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15,519 results for “r”
Replication package for How the R Community Creates and Curates Knowledge: An Extended Study of Stack Overflow and Mailing Lists
<p>This dataset was used in the paper: "How the R Community Creates and Curates Knowledge: An Extended Study of Stack Overflow and Mailing Lists", Journal of Empirical Software Engineering, to appear.</p>
raptr: Representative and Adequate Prioritization Toolkit in R
<p>1. An underlying aim in conservation planning is to maximize the long-term persistence of biodiversity. To fulfill this aim, the ecological and evolutionary processes that sustain biodiversity must be preserved. One way to conserve such processes at the feature level (eg. species, ecosystem) is to preserve a sample of the feature (eg. individuals, areas) that is representative of the intrinsic or extrinsic physical attributes that underpin the process of interest. For example, by conserving a sample of populations with local adaptations---physical attributes associated with adaptation---that is representative of the range of adaptations found in the species, protected areas can maintain adaptive processes by ensuring these adaptations are not lost. Despite this, current reserve selection methods overwhelmingly focus on securing an adequate amount of area or habitat for each feature. Little attention has been directed towards capturing a representative sample of the variation within each feature.</p> <p>2. To address this issue, we developed the <em>raptr R</em> package to help guide reserve selection. Users set "amount targets"---similar to conventional methods---to ensure that solutions secure a sufficient proportion of area or habitat for each feature. Additionally, users set "space targets" to secure a representative sample of variation in ecologically or evolutionarily relevant attributes (eg. environmental or genetic variation). We demonstrate the functionality of this package using simulations and two case studies. In these studies, we generated solutions using amount targets---similar to conventional methods---and compared them with solutions generated using amount and space targets.</p> <p>3. Our results demonstrate that markedly different solutions emerge when targeting a representative sample of each feature. We show that using these targets is important for features that have multimodal distributions in the process-related attributes (eg. species with multimodal niches). We also found that solutions could conserve a far more representative sample with only a slight increase in reserve system size.</p> <p>4. The <em>raptr R</em> package provides a toolkit for making prioritizations that secure an adequate and representative sample of variation within each feature. By using solutions that secure a representative sample of each feature, prioritizations may have a greater chance of achieving long-term biodiversity persistence.<br> </p>
Patterns of Etruscan urbanism (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Stoddart, S., Palmisano, A.,Redhouse, D.I., Barker, G., di Paola, G., Motta, L., Rasmussen, T., Samuels, T., and Witcher, R., 2020. <a href="https://doi.org/10.3389/fdigh.2020.00001">Patterns of Etruscan urbanism.</a> </strong><em>Frontiers in Digital Humanities</em>, <em>7 </em>(1).<strong> </strong></p> <p>The dataset included here provides a collection of archaeological sites dating from the ninth to the fifth century BC, uncovered by systematic field survey carried out in central Italy (Tuscany and Lazio). In addition, the digital archive related to this paper provides reproducible analyses in the form of six scripts written in R statistical computing language. The present repository contains also a R Markdwon tutorial to drive step by step any practitioner interested in running some analytical tools to assess regional centralisation and settlement hierarchies: site-size histograms, rank-size graphs, A-coefficient, and B-coefficient.</p> <p> </p> <p>List of versions:</p> <ul> <li><strong>3.0 </strong>15 April 2025 - Entails revising the R scripts to replace the deprecated 'rgdal' package with the 'sf' package.</li> <li><strong>2.0.</strong> 31 March 2020 — Includes a few minor error corrections (the files 'Tutorial.RMD' and 'Tutorial.html').</li> <li><strong>1.0</strong> 31 March 2020 — First public release of the dataset on Zenodo.</li> </ul> <p> </p>
A systems analysis of sustainability impacts of agricultural policies in India - R script and supporting files
<p>This includes : </p><ul><li>two R scripts used to implement the model (residue_burning. R) and generate results (residue_burning_calls.R)</li><li>three supporting .csv files used in the R scripts above </li></ul><p> </p>
Scientific Mapping Example with R package `bibliometrix`
<p>Example of the use of the <strong>R</strong> package <i>bibliometrix </i>for bibliometric analysis</p>
Data and R code used in Alonso-Crespo et al (2024) Exploring priority and year effects on plant diversity, productivity and vertical root distribution: first insights from a grassland field experiment
