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78 results for “community data analysis”
Data and analysis code from: Micro-scale geography of synchrony in a serpentine plant community
This package includes data and code to reproduce analyses of micro-scale geography of synchrony in the plant community at Jasper Ridge Biological Preserve. Plant cover and soil depth data come from long-term experimental plots established by Richard Hobbs. Plant cover is aggregated into 36 1m2 plots across three treatments (control, gopher exclosure, rabbit exclosure) from 1983 to 2015; included herein are data on the 6 most abundant species (Plantago erecta, Bromus hordeaceous, Lasthenia californica, Microseris douglasii, Vulpia microstachys, and Calycadenia multiglandulosa), total plant cover across all species, and records of gopher disturbance in the plots. The data package also includes time series of monthly precipitation and growing season Palmer’s Drought Severity Index for the same time period. An R Markdown file is included that reproduces all analyses described in the manuscript and reproduces all data figures. Data to support: Walter, Hallett et al. in review “Micro-scale geography of synchrony in a serpentine plant community
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey - Extended Data 4 - Analysis Data Sheet
<p>This dataset is extended data to the manuscript "Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey" by Schmidt C., Hanne J, Moore J, Meesters C, Ferrando-May E, Weidtkamp-Peters S, and members of the NFDI4BIOIMAGE initiative. [version 1; peer review: awaiting peer review] F1000Research 2022, 11:638, https://doi.org/10.12688/f1000research.121714.1</p> <p>This extended data includes:</p> <p>- Data Analysis Sheet and results table</p> <p>Note: The data is anonymized (i.e., all IP addresses as well as personal comments were deleted)</p> <p>The revised version was published after the peer-review process of the original article on zenodo.org</p>
Data archive: Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition
<p>Data belonging to the paper: </p> <p>Dick van Oevelen, Gerard C. A. Duineveld, Marc S. S. Lavaleye, Tina Kutti and Karline Soetaert (2017) Trophic structure of cold-water coral communities revealed from the analysis of 55 tissue isotopes and fatty acid composition. Marine Biology Research, DOI: https://doi.org/10.1080/17451000.2017.1398404</p> <p>Abstract:</p> <p>The trophic structure of cold-water coral reef communities at two contrasting locations, the 800-<br> m deep Belgica Mounds (Irish margin) and 300-m deep Træna reefs (Norwegian Shelf), was<br> investigated using stable isotope (δ13C and δ15N) and fatty-acid composition analysis. A<br> broad range of specimens, with emphasis on (commercial) fish species, and organic matter<br> sources were sampled using a variety of tools. Irrespective of the environmental and<br> geographical setting, the δ15N values indicated that the food web encompasses roughly 1.5<br> to 3 trophic levels. Mobile echinoderms, i.e. sea urchins and sea stars, had highest δ15N<br> values, indicative of a high trophic position in the food web. The fraction of bacterial fatty<br> acids in reef fauna was generally low (<5%), indicating that enhanced bacterial production in<br> the water column through seafloor seepage of nutrients (‘hydraulic theory’) does not form a<br> significant energy pathway into the food web. The high fraction of algal and essential fatty<br> acids in reef fauna and fish at both locations indicates a close coupling with surface<br> productivity, but the transport mechanism depends on the hydrographic setting. At Træna,<br> Calanus copepods and euphausiids form an additional link between primary production and<br> fish, which is largely absent at Belgica Mounds. At Belgica Mounds, the reef community is<br> primarily supported by phytodetritus, as evidenced by the high contribution of algal fatty<br> acids in faunal tissue and seasonal chlorophyll a deposition and marine snow at the reef. The<br> environmental setting of cold-water coral reefs influences the structure of the associated<br> food web.</p>
BIO4AFRICA_Survey Data Uganda - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_311022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Senegal - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_101022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Ghana - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_101022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
BIO4AFRICA_Survey Data Ivory Coast - Analysis of the needs and contexts of target farmers and rural communities with a gender lens_D1.1_311022_1
<p>The results of this survey support the identification of the needs, challenges, and context of target farmers and rural communities and how, why and under which circumstances the social, economic, regulatory, institutional, market and political circumstances could act as a barrier or an enabler for the uptake of bio-based solutions.</p>
