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317 results for “R code”
Data and R code supporting Battison et al. (2024) New Phytologist
<p>Data and R code supporting Battison et al. (2024) <span><span>Tracking tree demography and forest dynamics at scale using remote sensing. </span></span>New Phytologist</p> <p>If using these data and/or R code in your work please cite the original publication listed above, as well as this repository using the corresponding DOI.</p> <p> </p>
Low-intensity insect herbivory could have large effects on ecosystem productivity through reduced canopy photosynthesis. R code and data.
<p>R code and data to reproduce analysis in the publication: Visakorpi K., Gripenberg S., Malhi Y. and Riutta T. Low-intensity insect herbivory could have large effects on ecosystem productivity through reduced canopy photosynthesis. Web Ecology, 2024.</p> <p> </p> <p>File named "Visakorpietal2024_litteratureSurvey.csv" contains data collected from literature survey and to perform a meta-analysis. The columns contain the following data:</p> <p>Reference = unique identifier for each study</p> <p>group_id = if a study described several experiments or treatments, this column identifies them from each other.</p> <p>Plant_species = name of the plant species studied</p> <p>Herbivore_species = name of the herbivore species studies</p> <p>Plant_species_phylo and Plant_species_phylo2 = alternative ways to write the plant species name for phylogenetic analysis</p> <p>Plant_clade = Angiosperm or Gymnosperm</p> <p>Growth_form = seedling, sapling or tree</p> <p>Herbivore_order = phylogenetic order of the herbivore species</p> <p>Herbivore_family = phylogenetic family of the herbivore species</p> <p>Type_of_herbivory = chewing, sap-sucking, root-feeding, leafmining or bark-feeding</p> <p>Leaf_type = whether the leaf that was measured was damaged by herbivores, or intact</p> <p>Manipulation = whether herbivores were added (A) or removed (R)</p> <p>Year_published = year when the study was published</p> <p>PN_herb, SD_herb, se_herb, n_herb = photosynthetic rate, standard deviation, standard error, and sample size, of the treatment group (i.e. experiencing herbivory)</p> <p>PN_intact, SD_intact, se_intact, n_intact = photosynthetic rate, standard deviation, standard error, and sample size, of the control group (i.e. not experiencing herbivory)</p> <p>Indirect_effect, SD_indirect = the proportional difference in photosynthetic rates between the treatment and control values, and the standard deviation of the proportional difference</p>
Data and R code used in Hennecke et al. "Plant species richness and the root economics space drive soil fungal communities"
<p>To investigate how plant diversity and root traits relate to soil fungal communities, in 2021 we collected trait data from plots in the Jena Experiment (https://the-jena-experiment.de; funded by the DFG FOR 5000) and characterized fungal communities by sequencing, respiration and lipid fatty acid quantification. </p>
Dataset and R code for: "Task complexity matters: Investigating behavioural lateralisation in rats"
<h2>Dataset and R code used for the manuscript "Task complexity matters: Investigating behavioural lateralisation in rats"</h2> <p> </p> <p><strong>R project:</strong> Supplementary Task complexity.Rproj R project</p> <p><strong>R code: </strong>Task_Complexity_Stats_updated.Rmd </p> <p><strong>Dataset:</strong> Data_Task_complexity.xlsx </p> <p><strong>Models for repeatability estimation:</strong> mod_..._....rds </p>
Dataset and R code support the manuscript titled "Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling"
<p>This dataset and R code support the manuscript titled "Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling" submitted to the Journal of Chemical Information and Modeling.</p> <p>Table S 1: Chemicals with their experimental values of logKch , and values of logKow and<span> </span>logKaw used to calibrate chicken muscle protein-water 2p-LFER model.</p> <p>Table S 2: Chemicals with their experimental values of logKfish and values of logKow and<span> </span>logKaw used to calibrate fish muscle protein-water 2p-LFER model.</p> <p>Table S 3: Chemicals with their experimental values of logKBSA and values of logKow and<span> </span>logKaw used to calibrate bovine serum albumin-water 2p-LFER model.</p> <p>Table S 4: Chemicals with their experimental values of logKpw and values of logKow and<span> </span>logKaw used to calibrate combined chicken and fish muscle protein-water 2p-LFER model.</p> <p>Table S 5: Diversity of data for logKpw.</p> <p>Table S 6: Diversity of data for logKBSA.</p> <p>Table S 7: Comparison of Experimental and 2p-LFER Predicted Partition Coefficients for ionizable PFAS Compounds.</p> <p>Table S 8: List of neutral fluorotelomer PFAS Compounds.</p> <p>Table S 9: List of experimental in vivo and in vitro partitioning data for different tissues and species.</p> <p>Table S 10: List of experimental Milk-water partition coefficient and predicted values of Milk-water partitioning.</p> <p>Table S 11: Training set for logKpw</p> <p>Table S 12: Validation set for log Kpw</p> <p>Table S 13: Training set for log KBSA</p> <p>Table S 14: Validation set for log KBSA</p>
