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1,249 results for “R data”
finnpiatscheck/Environmental-Effects-on-a-Fig-Wasp-Community: Data sets and R scripts
<p>These are the data and R scripts used in the paper "Landscape-Level Analysis of a Fig-Pollinator-Antagonist Community: Spatial and Temporal Variation in a Fig Wasp Community and its Response to Biotic and Abiotic Factors".</p>
Data and R code for Reddin et al. 'Marine species and assemblage change foreshadowed by their thermal bias over Early Jurassic warming''
<p>This repository holds the raw and prepared datasets and R code to handle them for the manuscript Reddin et al. 'Marine species and assemblage change foreshadowed by their thermal bias over Early Jurassic warming'. Nature Communications</p>
Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
<p>Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package <i>mvtweedie</i> that extends capabilities of widely used packages in R (<i>mgcv</i> and <i>ggplot2</i>) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted puffins (<i>Fratercula cirrhata</i>) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980-2000) and then Pacific herring and capelin (2000-2020), while wolves (<i>Canis lupus ligoni</i>) in Southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. </p>
Data and R script for "Fear and cultural background drive sexual prejudice in France – A sentiment analysis approach"
<p>Data:</p> <p>corpus_integral.csv</p> <p>FEEL_1.csv</p> <p>mauvais.txt</p> <p>neg_hetero_corrected.txt</p> <p>participant_info_used.txt</p> <p>pos_hetero_corrected.txt</p> <p>R script:</p> <p>polarities.R</p> <p>sentiments_discrete.R</p>
A Nuclear Equation of State Inferred from Stellar r-Process Abundances: Data
<p>This repository contains the raw MCMC posteriors as H5 files for the three cases presented in "A Nuclear Equation of State Inferred from Stellar <em>r</em>-Process Abundances" (<a href="https://ui.adsabs.harvard.edu/abs/2021arXiv211006432H/abstract">Holmbeck et al., arXiv:2110.06432</a>).</p> <p>Also included are Python scripts with a variety of functions to read the H5 files and interpret the data with <a href="https://git.ligo.org/lscsoft/lalsuite">LALSuite</a>. These include:</p> <ul> <li>reading the data contained in the H5 file (likelihood, acceptance, and values for each MCMC step)</li> <li>generating a corner plot of the data</li> <li>finding the maximum likelihood in the posterior distribution</li> <li>calculating a neutron star mass-radius curve for a posterior EOS</li> <li>calculating pressure and density for a posterior EOS</li> <li>calculating observables (M_TOV, R_1.4, and L) associated with an EOS</li> </ul> <p>The scripts are written for Python3 compatibility and depend on:</p> <ul> <li><a href="https://pypi.org/project/lalsuite/">lalsuite</a></li> <li><a href="https://docs.h5py.org/en/stable/">h5py</a></li> <li><a href="https://numpy.org/">numpy</a></li> <li><a href="https://scipy.org/">scipy</a></li> <li><a href="https://matplotlib.org/">matplotlib</a></li> <li><a href="https://corner.readthedocs.io/en/latest/">corner</a></li> </ul> <p>For more information and how to use these scripts, see the comments in `example.py` or contact Erika Holmbeck.</p> <p>If any of our posterior samples are used in your work, we ask that you appropriately cite this repository and the original paper (<a href="https://ui.adsabs.harvard.edu/abs/2021arXiv211006432H/abstract">Holmbeck et al., arXiv:2110.06432</a>).</p>
Data and R files for the analysis of the innovative capacity and the network position of national manufacturing industries in world production
<p>Data and R files for the reproducibility of the results obtained in Kim and Ozaygen, Analysis of the innovative capacity and the network position of national manufacturing industries in world production.</p> <p>It also includes an R/Shiny application which runs at <a href="https://awekim.shinyapps.io/Manuf_shiny_R/">https://awekim.shinyapps.io/Manuf_shiny_R/ </a></p>
Data and R codes from: Exploring the effect of 195 years-old locks on species movement: Landscape genetics of painted turtles in the Rideau Canal, Canada
<p>Aquatic systems have been extensively altered by human structures (e.g., construction of dams/canals) and these have major impacts on the connectivity of wildlife populations through the loss and isolation of suitable habitats. Habitat loss and isolation affect gene flow and influence the persistence of populations in time and space by restricting movements. Isolation can result in higher inbreeding, lower genetic diversity, and greater genetic structure, which may render populations more vulnerable to environmental changes, and thus to extinction. Given the ubiquity and the persistence of dams and canals in space and time, it is crucial to understand their effects on the population genetics of aquatic species. Here, we documented the genetic diversity and structure of painted turtle (<em>Chrysemys picta</em>) populations in the Rideau Canal, Ontario, Canada. More specifically, we used 13 microsatellites to evaluate the influence of locks on genetic variation in 822 painted turtles from 22 sites evenly distributed along the 202-km canal. Overall, we found low, but significant, genetic differentiation suggesting that some dispersal is occurring throughout the canal. In addition, we showed that locks contribute to the genetic differentiation observed in the system. Clustering analysis revealed two distinct genetic groups whose boundary is associated with a series of six locks. Our results illustrate how artificial waterways, such as canal systems, can influence population genetic structure. We highlight the importance of adopting management plans that can mitigate the impacts of human infrastructure and preserve gene flow across the landscape to maintain viable populations.</p>