Data and code for reproducing analysis in 'Producing indicative allocations for Community Led Local Development funding in Scotland (2022-23)'
<p>The data and code in this folder can be used to reproduce work used to generate indicative allocations of Community Led Local Development funding (2022-23) to 21 Local Action Group (LAG) areas in Scotland. It accompanies a note ('Producing indicative allocations for Community Led Local Development funding in Scotland (2022-23)', <a href="https://doi.org/10.5281/zenodo.7418862">https://doi.org/10.5281/zenodo.7418862</a>) providing an overview of the analysis and its key outputs.</p>
Scripts of data selection and analysis: role of community size in driving spatial variation in riverine fish metacommunities around the world
<p>Here we describe how we obtained and analyzed data for the manuscript: High compositional dissimilarity among small communities is decoupled from environmental variation, accepted for publication in Oikos. (10.1111/oik.09802). A preprint is also available: https://doi.org/10.32942/osf.io/vngse</p> <p>We investigated the role of community size in mediate the strength of ecological drift and environmental selection in driving community spatial variation in metacommunities. </p>
ipaast project - community stakeholder survey data and basic analysis
<p>This data provides the basis for the report titled</p> <p>"Ready for integrated sustainable agricultural land management? </p> <p>Are practitioners in archaeology and agriculture informed, willing, enabled, and motivated to change how they work with remote and near-surface sensing data to collaboratively address contemporary challenges in sustainable agricultural land management? "</p> <p>Data were collected in compliance with the University of Glasgow's Research Ethics Policy (Application #100200154).</p> <p>As stated in the Methods section of this report:</p> <p>"The participatory survey was conducted between May 2021 and October 2022. </p> <p>Location: The preponderance of stakeholders engaged with are professional practitioners or researchers based in the UK, Belgium, Italy, Cyprus, Spain and France. Sessions occurred remotely (online/phone), as well as on site, during workshops at the University of Glasgow, the Dalswinton Estate, Dumfries, and Manor Farm, Yedingham. </p> <p>Participants </p> <p>Selection: A sub-group of 51 high-level participants were selected from a greater network of 86 stakeholders who were engaged with during the ipaast project. </p> <p>Sector: Farmers, researchers, heritage managers, geophysicists, remote sensing specialists, statisticians, soil scientists, service providers, sensor developers, and data archivists, who all deal directly, or indirectly with datasets relating to the measurement of soil and/or plant properties (physical, chemical, microbial) were represented (Table 1) </p> <p>Expertise: Engagement with mid- to late- career specialists was prioritised, with many participants having over 20 years of experience and most having over 10 years of experience (including time during the PhD). </p> <p> </p> <p>Interview method </p> <p>Engagement with stakeholders was primarily through one-to-one interviews and structured workshop discussions, conducted either in person, or remotely over video conference or phone. In some instances, participants provided written input (see Table 2 summary). Follow-up interviews or written exchanges were used to clarify or continue discussions when required. A semi-structured approach to interviews and discussions was preferred, with a mix of general questions (see sample questions), as well as questions specifically tailored to the participants specialist background and experience. </p> <p>Sample Questions: </p> <ul> <li> <p>What types of sensing data do you use/collect? </p> </li> </ul> <ul> <li> <p>Where/how do you access/collect these data? </p> </li> <li> <p>What are your main aims/applications in using or collecting these data? </p> </li> <li> <p>How often do you access/collect, or anticipate accessing/collecting, these data to be useful to you? </p> </li> <li> <p>What spatial resolution is necessary for these data to be useful to you? </p> </li> <li> <p>What, if anything, would encourage/discourage you from sharing your data? </p> </li> </ul> <ul> <li> <p>What kinds of additional data types or additional information (metadata) might help you to better understand and use data which you have previously collected or received? </p> </li> <li> <p>What do you see as the main impacts, if any, of ecosystem service frameworks and/or recent changes to rural/environmental regulations on your work? </p> </li> <li> <p>What attitudes to sensing data do you see from other stakeholders in rural affairs? </p> </li> </ul> <p>Documentation: Where viable, interviews and workshop discussions were recorded and transcribed; alternatively, notes were made during engagement by either the interviewer and/or dedicated participant observers (e.g. at workshops). Where notes were used, specific quotes and summary reports were checked with the participants for accuracy. "</p>