<p>This release contains the raw data, R code, and RootPainter model supporting the results described in Alonso-Crespo et al (2024) Exploring priority and year effects on plant diversity, productivity and vertical root distribution: first insights from a grassland field experiment.</p>
NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification
<p>Raw FASTQ files for the DNA-seq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.</p>
RecView: An interactive R application for locating recombination positions using pedigree data
<p><span>We present <em>RecView</em>, an interactive R application and </span><span>its homonymous R package</span><span>, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. </span><span>We demonstrate applicability of <em>RecView </em>using the genotype data from two offspring, as well as their grandparents and parents, of the great reed warbler (<em>Acrocephalus arundinaceus</em>).</span></p>
Data and R analysis code: Asian elephants distinguish sexual status and identity of unfamiliar elephants using urinary odours
<p class="MsoNormal"><span>Despite the ubiquity of odours in mammals, few studies have documented the natural olfactory abilities of many "non-model" species such as the Asian elephant. As Asian elephants are endangered, we may apply odours to more effectively manage threatened populations. We implemented a habituation–discrimination paradigm for the first time in Asian elephants to test the ability of elephants to discriminate between unfamiliar male elephant urine, hypothesizing that elephants would successfully distinguish non-musth from musth urine and also distinguish identity between two closely related individuals. We conducted two bioassay series, exposing three female and three male zoo-housed elephants to the same urine sample (non-musth urine in the first series, and urine from an unfamiliar individual in the second) over five days. On the sixth day, we simultaneously presented each elephant with a novel sample (either musth urine or urine from a second unfamiliar individual) alongside the habituated urine sample, comparing rates of chemosensory response to each sample to indicate discrimination. All elephants successfully discriminated non-musth from musth urine, and also urine from two unfamiliar half-brothers. Our results further demonstrate the remarkable olfactory abilities of elephants with promising implications for conservation and management.</span></p>
Enquête par questionnaire humanités "Manipuler des données en Sciences Humaines et Sociales (SHS) : R, Python, ou autre ?"
<p>Ce sondage réalisé avec Framaform https://framaforms.org/manipuler-des-donnees-en-sciences-humaines-et-sociales-shs-r-python-ou-autre-1675889669 était destiné à tous les personnels impliqués dans la recherche et / ou l'enseignement en sciences humaines et sociales mobilisant du traitement de données (humanités numériques, sciences sociales computationnelles, etc.). Il a été diffusé sur la liste de diffusions DH, sur les sites de l'Observatoire des Humanités numériques de l'ENS PSL et de l'INSHS du CNRS.</p><p>L'enquête visait à mieux connaître les usages de la programmation chez les chercheurs, enseignants-chercheurs, étudiants et personnels de soutien à la recherche. Les résultats obtenus permettent de proposer un état des lieux de l'existant afin d'accompagner et d'améliorer les pratiques en proposant des ressources pour s'informer ou se former.</p><p>217 personnes ont répondu à cette enquête ce qui nous a permis de dresser un panorama réaliste des pratiques actuelles relevant de la programmation en SHS.</p><p>Le fichier .json permet de recoder le nom des colonnes.</p><p>Un notebook d'analyse est disponible ici : https://github.com/emilienschultz/digit_hum_2023/blob/main/2023_Digit_Hum_Exploration_sondage_v2.ipynb</p>
LiDAR and Photogrammetry Point Clouds and R code
<p>Some examples of point clouds from lidar and photogrammetry, from drone and from helicopter surveys.</p> <p>These data are used in the course "Remote Sensing" to forestry students at University of Padova, TESAF Department</p> <p> </p>
Hombre con martillo neumático. R. Contel (1936)
Hombre con martillo neumático: Escultura en bronce (1936) de Rafael Pérez Contel cedida por la Diputación Provincial de Valencia. Un homenaje al trabajo y el esfuerzo. Alzira. Museu MUMA Source: Objaverse 1.0 / Sketchfab
Rešketėnų šventvietė Telšių r. Akmuo su dubeniu
Rešketėnų šventvietė (Telšių r.). Akmuo su dubeniu / Rešketėnai Sacred Site (Telšiai District). Stone with a flat-bottomed bowl 2001 m. miške prie Rešketėnų kaimo (Telšių r.) buvo aptiktas akmuo su plokščiadugniu dubeniu, būdingas kuršių šventvietėms. Kitais metais jis buvo atgabentas prie Telšių Alkos muziejaus. 2020 m. Rešketėnų šventvietėje surengti archeologiniai tyrimai (vad. V. Vaitkevičius, Klaipėdos universitetas) / In 2001, in the forest nearby Rešketėnai village (Telšiai district) stone with a flat-bottomed bowl, characteristic of the Curonian tribe, was discovered. It was taken to the Telšiai Alka Museum next year. In 2020 Rešketėnai Sacred Site was investigated by archaeologist V. Vaitkevičius (Klaipėda University) Created in RealityCapture by Capturing Reality from 241 images in 01h:22m:26s. Source: Objaverse 1.0 / Sketchfab