R code to accompany 'Teleconnection-based evaluation of seasonal forecast quality''
<p>R code for the diagnostic published in 'Teleconnection-based evaluation of seasonal forecast quality' DOI: 10.1007/s00382-020-05327-x</p>
R code and dataset to "Monetizing Spillover Effects in the Creative Industries: the Impact of Live Music Performances on Youtube Searches"
<p>Content:</p> <ol> <li>The script<strong> main_script.R</strong> includes code to run a regression discontinuity (RD) design and validation and falsification of estimated results</li> <li>The folder <strong>data</strong> contains two files: <ol> <li>bands_2016_2019.csv: a dataset of performers with additional information for each one.</li> <li>festivals_2016_2019.csv: a dataset of video search activity (as retrieved from Google Trends) for performers in file bands_2016_2019.csv</li> </ol> </li> <li>The folder <strong>source</strong> contains two additional R scripts: <ol> <li>data_preparation.R: generates the long dataset used to estimate RD effects</li> <li>status_simulation.R: randomly assigns treattment status to performers and estimates RD effects. Note this may take a long time to run. Parallel code is used: the number of cores has been set to 4. </li> </ol> </li> <li>The folder simulation_results contains simulated data after running the script status_simulation.R.</li> </ol>
Aquatic animal antimicrobial resistance trends dataset and R code
<p>First release of aquatic animal AMR R scripts and dataset accompanying "Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia" (doi: 10.1038/s41467-021-25655-8)</p>
Compiled comparative data and the R code from: "Why do some primate mothers carry their infant's corpse? A cross-species comparative study"
<p>Non-human primates respond to the death of a conspecific in diverse ways, some of which may present phylogenetic continuity with human thanatological responses. Of these responses, infant corpse carrying by mothers (ICC) is the most frequently reported. Despite its prevalence, quantitative analyses of this behaviour are scarce and inconclusive. We compiled a database of 409 published cases across 50 different primate species of mothers' responses to their infants' deaths and used Bayesian phylogenetic regressions with an information-theoretic approach to test hypotheses proposed to explain between- and within-species variation in ICC. We found that ICC was more likely when the infant's death was non-traumatic (e.g. illness) versus traumatic (e.g. infanticide), and when the mother was younger. These results support the death detection hypothesis, which proposes that ICC occurs when there are fewer contextual or sensory cues indicating death. Such an interpretation suggests that primates are able to attain an awareness of death. In addition, when carried, infant age affected ICC duration, with longer ICC observed for younger infants. This result suggests that ICC is a by-product of strong selection on maternal behaviour. The findings are discussed in the context of the evolution of emotion, and implications for evolutionary thanatology are proposed.</p>
Data and R code from: Nature calls: intelligence and natural foraging style predict welfare problems in captive parrots
<p>Around half of all parrots (a highly threatened order) live in captivity. Here, some species thrive. Others, however, breed poorly or display stereotypic behaviours indicating stress. Using data on the prevalence of three types of stereotypic behaviour in pet (50 species; 1,378 individuals) and aviculture hatch rates (115 species; 10,255 breeding pairs), we applied Phylogenetic Comparative Methods (PCMs) to test hypothesised causes of this variation (relating to species' rarity and constraints on natural behaviour). In the first empirical evidence that high intelligence increases vulnerability to poor captive welfare, species with large relative brain sizes were found to be most at risk of oral and whole-body stereotypic behaviour. This suggests that if they are to be kept in private homes, such parrots must be offered substantially more cognitive stimulation. Self-harming behaviours involving feather damage were predicted by naturally relying on food items that require substantial handling, highlighting inadequacies in captive diets (often highly processed); while relatively low hatch rates in aviculture were predicted by small captive population sizes, potentially due to genetic bottlenecks, inbreeding, and/or low availability of compatible mates. These novel findings should help advance captive parrot husbandry, and inspire further research applying PCMs to understand and improve animal welfare.</p>
Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data
<p><span>Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses; ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972-2018; iii) and compiled historical reports on distemper dating back to the 18<sup>th</sup> century. We find that CDV and PDV diverged in the early 17<sup>th</sup> century. Modern CDV strains last shared a common ancestor in the 19<sup>th</sup> century with a marked radiation during the 1930s-50s. Modern PDV strains are of more recent origin, diverging in the 1970s-80s. Based on the compiled information on distemper distribution, the diverse host range of CDV and basal phylogenetic placement of terrestrial morbilliviruses, we hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the North Atlantic. Moreover, given the estimated timing of distemper origin and radiation, we hypothesize a prominent role of environmental change such as the Little Ice Age, and human activities like globalisation and war in distemper virus evolution. </span></p>
Dataset and R code for the manuscript:Interspecific facilitation drives coexistence by favouring rare sensitive species and reducing performance disparities
<p>The following directory contains the data necessary to replicate the results obtained in the manuscript entitled: <strong>Interspecific facilitation drives coexistence by favouring rare sensitive species and reducing performance disparities </strong></p> <p>We provided an R workspace containing the data "Dataset1.RData", a "ReadMe.txt" archive with detailed information of the variables included in "Dataset1.RData", and the R code necessary to replicate the results and figures ("Rcode1.txt")</p>
Dataset and R code: Prior exposure to B. pertussis shapes the mucosal antibody response to acellular pertussis booster vaccination
<p>The R code and dataset for the figures created in the Nature communications manuscript titled "<strong>Prior exposure to <em>B. pertussis </em>shapes the mucosal antibody response to acellular pertussis booster vaccination"</strong>.</p> <p>contains:</p> <p>- excel dataset including the parameters needed for the figures</p> <p>- R code document with the code used to produce the figures and statistical analyses</p>
Data and R code for statistical analyses on trap experiments
<p>Data and R code for statistical analyses related to trap experiments used in the article titled "<strong>Attractant activity of host-related chemical blends on the Poultry Red Mite at different spatial scales".</strong></p> <p>Data are provided as two .csv files and codes as one .rmd file and one .R file as follows:</p> <p>- 6-trap laboratory experiments (data_PRM_lab_6-trap_experiments.csv and Lab_6-trap-experiments.rmd)</p> <p>- field experiments (data_PRM_field_trapping.csv and Field_trap_analyses.R).</p>
Evaluating drivers of female dominance in the spotted hyena: R code and data
<p><strong>Introduction</strong>: Dominance relationships in which females dominate males are rare among mammals. Mechanistic hypotheses explaining the occurrence of female dominance suggest that females dominate males because 1) they are intrinsically more aggressive or less submissive than males, and/or 2) they have access to more social support than males.</p> <p><strong>Methods</strong>: Here, we examine the determinants of female dominance across ontogenetic development in spotted hyenas (<em>Crocuta crocuta</em>) using 30 years of detailed behavioral observations from the Mara Hyena Project to evaluate these two hypotheses.