Data and tools of the landscape and cost analysis of data repositories currently used by the Swiss research community
<p>This file collection is part of the ORD Landscape and Cost Analysis Project (DOI: 10.5281/zenodo.2643460), a study jointly commissioned by the SNSF and swissuniversities in 2018.</p> <p>Please cite this data collection as:<br> von der Heyde, M. (2019). Data and tools of the landscape and cost analysis of data repositories currently used by the Swiss research community. Retrieved from https://doi.org/10.5281/zenodo.2643495</p> <p>Connected data papers are:<br> von der Heyde, M. (2019). Open Data Landscape: Repository Usage of the Swiss Research Community: Description of collection, collected data, and analysis methods [Data paper]. Retrieved from https://doi.org/10.5281/zenodo.2643430<br> von der Heyde, M. (2019). International Open Data Repository Survey: Description of collection, collected data, and analysis methods [Data paper]. Retrieved from https://doi.org/10.5281/zenodo.2643450</p> <p>Connected data sets are:<br> von der Heyde, M. (2019). Data from the Swiss Open Data Repository Landscape survey. Retrieved from https://doi.org/10.5281/zenodo.2643487<br> von der Heyde, M. (2019). Data from the International Open Data Repository Survey. Retrieved from https://doi.org/10.5281/zenodo.2643493</p> <p> </p> <p><strong>Contact</strong></p> <p>Swiss National Science Foundation (SNSF)</p> <p>Open Research Data Group</p> <p>E-mail: <a href="mailto:ord@snf.ch">ord@snf.ch</a></p> <p> </p> <p>swissuniversities</p> <p>Program "Scientific Information"</p> <p>Gabi Schneider</p> <p>E-Mail: <a href="mailto:isci@swissuniversities.ch">isci@swissuniversities.ch</a></p>
Data and analysis scripts for: Co-occurrence patterns at four spatial scales implicate reproductive processes in shaping community assembly in clovers
Open the record for dataset details and reuse information.
Data from: Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments
Open the record for dataset details and reuse information.
Data for a meta-analysis of the effect of kelp forests on fish communities around the world from observational and experimental studies spanning 1983-2020
Data for Pérez-Matus, A., Micheli, F., Konar, B., Shears, N., Low, N., Okamoto, D., Wernberg, T., Krumhansl, K., Ling, S., Kinsgford, M., Navarrete-Fernandez, T., Ruz, C., and Byrnes, J. 2024. Kelp forests as nursery and foundational habitat for reef fish. Ecology. For the definitive analysis, see the paper. Code is at https://github.com/jebyrnes/fish_kelp_meta. This data set concerns the effects of kelp on fish community composition. Data was mined as part of the National Center for Ecological Analysis and Synthesis (NCEAS) working group on "Global impacts of climate change on kelp forest ecosystems." It consists of digitized information from studies searched (see methods) examining fish community composition with and without kelp. To summarize the study, conservation of marine biodiversity requires an understanding of the habitats needed to support and replenish species of interest. It also requires knowledge about the abundance and diversity of multi-species assemblages. Variation in the distribution and composition of kelp forests, one of the most productive marine coastal habitats globally, can have major influences on reef fishes – a group of ecologically and socio-economically important species. In the face of widespread and escalating loss of kelp forests, quantification of these effects is urgently needed to assess and project cascading impacts on biodiversity. Here, we evaluate relationships between kelp forests and associated reef fish populations using a global meta-analysis of experimental kelp removals and comparative surveys of kelp and adjacent non-kelp habitats. These analyses show that kelp forests increase the abundance of reef fishes, though the significance of this effect varied depending on the structural complexity of kelp forests. In experimental studies, kelp forests have a significant positive effect on fish species richness, revealing that kelp act as true foundation species by supporting the diversity of associated multi-species assemblag
Data for a global meta-analysis of passive experimental warming effects on plant traits and community properties
This database contains the data used in a global meta-analysis of warming effects on plants. L0 data are available upon request; they include the raw data from 126 warming experiments. The L1 data are the result of merged L0 data and are cleaned for typos and are standardized names. L1 data contain plant trait and community property measurements in both warmed and ambient conditions. L2 data contain the effect sizes of warming for each study. These data came from 126 warming experiments across the globe.