Data and R code - ISRR11/Rooting2021 Meeting Report
<p>This repository contains the raw data and R code used to analyse the results of the online root phenotyping survey that was created and disseminated by ISRR Ambassadors during the ISRR11/Rooting2021 meeting.</p>
Coded data and R scripts for the article-Toward a dynamic behavioral profile of the Mandarin Chinese temperature term re
<p>These are the coded dataset and R scripts for the article "Towards a dynamic behavioral profile of Mandarin Chinese temperature term re: A diachronic semasiological approach".</p>
R code and example data for using genogeographic clustering approach
<p>While in recent years there have been considerable advances in discerning spatial genetic patterns within species, the task of identifying common patterns across species is still challenging. Approaches using new data from co-sampled species permit rigorous statistical analysis but are often limited to a small number of species; meta-analyses of published data can encompass a much broader range of species, but are usually restricted by uneven data properties. There is a need for new approaches that bring greater statistical rigour to meta-analyses, and are also able to discern more than a single spatial pattern among species.</p> <p>We propose a new approach for comparative multi-species meta-analyses of published population genetic data that addresses many existing limitations. This analysis takes a three-stage approach: (i) use common genetic metrics to measure location-specific diversity across the sampled range of each species, (ii) use an innovative graphing technique to describe spatial patterns within each species, and (iii) quantitatively cluster species by their similarity in pattern. We apply this technique to 21 species of intertidal invertebrate from the New Zealand coastline, to resolve common spatial patterns from disparate profiles of genetic diversity.</p> <p>The genogeographic curves are shown to successfully capture the known spatial patterns within each intertidal species, and readily permit statistical comparison of those patterns, regardless of sampling and marker inconsistencies. The species clustering technique is shown to discern groups of species that clearly share spatial patterns within groups but differ significantly among groups. The species groups defined were not identifiable a <em>priori</em> from their taxonomy or life history, but their spatial genetic patterns appear biologically relevant.</p> <p>Genogeographic species clustering provides a novel approach to discerning multiple common spatial patterns of diversity among a large number of species. It will permit more rigorous comparative studies from diverse published data, and can be easily extended to a wide variety of alternative measures of genetic diversity or divergence. We see the approach best used as an exploratory method, to uncover the patterns often hidden in multi-species communities, likely to be followed by more targeted model-testing analyses.</p>
Data for Rapid phenotypic differentiation and local adaptation in Japanese knotweed s.l. (Reynoutria japonica and R. × bohemica, Polygonaceae) invading novel habitats
<p><span><strong>PREMISE:</strong> Many plant invaders like the Japanese knotweeds are thought to colonize new habitats with low genetic diversity. Such species provide an opportunity to study rapid adaptation to complex environmental conditions.</span></p> <p><span><strong>METHODS:</strong> Using replicate reciprocal transplants of clones across three habitats, we described patterns of phenotypic response and assessed degree of local adaptation.</span></p> <p><span><strong>KEY RESULTS:</strong> We found plants from beach habitats had decreased height, number of leaves, leaf area, and biomass allocation to roots and shoots compared to plants from marsh and roadside habitats when grown in their home habitat. In the marsh habitat, marsh plants were generally larger than beach plants, but not different from roadside plants. There were no differences among plants from different habitats grown in the roadside habitat. Despite this evidence of differentiation in beach and marsh habitats, we found mixed evidence for local adaptation. In their "home site" plants from the marsh habitat had greater biomass than plants from the beaches but not compared to plants from roadsides. Biomass comparisons in other habitats were either maladaptive or not significant. However, plants from the roadside had greater survival in their "home site" compared to foreign plants. There were no differences in survival in the other habitats.</span></p> <p><span><strong>CONCLUSIONS:</strong> We found phenotypic differentiation associated with habitats despite the low reported genetic diversity for these populations. Our results partially support the hypothesis of local adaptation in marsh and roadside habitats. Identifying whether these patterns of differentiation result from genetic or heritable non-genetic mechanisms will require further work.</span></p>
R script with data for vegetation and macropod scat analysis
