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1,249 results for “R data”
Figure 2 from: Mille C, Jourdan H, Cazères S, Maw E, Foottit R (2020) New data on the aphid (Hemiptera, Aphididae) fauna of New Caledonia: some new biosecurity threats in a biodiversity hotspot. ZooKeys 943: 53-89. https://doi.org/10.3897/zookeys.943.47785
Figure 2 Aphid interceptions in New Caledonia from 2008 to 2018 on fresh imported fruits and vegetables.
Figure 1 from: Milotic T, Desmet P, Anselin A, De Bruyn L, De Regge N, Janssens K, Klaassen R, Koks B, Schaub T, Schlaich A, Spanoghe G, T'jollyn F, Vanoverbeke J, Bouten W (2020) GPS tracking data of Western marsh harriers breeding in Belgium and the Netherlands. ZooKeys 947: 143-155. https://doi.org/10.3897/zookeys.947.52570
Figure 1 INBO researcher Anny Anselin holding Peter (animal ID L143457), one of the tagged Western marsh harriers in the MH_WATERLAND dataset (tag ID 623).
Figure 2 from: Milotic T, Desmet P, Anselin A, De Bruyn L, De Regge N, Janssens K, Klaassen R, Koks B, Schaub T, Schlaich A, Spanoghe G, T'jollyn F, Vanoverbeke J, Bouten W (2020) GPS tracking data of Western marsh harriers breeding in Belgium and the Netherlands. ZooKeys 947: 143-155. https://doi.org/10.3897/zookeys.947.52570
Figure 2 Left: Map giving an overview of the extent of the three datasets including the winter migration tracks; top right: summering data in H_GRONINGEN; middle right: summering data of MH_WATERLAND; and bottom right: summering data in MH_ANTWERPEN.
Evidence that male sea lamprey increase pheromone release after perceiving a competitor: raw data, R-code, R analyses
<p class="CxSpFirst">Sexual signals evolve via selective pressures arising from male-male competition and female choice, including those originating from unintended receivers that detect the signal. For example, males can acquire information from other males signaling to females and alter their own signal. Relative to visual and acoustic signals, less is known about how such communication networks influence chemical signaling among animals. In sea lamprey (<i>Petromyzon marinus</i>), chemical communication system is essential for reproduction, offering a useful system to study a pheromone communication network that includes signalers and both intended and unintended receivers. Male sea lamprey aggregate on spawning grounds where individuals build nests and signal to females using sex pheromones. We examined how exposure to a major component of the male pheromone, 3keto-petromyzonol sulfate (3kPZS), influenced male pheromone signaling, and whether females had a preference for males that altered their signal. Exposure to 3kPZS, at a concentration of 5x10<sup>-10 </sup>M, simulated the presence of other male(s) and led to increased 3kPZS release rates within 10 min, followed by a return to baseline levels within 30 min. Exposure also led to increases in hepatic synthesis and circulatory transport of pheromone components. In behavioral assays, females preferred the odor of males that had been exposed to 3kPZS; therefore, males likely benefit from upregulating 3kPZS release after detecting competition for mates. Here, we define how a specific pheromone component influences chemical signaling during intrasexual competition, and show a rare example of how changes in chemical signaling strategies resulting from male competition may influence mate choice.</p>
Figure 6 from: Altenhöner R, Blümel I, Boehm F, Bove J, Bicher K, Bracht C, Brand O, Dieckmann L, Effinger M, Hagener M, Hammes A, Heller L, Kailus A, Kohle H, Ludwig J, Münzmay A, Pittroff S, Razum M, Röwenstrunk D, Sack H, Simon H, Schmidt D, Schrade T, Walzel A-V, Wiermann B (2020) NFDI4Culture - Consortium for research data on material and immaterial cultural heritage. Research Ideas and Outcomes 6: e57036. https://doi.org/10.3897/rio.6.e57036
Figure 6 Multimodal data types. Example 1: Motion Bank, Example 2: Digital Mozart Score Viewer, Example 3: Inscriptions in their Spatial Context (IBR).
Quina retouch does not maintain edge angle over reduction - R code and data
<p>R code and data used in the paper "Quina retouch does not maintain edge angle over reduction" in <em>Lithic Technology</em>.</p>
Supplementary material 1 from: Walton S, Livermore L, Bánki O, Cubey RWN, Drinkwater R, Englund M, Goble C, Groom Q, Kermorvant C, Rey I, Santos CM, Scott B, Williams AR, Wu Z (2020) Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes 6: e57602. https://doi.org/10.3897/rio.6.e57602
Tools and services evaluation speadsheet
Figure 1 from: Walton S, Livermore L, Bánki O, Cubey RWN, Drinkwater R, Englund M, Goble C, Groom Q, Kermorvant C, Rey I, Santos CM, Scott B, Williams AR, Wu Z (2020) Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes 6: e57602. https://doi.org/10.3897/rio.6.e57602
Figure 1 An overview of potential Specimen Data Refinery workflows based on image inputs and their derivatives, datasets and services.