</p> <p><strong>Results</strong>: Among adult hyenas, we find that females spontaneously aggress at higher rates than males, whereas males spontaneously submit at higher rates than females. Once an aggressive interaction has been initiated, adult females are more likely than immigrant males to elicit submission from members of the opposite sex, and both adult natal and immigrant males are more likely than adult females to offer submission in response to an aggressive act. We also find that adult male aggressors are more likely to receive social support than adult female aggressors, and that both adult natal and immigrant males are 2-3 times more likely to receive support when attacking a female than when attacking another male. Across all age classes, females are more likely than males to be targets of aggressive acts that occur with support. Further, receiving social support does slightly help immigrant males elicit submission from adult females compared to immigrant males acting alone, and it also helps females elicit submission from other females. However, adult females can dominate immigrant males with or without support far more often than immigrant males can dominate females, even when the immigrants are supported against females.</p> <p><strong>Discussion</strong>: Overall, we find evidence for both mechanisms hypothesized to mediate female dominance in this species: 1) male and female hyenas clearly differ in their aggressive and submissive tendencies, and 2) realized social support plays an important role in shaping dominance relationships within a clan. Nevertheless, our results suggest that social support alone cannot explain sex-biased dominance in spotted hyenas. Although realized social support can certainly influence fight outcomes among females, adult females can easily dominate immigrant males without any support at all.</p>
Data, sample sizes, and R code for analysis of: Variation in mutation (co)variances
<p>Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode <em>Caenorhabditis elegans </em>that accumulated mutations in a nearly-neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of <em>C. elegans </em>genotypes allows selection on new phenotypic dimensions of locomotion behavior.</p>
Light-by-nitrogen greenhouse experiment dataset and R code (v2.1)
<p>Release corrects errors in some reported chlorophyll absorbance values in "data_sheets/LxN_phys_data.csv" and updates the "data_sheets/LxN_phys_metadata.csv" metadata file.</p>
Datasheets and R-codes for flood mortality and income inequality project
<p>This zipped folder contains the compiled datasheets, raw figures, tables and R-codes for the analysis conducted in 2023 by Sara Lindersson, as reported in the following preprint:</p> <p>Sara Lindersson, Elena Raffetti, Maria Rusca, Luigia Brandimarte, Johanna Mård and Giuliano Di Baldassarre. <em>The wider the gap between rich and poor, the higher the flood mortality.</em> 2023. PREPRINT (revised manuscript)</p> <ul> <li>Dataset v. 1.0 corresponds to the first version of the manuscript, submitted in 2022.</li> <li>Dataset v. 2.0 corresponds to the revised manuscript, submitted in 2023.</li> </ul>
Data and R code for: Temperature-induced multispecies cohort effects in sympatric snakes
<p>In reptiles, reproductive maturity is often determined by size rather than age. Consequently, growth early in life may influence population dynamics through effects on generation time and survival to reproduction. Because reproductive phenology and pre- and post-natal growth are temperature-dependent, environmental conditions may induce multi-species cohort effects on body size in sympatric reptiles. I present evidence of this using ten years of neonatal size data for three sympatric viviparous snakes, Dekay's Brownsnakes (<i>Storeria dekayi</i>), Red-bellied Snakes (<i>S. occipitomaculata</i>) and Common Gartersnakes (<i>Thamnophis sirtalis</i>). End-of-season neonatal size varied in parallel across species such that snout-vent length was 36-61% greater and mass was 65-223% greater in years when gestating females could achieve higher April-May (vs. June-July or August-September) operative temperatures. Thus, temperature had a larger impact during follicular enlargement and ovulation than during gestation or post-natal growth. Multi-species cohort effects like these may affect population dynamics and increase with climate change.</p>
Dataset and R code for the manuscript: Interspecific facilitation favors rare species establishment and reduces performance disparities among adults
<p>The following directory contains the data necessary to replicate the results obtained in the manuscript entitled: <strong>Interspecific facilitation favors rare species establishment and reduces performance disparities among adults.</strong></p> <p>We provided an R workspace containing the data "Dataset1.RData", a "ReadMe.txt" archive with detailed information on the variables included in "Dataset1.RData", and the R code necessary to replicate the results ("Rcode1.txt")</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.