools to estimate network performance under different signal optimization strategies. In recent years, new data collection technologies are emerging including high resolution controller data, more advanced detection technologies such as video image detection that are based on vehicle tracking and possible integration with microwave detectors, automatic-vehicle based identification technologies, third party crowdsourcing data, connected vehicles, and connected automated vehicles data.  The objective of the proposed study is to propose methods and algorithms to combine data collected from existing and emerging sources with enhanced models and optimization algorithms to optimize and manage signal operations. The results from applying the developed methods and algorithms will be compared with traditional signal timing and optimization methods currently used by transportation agencies.

opencc-by-4.0Jul 2021View details →

Field Data associated with study: Investigating the water movements around a shallow shipwreck in Big Tub Harbour of Lake Huron: implications for managing underwater shipwrecks.

Field data (Water temperature, pressure, currents, summary of boat presence data) used in analysis of the study (and paper with the same name) titled: Investigating the water movements around a shallow shipwreck in Big Tub Harbour of Lake Huron: implications for managing underwater shipwrecks.

opencc-zeroSep 2021View details →

Data from: Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity

The long-term contribution of nitrification to nitrous oxide (N2O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2O, we test the relative importance of nitrification-derived N2O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2O fluxes was 13-17% in a conventionally fertilized annual cropping system, 27-42% in a low-input cover-cropped annual cropping system, and 52-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be less than 10% of these values because of low N2O yields in cultured nitrifiers (typically 0.04 to 8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2O was produced by ammonia oxidizing bacteria (AOB) rather than archaea (AOA), who appeared responsible for no more than 30% of nitrification-derived N2O production in all but one ecosystem. Although the proportion of nitrification-derived N2O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2O (higher Vmax) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2O in all ecosystems examined.

opencc-by-4.0Oct 2021View details →

Introduction to Research Data Management for Ecologists Distributed Graduate Seminar

This video was made to introduce students who had registered for the Spring 2021 Research Data Management for Ecologists distributed graduate seminar that was offered at Florida International University, University of New Mexico, and University of Wisconsin, Madison.

Data for the article "Management of social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study"

Data for the paper "Social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study". ANimated GIFs, GPS data, activity data and proximity data. Herdsmen use different techniques, as per varying geographies and cultures, to keep the cohesion within herds and avoid animals getting lost or predated. However, there is no study on the social behaviour of yaks and on herdsmen management practices. Therefore, this ethology study was initiated by ethnographic inquiries. We collected data from two herds living at the same settlement (Yak kharka, 4,100 m altitude, Nepal) by equipping them with loggers. One of the herdsman used the tether rope while other did not. Moreover, the Thaku herd had a more proactive shepherd than the Phurba one. In each herd, 17 animals were equipped with one actigraph wgt3x-BT to measure activity using accelerometer and spatial associations using proximity recorder. One of the herds was equipped with GPS (N=11) as well. Using GPS locations and activity, we showed that the two herds were cohesive and synchronised their activities but the herd with the tether rope was more cohesive.

opencc-zeroNov 2022View details →

Data for: Evaluating Golden-winged Warbler use of alder and aspen communities managed with shearing in the western Great Lakes

Best management practices are often written by researchers to guide land managers and landowners in the creation of habitat for wildlife species of interest. These documents are based on research evaluating the habitat needs of a species, but also describe tools and strategies managers can implement to create or restore desired conditions. Shrub and sapling shearing is a management practice often used to improve habitat for early-successional species, yet little monitoring or research has focused on wildlife response to shearing. The goal of this research was to formally evaluate the effect of shrub and sapling shearing as a best management strategy for Golden-winged Warbler (Vermivora chrysoptera) conservation at a regional scale. Specifically, we surveyed for male Golden-winged Warblers during the breeding season in sheared sites and untreated reference sites across portions of the western Great Lakes to assess the effects of 1) management status (i.e., sheared aspen or alder vs un-treated sites), and 2) the patch-level vegetation characteristics on male abundance. We found that male Golden-winged Warbler abundance was twice as high in sheared sites than in mature reference sites and peaked when sapling cover was ~40%. Male abundance was also negatively associated with percent cover of forbs and non-vegetated ground. These findings highlight the importance of patch-level heterogeneity when implementing shearing treatments for Golden-winged Warblers, and demonstrate the potential need for pre-treatment site assessments to help focus conservation efforts for this species. Ultimately, our results support the use of a site-specific, nuanced approach to shearing implementation to maximize cost efficiency and desired species outcomes.