The performance of permutations and exponential random graph models when analysing animal networks (R code and data)
<p>Social network analysis is a suite of approaches for exploring relational data. Two approaches commonly used to analyse animal social network data are permutation-based tests of significance and exponential random graph models. However, the performance of these approaches when analysing different types of network data has not been simultaneously evaluated. Here we test both approaches to determine their performance when analysing a range of biologically realistic simulated animal social networks. We examined the false positive and false negative error rate of an effect of a two-level explanatory variable (e.g. sex) on the number and combined strength of an individual's network connections. We measured error rates for two types of simulated data collection methods in a range of network structures, and with/without a confounding effect and missing observations. Both methods performed consistently well in networks of dyadic interactions, and worse on networks constructed using observations of individuals in groups. Exponential random graph models had a marginally lower rate of false positives than permutations in most cases. Phenotypic assortativity had a large influence on the false positive rate, and a smaller effect on the false negative rate for both methods in all network types. Aspects of within- and between-group network structure influenced error rates, but not to the same extent. In grouping-event based networks, increased sampling effort marginally decreased rates of false negatives, but increased rates of false positives for both analysis methods. These results provide guidelines for biologists analysing and interpreting their own network data using these methods.</p>
Data and R code for What you see is where you go: visibility influences movement decisions of a forest bird navigating a 3D structured matrix
<p>Animal spatial behaviour is often presumed to reflect responses to visual cues. However, inference of behaviour in relation to the environment is challenged by the lack of objective methods to identify the information that effectively is available to an animal from a given location. In general, animals are assumed to have unconstrained information on the environment within a detection circle of a certain radius (the perceptual range; PR). However, visual cues are only available up to the first physical obstruction within an animal's PR, making information availability a function of an animal's location within the physical environment (the effective visual perceptual range; EVPR). By using LiDAR data and viewshed analysis, we model forest birds' EVPRs at each step along a movement path. We found that the EVPR was on average 0.063% that of an unconstrained PR and, by applying a step-selection analysis, that individuals are 1.57 times more likely to move to a tree within their EVPR than to an equivalent tree outside it. This demonstrates that behavioural choices can be substantially impacted by the characteristics of an individual's EVPR and highlights that inferences made from movement data may be improved by accounting for the EVPR.</p>
Supplementary material 3 from: Eddy B, Muggridge M, LeBlanc R, Osmond J, Kean C, Boyd E (2020) An Ecological Approach for Mapping Socio-Economic Data in Support of Ecosystems Analysis: Examples in Mapping Canada's Forest Ecumene. One Ecosystem 5: e55881. https://doi.org/10.3897/oneeco.5.e55881
Supplement C - Labour Force Distribution Maps of Natural Resource Sectors in Canada
Supplementary material 2 from: Eddy B, Muggridge M, LeBlanc R, Osmond J, Kean C, Boyd E (2020) An Ecological Approach for Mapping Socio-Economic Data in Support of Ecosystems Analysis: Examples in Mapping Canada's Forest Ecumene. One Ecosystem 5: e55881. https://doi.org/10.3897/oneeco.5.e55881
Supplement B - GIS Procedure for Mapping Labour Force Distribution
Supplementary material 1 from: Eddy B, Muggridge M, LeBlanc R, Osmond J, Kean C, Boyd E (2020) An Ecological Approach for Mapping Socio-Economic Data in Support of Ecosystems Analysis: Examples in Mapping Canada's Forest Ecumene. One Ecosystem 5: e55881. https://doi.org/10.3897/oneeco.5.e55881
Supplement A - GIS Procedure for Population Estimation
Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model
<p>Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated <i>in vitro</i>; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 non-diseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for five phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors (TDVF). Toxicokinetic modeling was used for probabilistic <i>in vitro</i>-to-<i>in vivo </i>extrapolation in order to derive population-wide margins of safety (MOS) for pharmaceuticals and margins of exposure (MOE) for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. TDVF estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally-assumed default of ~3. Population variability-based MOS for pharmaceuticals were correctly predicted to be relatively narrow, between 10-100; however, MOE for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at general population exposures even to sensitive sub populations. This study represents a first of its kind human <i>in vitro</i> model that can be used to characterize toxicodynamic population variability in cardiotoxic risk.</p>
Data and R code for: Tariel J., Plénet S., and Luquet É. (2020). How do developmental and parental exposures to predation affect personality and immediate behavioural plasticity in the snail Physa acuta?
