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15,519 results for “r”
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>
Mimulus cardinalis plasticity analyses and R scripts for: Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower
<p>A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers (<i>Mimulus cardinalis</i>) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer-origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler-origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40ºC) rather than cooler (20ºC) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40ºC, was also found for the cooler-origin northern versus the warmer-origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another.</p>
Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0) in R
<p>We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats. Here, we provide the R-code for calculation and comparison chronologies with embedded manual, metadata for code runs, Bacon output graphs of each record, graphs comparison of original chronologies and LegacyAge 1.0, and a short shared-screen video of the R-code to show the usage on two example records separately.</p> <p>Supplement to: Li, C., Postl, A. K., Böhmer, T., Cao, X., Dolman, A. M., and Herzschuh, U.: Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0), Earth Syst. Sci. Data Discuss. [preprint], https://doi.org/10.5194/essd-2021-212, in review, 2021.</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>
Sex-specific variation in R-loop formation in Drosophila melanogaster
<p>Source Data for manuscript, "Sex-specific variation in R-loop formation in <em>Drosophila melanogaster</em>".</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>
comspat: an R package to analyze within-community spatial organization using species combinations
<p>The diversity of species combinations observable in sampling units reflects a species' uneven distribution and preference for specific abiotic and biotic conditions – a phenomenon most commonly expressed in terms of ecological assembly rules of plant communities and other sessile organisms (e.g., subtidal algae, invertebrates and coral reefs). We present comspat, a new R package that uses grid or transect data sets to measure the number of realized (observed) species combinations (NRC) and the Shannon diversity of realized species combinations (compositional diversity; CD) as a function of spatial scale. NRC and CD represent two measures from a model family developed by Pál Juhász-Nagy based on Information Theory. Classical Shannon diversity measures biodiversity based on the number and relative abundance of species, whereas the specific version of Shannon diversity presented here characterizes biodiversity and provides information on species coexistence relationships; both measures operate at fine-scale within the sampling unit or within the community. comspat offers two commonly applied null models, complete spatial randomness and random shift, to disentangle the textural, intraspecific, and interspecific effects on the observed spatial patterns. Combined, these models assist users in detecting and interpreting spatial associations and inferring assembly mechanisms. Our open-sourced package provides a vignette that describes the method and reproduces the figures from this paper to help users contextualize and apply functions to their data.</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>
Dataset and R code from: Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions
<p class="MsoNormal">Land abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with climatic niches and habitat preferences. Hierarchical models that unified species occurrence and habitat preferences revealed that negative responses to land abandonment were associated with species that have cold climatic niches and utilize open habitats, suggesting that species negatively impacted by land abandonment will decline more due to future climate warming. Maps representing species gains and losses due to land abandonment, which were created from the model estimates, showed similar geographic patterns, but some areas exhibited high species losses relative to gains. Our hierarchical modelling approach was useful for scaling up local-scale effects of land abandonment to a macro-scale assessment, which is crucial to developing spatial conservation strategies in the era of depopulation.</p>
R Skills Building for Cancer Scientists
<p>These datasets are being used in our course but are originally from the course run by the Bioinformatics Core<br> at the Cancer Research UK Cambridge Institute (Contributions : Matthew Eldridge, Chandra Chilamakuri, Mark Fernandes, Ashley Sawle, Kamal Kishore, Sergio Martinez Cuesta, Rory Stark).</p>
SeaTemCon_R code for "The Holocene temperature conundrum answered by mollusk records from East Asia"
<p>This repository includes the code that can be used to calculate the contribution percentages of seasonal temperatures to the annual temperature for the paper entitled "The Holocene temperature conundrum answered by the mollusk records from East Asia".</p>
Figure 226. R in Revision of the genus Reddyanus from Southeast Asia, with description of five new species from Cambodia, Malaysia, Thailand and Vietnam (Scorpiones: Buthidae)
Figure 226. R. zideki, male from Malaysia, Templer park in vivo habitus.
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>
Cambios en el porcentaje del material foliar remanente de las diferentes especies de manglar en los dos (2) tipos de tratamiento de malla (MF – MG) durante las cuatro semanas de muestreo, en el delta del río Ranchería - brazo Riito. RM: R. mangle, LR: L. racemosa, AG: A. germinans.
<p>Publicado en:</p> <p>Hernández Escobar, L., Granados-Martínez, C. & Fuentes-Reinés, J. (2022). Descomposición acuática de la hojarasca foliar en tres especies de mangle en la desembocura del río Ranchería (Brazo Riíto) y su relación con los macroinvertebrados en el municipio de Riohacha, departamento de La Guajira. <em>Ciencia e Ingeniería</em>, 9 (1):e6709388. https://www.doi.org/10.5281/zenodo.6709388</p>
Velocidades de descomposición del material foliar de A. germinans, L. racemosa y R. magle reportados para tres lugares del trópico.
<p>Publicado en:</p> <p>Hernández Escobar, L., Granados-Martínez, C. & Fuentes-Reinés, J. (2022). Descomposición acuática de la hojarasca foliar en tres especies de mangle en la desembocura del río Ranchería (Brazo Riíto) y su relación con los macroinvertebrados en el municipio de Riohacha, departamento de La Guajira. <em>Ciencia e Ingeniería</em>, 9 (1):e6709388. https://www.doi.org/10.5281/zenodo.6709388</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.