Data set for "Landscape-variability of the carbon balance across managed boreal forests"

This data set is a compilation of biometric- and chamber-based annual CO2 flux estimates obtained during the period 2016–2018. Data were collected in 50 main forest stands within the Krycklan Catchment Study (KCS, https://www.slu.se/Krycklan), a multi-scale long-term monitored boreal catchment spanning 68 km2 in northern Sweden. Seven additional old forest stands were also included with the aim to reconcile our CO2 flux estimates for the old age class. Selected forest stands encompassed different landscape attributes: 1) soil type (i.e., sediment and till), 2) dominant tree species (i.e., pine and spruce), and 3) stand age class (i.e., initiation, young, middle-aged, mature, and old stands). Annual CO2 fluxes included are the following: net ecosystem production (NEP), net primary production (NPP), net primary production of trees (NPPt), net primary production of understory (NPPu) as well as total heterotrophic respiration (RH) and its soil and dead wood components (RHs and RHdw, respectively). All component CO2 fluxes are presented as positive terms, whereas positive and negative NEP refers to net C sink and source, respectively. It also includes a set of potential abiotic and biotic drivers controlling NEP and its component fluxes at the landscape-scale. This data set is composed of three Microsoft Excel worksheets: readme, metadata, and data. More details can be found in Peichl et al. (2022) Landscape-variability of the carbon balance across managed boreal forests. Global Change Biology, 00, 1–14. https://doi.org/10.1111/gcb.16534. Contact information: Professor Matthias Peichl (<a href="mailto:matthias.peichl@slu.se">Matthias.Peichl@slu.se</a>) Ph.D. Eduardo Martínez García (<a href="mailto:eduardo.martinez@slu.se">Eduardo.Martinez@slu.se</a>, <a href="mailto:edu.martinez.garcia@gmail.com">edu.martinez.garcia@gmail.com</a>) Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd 17, SE-901 83, Umeå, Sweden

opencc-zeroNov 2022View details →

Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas

Tropical savannas are characterised by high primary productivity and high fire frequency, such that much of the carbon captured by vegetation is rapidly returned to the atmosphere. Hence, there have been suggestions that management-driven reductions in savanna fire frequency and/or severity could significantly reduce greenhouse gas emissions and sequester carbon in tree biomass. However, a key knowledge gap is the extent to which savanna tree biomass will respond to modest shifts in fire regimes due to plausible, large-scale management interventions. Here, we: (1) characterise relationships between the frequency and severity of fires and key demographic rates of savanna trees, based on long-term observations in vegetation monitoring plots across northern Australia; (2) use these relationships to develop a process-explicit demographic model describing the effects of fire on savanna tree populations; and (3) use the demographic model to address the question: to what extent is it feasible, through the strategic application of prescribed burning, to increase tree biomass in Australian tropical savannas? Our long-term tree monitoring dataset included observations of 12,344 tagged trees in 236 plots, monitored for between 3 and 24 years. Analysis of this dataset showed that frequent high-severity fires significantly reduced savanna tree recruitment, survival and growth. Our demographic model suggested that: (1) despite the negative effects of frequent high-severity fires on demographic rates, savanna tree biomass appears to be suppressed by only a relatively small amount by contemporary fire regimes, characterised by a mix of low- to high-severity fires; and (2) plausible, management-driven reductions in the frequency of high-severity fires are likely to lead to increases in tree biomass of about 11.0 t DM ha–1 (95% confidence interval: -1.2–20.8) over a century. Accounting for this increase in carbon storage could generate significant carbon credits, worth on average three times those generated annually by current greenhouse gas (methane and nitrous oxide) abatement projects, and has the potential to significantly increase the economic viability of fire/carbon projects, thereby promoting ecologically sustainable management of tropical savannas in Australia and elsewhere. This growing industry has the potential to bring much-needed economic activity to savanna landscapes, without compromising important natural and cultural values.

A Scalable Data Management System Data Model facilitating the integration of any inspection system and the automated data digitalization process.

In the context of the EU-funded project PILOTING (No. 871542), a scalable Data Management System (DMS) was deployed and facilitated the easy integration of nine different robotic systems and various payloads and the storing of all the data observations produced during the inspections. In particular, a three-phase methodology was adopted for the creation of the DMS Data Model (DMS-DM) in order to define the architectural design of the DMS.  The first phase was to semantically define the entities of the PILOTING ecosystem, identifying assets and activities that were important to the data providers, and including them in the data model design. The second phase was to identify relationships between the entities, focusing on information that must pre-exist for entities to be semantically accurate, hierarchies between entities, especially physical assets, and the data needed to form the inspection plan. For the third phase, the information collected by the previous two stages of the data model construction was used to create the overall data model, taking into consideration the possible integration with third parties and the needs of the I&M Visualization portal.  The constructed document is attempted to present the designed Entity-Relationship-Diagram (ERD) of the DMS-DM. Additional definitions of the existing entities and the relations between them are also depicted.