<p>Data and R code of the article: Tariel J., Plénet S., and Luquet É. (2020) How do developmental and parental exposures to predation affect personality and immediate behavioural plasticity in the snail <em>Physa acuta</em>? doi:<a href="http://doi.org/10.1098/rspb.2020.1761">10.1098/rspb.2020.1761</a></p> <p>The dataset is provided (<em>data -Tariel, Plénet and Luquet (2020).csv</em>). This dataset is analyzed in the R script (<em>Juliette Tariel - R analysis.Rmd</em>). A knitted version of the R script is also provided in pdf format (<em>Juliette Tariel - R analysis.pdf</em>). Finally, a zip file is provided and contains several outputs, such as MCMCglmm objects or confint objects (<em>R outputs used in the analysis.zip</em>)</p> <p><strong>Signification of variables names:</strong></p> <ul> <li>ID: snail's identification number</li> <li>ID Family: identification number of the family of the F2 snail</li> <li>ID F1 mother: identification number of the mother of the F2 snail</li> <li>ID F1 father: identification number of the father of the F2 snail</li> <li>ID F0 grand-mother: identification number of the grand-mother of the F2 snail</li> <li>ID F0 grand-father: identification number of the grand-fathrt of the F2 snail</li> <li>Mass: total wet mass (body and shell) in grams</li> <li>Parental: parental environment (control C or predator-cue P)</li> <li>Developmental: developmental environment (C or P)</li> <li>Immediate: immediate environment (C or P)</li> <li>Trial_number</li> <li>Time: time to crawl-out of the water in seconds</li> </ul>
Supplementary Data (S1) and R Codes
<p>Supplementary Data (Data S1), including Read.me tab</p> <p>R Codes with table of contents</p>
Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R
Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs, and (iv) describing several spatial components of clonality. RClone allows the one shot analysis of multi-population datasets without size limitation, suitable for datasets now increasingly produced through Next Generation Sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClone_quickmanual) or several populations (RClone_qmsevpops).
Data from: Tuning Geometric Morphometrics: an R tool to reduce information loss caused by surface smoothing
The application of Geometric Morphometrics has remarkably increased since 3D imaging techniques have become widespread, such as high-resolution computerised tomography, laser scanning and photogrammetry. Acquisition, 3D rendering and simplification of virtual objects produce faceting and topological artefacts, which can be counteracted by applying decimation and smoothing algorithms. Nevertheless, smoothing algorithms can have detrimental effects. This work aims at developing a method to assess the amount of information loss or recovery after the application of 3D surface smoothing. The method presented here is conceived to optimise the smoothing procedure for 3D surfaces used in Geometric Morphometrics. We implemented the method in a tool running in the r statistical environment. The tool requires one surface, one landmark set and one surface semilandmark set to estimate the best smoothing settings, including algorithm type, iteration and scale factor value. Additional parameters can be tuned by the user. We describe the method in detail, reporting the tool usage, including its main settable parameters. One example is provided as a further explanation of the method. Our method reduces the chances of losing information in Geometric Morphometrics applications and is a unique attempt of standardising a widespread, potentially damaging procedure. The tool represents an advance in the application of Geometric Morphometrics.
Data from: pavo: an R package for the analysis, visualization and organization of spectral data
1. Recent technical and methodological advances have led to a dramatic increase in the use of spectrometry to quantify reflectance properties of biological materials, as well as models to determine how these colours are perceived by animals, providing important insights into ecological and evolutionary aspects of animal visual communication. 2. Despite this growing interest, a unified cross-platform framework for analyzing and visualizing spectral data has not been available. We introduce pavo, an R package that facilitates the organization, visualization, and analysis of spectral data in a cohesive framework. pavo is highly flexible, allowing users to (a) organize and manipulate data from a variety of sources, (b) visualize data using R's state-of-the-art graphics capabilities, and (c) analyze data using spectral curve shape properties and visual system modeling for a broad range of taxa. 3. In this paper, we present a summary of the functions implemented in pavo and how they integrate in a workflow to explore and analyze spectral data. We also present an exact solution for the calculation of colour volume overlap in colourspace, thus expanding previously published methodologies. 4. As an example of pavo's capabilities, we compare the colour patterns of three African Glossy Starling species, two of which have diverged very recently. We demonstrate how both colour vision models and direct spectral measurement analysis can be used to describe colour attributes and differences between these species. Different approaches to visual models and several plotting capabilities exemplify the package's versatility and streamlined workflow. 5. pavo provides a cohesive environment for handling spectral data and addressing complex sensory ecology questions, while integrating with R's modular core for a broader and comprehensive analytical framework, automated management of spectral data, and reproducible workflows for colour analysis.
Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).
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.