<p>Fire and herbivores alter vegetation structure and function. Future fire activity is predicted to increase, and quantifying changes in vegetation communities arising from post-fire herbivory is needed to better manage natural environments.</p> <p>We investigated the effects of post-fire herbivory on understory plant communities in a coastal eucalypt forest in south-eastern Australia. We quantified herbivore activity, understory plant diversity, and dominant plant morphology following a wildfire in 2017 using two sizes of exclosures. Statistical analysis incorporated the effect of exclusion treatments, time since fire (TSF), and the effect of a previous prescribed burn.</p> <p>Exclusion treatments altered herbivore activity, but TSF did not. Herbivory reduced plant species richness, diversity and evenness and promoted the dominance of the most abundant plants within the understory. Increasing TSF reduced community diversity and evenness and influenced morphological changes to the dominant understory plant species, increasing size and dead material while decreasing abundance. We found the legacy effects of a previous prescribed burn had no effect on herbivores or vegetation within our study.</p> <p>Foraging by large herbivores resulted in a depauperate vegetation community. As post-fire herbivory can alter vegetation communities, we postulate that management burning practices may exacerbate herbivore impacts.</p> <p>Future fire management strategies to minimise herbivore-mediated alterations to understory vegetation could include aggregating management burns into larger fire sizes or linking fire management with herbivore management. Restricting herbivore access following fire (planned or otherwise) can encourage a more diverse and species-rich understory plant community. Future research should aim to determine how vegetation change from post-fire herbivory contributes to future fire risk.</p>
Data for 'Using 40 years of spot measurements to assess stream temperature response and recovery for different harvesting systems in northern hardwood forests' by Jason Leach, Danielle Hudson and R. Dan Moore. Submitted to Hydrological Processes.
<p>This dataset contains spot stream temperature measurements taken at 5 headwater streams draining forested hillslopes (C31, C32, C33, C34, C35) in the Turkey Lakes Watershed, approximately 65 km northwest of Sault Ste. Marie, Ontario, Canada.</p>
Dataset and R script for Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products
<p>We provide raw data and R script for analysis of data published in:</p> <p>1) Daher, E.; Cinosi, N.; Chierici, E.; Rondoni, G.; Famiani, F.; Conti, E. Field and Laboratory Efficacy of Low-Impact Commercial<br> Products in Preventing Olive Fruit Fly, Bactrocera oleae, Infestation. Insects 2022, 13, 213. https://doi.org/10.3390/insects13020213</p> <p>2) Daher, E.; Chierici, E.; Cinosi, N.; Rondoni, G.; Famiani, F.; Conti, E. Collection and Processing of Behavioural Data of the Olive Fruit Fly, <em>Bactrocera oleae</em>, when Exposed to Olive Twigs Treated with Different Commercial Products. <em>Data </em><strong>2022</strong>, <em>7</em>,</p>
Calibration data for IMACLIM-R electricity nexus - alpha version
<p>First release of the calibration data for the electricity nexus of IMACLIM-R (<a href="https://www.iamconsortium.org/resources/model-resources/imaclim-r/">https://www.iamconsortium.org/resources/model-resources/imaclim-r/</a>).</p> <p>Ongoing/missing:</p> <ul> <li>operation and maintenance costs</li> <li>installed capacity</li> </ul>
Edited DHS data for R training
<p>Edited DHS data for R training</p>
Synthetic data for R training
<p>Synthetic data for R training</p>
Data and R scripts for: Identifying existing management practices in the control of Striga asiatica within rice–maize systems in mid-west Madagascar
<p>Infestations by the parasitic weed genus <i>Striga</i> result in significant losses to cereal crop yields across sub-Saharan Africa. The problem disproportionately affects subsistence farmers who frequently lack access to novel technologies. Effective <i>Striga </i>management therefore requires the development of strategies utilising existing cultural management practices. We report a multi-year, landscape-scale monitoring project for <i>Striga</i> asiatica in the mid-west of Madagascar, undertaken over 2019-2020 with the aims of examining cultural, climatic and edaphic factors currently driving abundance and distribution. Long-distance transects were established across the middle-west region of Madagascar, over which <i>Striga asiatica</i> abundance in fields was estimated. Analysis of the data highlights the importance of crop variety and legumes in driving <i>Striga </i>density. Moreover, the dataset revealed significant effect of precipitation seasonality, mean temperature and altitude in determining abundance. A composite management index indicated the effect of a range of cultural practices on changes in <i>Striga </i>abundance<i>. </i>The findings support the assertion that single measures are not sufficient for the effective, long-term management of <i>Striga</i>. Furthermore, the composite score has potential as a significant guide of integrated <i>Striga </i>management beyond the geographic range of this study. </p>
Data and R script: Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era
<p>Raw data and R code necessary to reproduce the results of the paper entitled "Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era" published in Frontiers in Ecology and the Environment.</p> <p> </p>
Data for testing the SIAMCAT R package
<p>Datasets needed for the vignettes of the <a href="https://siamcat.embl.de/">SIAMCAT</a> R package</p>
ScienceDex guides
Understand access before you commit
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.