A Versatile and Secure Data Management System API facilitating the Interconnection of any software component and Easy Data Access.

In the context of the EU-funded project PILOTING (No. 871542), a versatile Data Management System (DMS) was deployed and facilitated the easy integration of nine different robotic systems and various payloads and the storing of all the data observations produced during the inspections. The DMS is designed under the DMS-Data Model (DMS-DM) and operates on top of a representational state transfer (REST) application programming interface (API) that provides a simplified way to exchange data through HTTP(S) requests from a client to the server. One of its key advantages is that it provides a great deal of flexibility so the model could accommodate extensions if needed. Data is not tied to resources or methods, so REST can handle multiple types of calls, return different data formats and even change structurally with the correct implementation of hypermedia.  It supports CRUD operations via GET, POST, PUT, PATCH, and DELETE HTTP methods and stores the data on a PostgreSQL object-relational database system. The REST API has been created with Python's Django (web framework) and Django REST Framework, a powerful and flexible toolkit for building Web APIs.  The constructed document presents the communication endpoints (DMS API’s Uniform Resource Identifiers (URIs)) under which an authorized user can have access to the DMS API and subsequently to the collected data.

opencc-zeroNov 2022View details →

Data for: A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for non-model organisms. Here we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD-capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen that were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false positive rates of parent-offspring and full-sibling kinship identification was found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

opencc-zeroDec 2022View details →

Data for: The role of landscape in shaping bird community and implications for landscape management at Nanjing Lukou International Airport

Understanding the patterns of bird diversity and its driving force is necessary for bird strike prevention. In this study, we investigated the effects of landscape attributes on phylogenetic and functional diversity of bird communities at Nanjing Lukou International Airport (NLIA). Bird identifications and counting of individuals were carried out from November 2017 to October 2019. Based on the land cover data, the landscape was divided into four main types, including farmlands, woodlands, wetlands and urban areas. Bird phylogenetic and functional diversity were strongly affected by landscape matrix types. Bird species, phylogenetic and functional richness were highest in woodlands, while phylogenetic and functional structure were most complex in wetlands. We found that related carnivorous birds occupied most niches at the NLIA. Moreover, bird assemblages exhibited phylogenetic and functional clustering in all landscape matrix types, which meant environmental filtering governed community assembly. Landscape attributes of different matrix types influenced phylogenetic and functional diversity of bird communities. Landscape diversity affected bird functional structure positively, and the mean of patch area in the landscape had the strongest explanatory effects. To prevent bird strikes, we suggest that more small-area woodlands with low levels of aggregation can be considered and farmlands should be patchier and more regular. At landscape level, the number of patches can be adjusted to reduce the frequency of bird activities.

opencc-by-4.0Dec 2022View details →

PAReTT: a Python package for the Automated Retrieval and management of divergence time data from the TimeTree resource for downstream analyses (Dataset)

Dataset for article by the same title submitted the the Journal of Molecular Evolution.

opencc-by-4.0Jan 2023View details →

Data management table for PhD project:Reconquering the city: Pastoral agency and spatial impact of workers' parishes in Belgium (1884-1914)

In this data management table I organized additional information on all the sorts of data I am or will be using in the course of my research project. The content of the table sheds a light on why, how and for who I work on these different kinds of data.

opencc-zeroFeb 2023View details →

Data for: Causal mechanisms for negative impacts of energy development inform management triggers for sagebrush birds

Estimated population trends can identify declining species to focus biological conservation, but monitoring may fail to illuminate causes of population change and strategies for reversing declines. Monitoring programs can relate trends with environmental attributes to test causal hypotheses, but typical analytical approaches do not explicitly support causal inference, diluting available data for informing conservation. The U.S. Bureau of Land Management (BLM) extended Integrated Monitoring in Bird Conservation Regions with a quasi-experimental sampling design over a 10-year period (2010–2019) to evaluate impacts of oil and gas development on sagebrush birds within the Atlantic Rim Natural Gas Development Project in southern Wyoming. We analyzed resulting data using a multi-scale community occupancy model to estimate trends in species occupancy and richness relevant to management triggers. Additionally, we employed path analysis to evaluate mechanisms underlying observed trends to inform potential management responses. Fine-scale occupancy for sage thrasher (Oreoscoptes montanus) declined within the high-development stratum at a rate sufficient to meet an a priori management trigger established by the BLM. Two additional sagebrush-associated species, Brewer's (Spizella breweri) and sagebrush sparrow (Artemisiospiza nevadensis), exhibited negative development relationships with trend, as did overall species richness, and richness of grassland, sagebrush, and generalist guilds. We identified well pad density and invasive plants associated with energy development as causal factors contributing to these negative development impacts. We demonstrate an analytical approach for both estimating occupancy trends and identifying underlying causes to inform conservation action. Reducing the development footprint, including well pad density and associated invasive plants, could help reduce or limit impacts on birds within this landscape.