Panel 28, Ashurbanipal's palace room R
Gypsum wall panel relief: return from the hunt. Men carry dead lions. Was on corridor leading to eastern gate out of the palace. The king probably passed this way on his way back from the hunt. Dating to 645 BC-635 BC from the North Palace of Ashurbanipal, Room R Panel 28 Dimensions: Length 144.78cm, Width 114.30cm Created from 101 photographs taken with a Sony A6000, processed in Photoscan, Meshlab and Imagick. Source: Objaverse 1.0 / Sketchfab
Richardson Model R-5 Slam Fire Shotgun Low Poly
* 2048x2048 texture + normal map * low poly game ready model Richardson Model R-5 Single Shot Shotgun 12 ga. Barrel length 24" Excellent Bore , Marked clearly on top of the Receiver is "Richardson Industries, Inc. New Haven Conn.USA Model R-5 12ga. For those of you out their not familiar with a slamfire shot-gun, this is a factory gun made after WW2 by the Richardson Industries, a company owned by the famous Lt Iliff D. Richardson, during WW2 Lt Richardson fought the Japanese on the Philippines, it is their that he developed this unusual simple shotgun Source: Objaverse 1.0 / Sketchfab
Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology
<p>Before commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, Polymerase Chain Reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole genomic sequencing coverage that meets regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234 and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.</p>
Raw data and R code for statistical analyses from: Sensory trap leads to reliable communication without a shift in nonsexual responses to the model cue
<p>The sensory trap model of signal evolution suggests that males manipulate females into mating using traits that mimic cues used in a nonsexual context. Despite much empirical support for sensory traps, little is known about how females evolve in response to these deceptive signals. Female sea lamprey (<em>Petromyzon marinus</em>) evolved to discriminate a male sex pheromone from the larval odor it mimics and orient only towards males during mate search. Larvae and males release the attractant 3-keto petromyzonol sulfate (3kPZS), but spawning females avoid larval odor using the pheromone antagonist, petromyzonol sulfate (PZS), which larvae but not males, release at higher rates than 3kPZS. We tested the hypothesis that migratory females also discriminate between larval odor and the male pheromone and orient only to larval odor during anadromous migration, when they navigate within spawning streams using larval odor before they begin mate search. In-stream behavioral assays revealed that, unlike spawning females, migratory females do not discriminate between mixtures of 3kPZS and PZS applied at ratios typical of larval versus male odorants. Our results indicate females discriminate between the sexual and nonsexual sources of 3kPZS during but not outside of mating and show sensory traps can lead to reliable sexual communication without females shifting their responses in the original context.</p>
Dataset and R-scripts to the manuscript: Beyond salinity: plants show divergent responses to soil ion composition
<p>Dataset and R-scripts to the article: Pätsch R., Midolo G., Dítě Z., Dítě, D., Wagner, V., Pavonič, M., Danihelka, J., Preislerová Z., Ćuk M., Stroh H.G., Tóth T., Chytrá H., Chytrý M. (2024) Beyond salinity: plants show divergent responses to soil ion composition. <em>Global Evology and Biogeography, </em>00, e13821. <a href="https://doi.org/10.1111/geb.13821%E2%80%8B" target="_blank" rel="noopener">https://doi.org/10.1111/geb.13821</a></p>
Figure, 18. Tegulaster alba (R = 5 mm, paratype, NMV F45118): a, abactinal view; b, actinal view. in A molecular and morphological revision of genera of Asterinidae (Echinodermata: Asteroidea)
Figure, 18. Tegulaster alba (R = 5 mm, paratype, NMV F45118): a, abactinal view; b, actinal view.
Dataset and R-codes for Publication: "Best performances of visible-near infrared models in soils with little carbonate - a field study in Switzerland" (accepted version)
<p><span>In this upload you can find the R-codes and dataset for the Publication: </span></p> <p><span>"Best performances of visible-near infrared models in soils with little carbonate - a field study in Switzerland" by Simon Oberholzer Laura Summerauer, Markus Steffens and Chinwe Ifejika Speranza accepted in SOIL (https://doi.org/10.5194/egusphere-2023-1087)</span></p> <p><span>To reproduce the results of the manuscript, start with the R-file “ResampleandPreprocess.R” to prepare spectral data and then continue with the R-file “PLSRmodelling_GroupedCV.R” for the modelling.</span></p> <p><span>The R-files “control_train.R” and “rep_grouped_kfold_CV.R” are helper-functions for the grouped cross-validation. The file metadata.csv explains the column names in the spectral data (spcdata.RDS).</span></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.