Plant-mediated root methane emissions and oxidation in a thermokarst bog complex in the Bonanza Creek LTER Experimental Forest V - Raw Microbial Community Analysis Data 2015
Vascular plants are important in the wetland methane cycle but their effect on production, oxidation, and transport has high uncertainty, limiting our ability to predict emissions. Vegetation operated on top of baseline methane emissions, which varied with proximity to the thawing permafrost margin. Emissions from vegetated plots increased over the season, resulting in cumulative seasonal methane emissions that were 4.1-5.2 g m-2 season-1 greater than unvegetated plots. Mass balance calculations signify these greater emissions were due to increased methane production (3.0-3.5 g m-2 season-1) and decreased methane oxidation (1.1-1.6 g m-2 season-1). Minimal oxidation occurred along the plant-transport pathway and oxidation was suppressed outside the plant pathway. Our data indicate suppression of methane oxidation was stimulated by root exudates fueling competition among microbes for electron acceptors. Root exudates are known to fuel methane production and our work provides evidence they also decrease methane oxidation. This dataset contains 2015 results from monthly DNA analyses taken on cores from natural conditions in a bog complex in the Bonanza Creek LTER.
Data from: Bringing multivariate support to multiscale codependence analysis: assessing the drivers of community structure across spatial scales
1. Multiscale codependence analysis (MCA) quantifies the joint spatial distribution of a pair of variables in order to provide a spatially-explicit assessment of their relationships to one another. For the sake of simplicity, the original definition of MCA only considered a single response variable (e.g. a single species). However, that definition would limit the application of MCA when many response variables are studied jointly, for example when one wants to study the effect of the environment on the spatial organisation of a multi-species community in an explicit manner. 2. In the present paper, we generalize MCA to multiple response variables. We conducted a simulation study to assess the statistical properties (i.e. type I error rate and statistical power) of multivariate MCA (mMCA) and found that it had honest type I error rate and sufficient statistical power for practical purposes, even with modest sample sizes. We also exemplified mMCA by applying it to two ecological data sets. 3. The simulation study confirmed the adequacy of mMCA from a statistical standpoint: it has honest type I error rates and sufficient power to be useful in practice. Using mMCA, we were able to detect variation in fish community structure along the Doubs River (in France), which was associated with large spatial structures in the variation of physical and chemical variables related to water quality. Also, mMCA usefully described the spatial variation of an Oribatid mite community structure associated with a gradient of water content superimposed on various smaller-scale spatial features associated with vegetation cover in the peat blanket surrounding Lac Geai (in Québec, Canada). 4. In addition to demonstrating the soundness of mMCA in theory and practice, we further discuss the strengths and assumptions of mMCA and describe other potential scenarios where it would be helpful to biologists interested in assessing influence of environmental conditions on community structure in a spatially-explicit way.
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.
Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
<p>A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of <i>Stipa</i><i> grandis</i> in grazed and ungrazed <i>S. grandis</i> communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of <i>S. grandis</i> by using the pair correlation function <i>g</i>(<i>r</i>) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of <i>S. grandis</i> were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.</p>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.