opencc-zeroMar 2023View details →

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

opencc-by-4.0Apr 2023View details →

Data from: Bat activity is related to habitat type and structure in managed pine barrens in New England

Background. Several insectivorous bat species are found in New England, yet research on them is still scarce. Current research shows the ecological importance of bats due to their control of insect populations, but they are endangered by habitat loss and White Nose Syndrome, among other threats. Pine barrens are an uncommon ecosystem found in New England that supports other rare taxa and could be important for these bat species. Methods. With hand-held audio recorders, we surveyed for bats in Montague Plains Wildlife Management Area in Massachusetts and Concord Pine Barrens in New Hampshire in June 2022. Our study objectives were to 1) describe the most common bat species and 2) compare bat activity across different habitat types at two managed pine barrens in New England. In particular, we examined bat activity related to habitat type (scrub oak, mature pitch pine, treated pitch pine, hardwood forest), habitat structure (i.e., canopy closure), and time since prescribed fire. We analyzed our data through linear mixed effects modeling and Fisher’s exact tests. Results. Overall, we were able to measure the presence of five out of the nine total species found in the area, including the endangered Myotis lucifugus (little brown bat). We recorded 293 bat calls, with the majority of calls from big brown bats (71%). We found significant differences (P < 0.05) in bat activity in relation to habitat types and structure. The index of bat activity was greatest in pitch pine and hardwood forests and lowest in scrub oak and treated pitch pine habitats. With preliminary data, we also found that there was more bat activity in areas that had not been burned recently. Discussion. These findings demonstrate the importance of pine barrens as an ecosystem that supports bats in New England. According to the activity of bats in our study, closed canopy and mature pitch pine habitats may be prioritized in conservation efforts at managed barrens for bat species. Further research is recommended to better understand the relationship between prescribed fires, which are common in managed barrens, and bat activity.

opencc-zeroApr 2023View details →

Data for: Effects of habitat management on rodent diversity, abundance, and virus infection dynamics

As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife. We compared the effects of grassland management regimes (prescribed burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing grassland sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses. We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity, but burned sites had a higher proportion of grassland species than unmanaged sites; cut sites had the highest proportion of grassland species but the lowest rodent abundance and diversity. A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland species, accounted for 97% of the rodents seropositive for orthohantavirus. Our study indicates that prescribed burns lead to a diverse and abundant community of grassland rodent species when compared to other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from robust host population densities supported by the increased habitat quality of these sites. Ultimately, these results provide empirical evidence that can inform grassland restoration and ongoing management strategies.

opencc-zeroMay 2023View details →

Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests

Declining biodiversity is a global challenge to sustainability and resilience of ecosystems facing multiple novel stressors, including climate change and invasive pests-pathogens. Northern hardwood forests (NHF) of the Great Lakes region have experienced declines in canopy tree diversity since European colonization, with current tree regeneration patterns in some areas suggesting perpetuation of this trend. However, regional (106 ha) patterns and possible causes are underexplored. To address this information gap, we used data from 141 managed NHF stands, Michigan, USA to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand-level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6 – 7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (Fraxinus americana and Fagus grandifolia, insect/pathogen limited; Ostrya virginiana, small maximum size). For the 11 most common species, conspecific canopy density (+, significant for 11 seedlings, 11 species) and stand basal area (-, saplings, 3 species) were the most consistent drivers of density, with less consistent effects for deer use, site quality, and substrate. Patterns of relative density by size class among the 18 species present on > 10 % of sites were consistent with theories of establishment or recruitment limitations due to deer browsing, deep shade, or limited suitable substrate. For seven species (including e.g., Tsuga canadensis, Betula alleghaniensis, Populus grandidentata, Tilia americana), relative abundance was lowest in the seedling layer and increased in larger size classes, suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (Acer saccharum, Quercus rubra.), patterns of reduced sapling relative abundance compared to seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., Fagus grandifolia, Ostrya virginiana, Pinus strobus) had highest relative density for saplings suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most abundant for Acer rubrum and Prunus spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. Americana, consistent with recent pest-related canopy mortality. Our results suggest sustained low diversity and shifting composition are being driven by limited local seed availability, deep shading, limited seedling establishment substrate, and abundant deer. Management aimed at overcoming these specific limitations may be necessary to promote future NHF resilience.