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15,519 results for “r”
Linked collectors and determiners for: Rubus neohunanensis, a new name for a bramble taxon misidentified as R. hunanensis in previous Chinese taxonomic literature.
Natural history specimen data linked to collectors and determiners held within, "Rubus neohunanensis, a new name for a bramble taxon misidentified as R. hunanensis in previous Chinese taxonomic literature". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/95210b28-c75b-4123-805d-b4c2a941fd25">https://bionomia.net/dataset/95210b28-c75b-4123-805d-b4c2a941fd25</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/95210b28-c75b-4123-805d-b4c2a941fd25">https://gbif.org/dataset/95210b28-c75b-4123-805d-b4c2a941fd25</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Taxonomic studies on the genus Reevesia (Malvaceae: Helicteroideae) I: the identities of R. thyrsoidea.
Natural history specimen data linked to collectors and determiners held within, "Taxonomic studies on the genus Reevesia (Malvaceae: Helicteroideae) I: the identities of R. thyrsoidea". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bf67e644-d0d6-48f9-b55f-6a35940adb2e">https://bionomia.net/dataset/bf67e644-d0d6-48f9-b55f-6a35940adb2e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bf67e644-d0d6-48f9-b55f-6a35940adb2e">https://gbif.org/dataset/bf67e644-d0d6-48f9-b55f-6a35940adb2e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Diptera R. Frey (MZH/Luomus).
Natural history specimen data linked to collectors and determiners held within, "Diptera R. Frey (MZH/Luomus)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/489cf6d8-4171-46bd-94b1-ca514fb2043f">https://bionomia.net/dataset/489cf6d8-4171-46bd-94b1-ca514fb2043f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/489cf6d8-4171-46bd-94b1-ca514fb2043f">https://gbif.org/dataset/489cf6d8-4171-46bd-94b1-ca514fb2043f</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Towards a revision of Pseudobombax Dugand (Malvaceae- Bombacoideae): typification of names published by E. Hassler and R. Chodat in the related genus Bombax L..
Natural history specimen data linked to collectors and determiners held within, "Towards a revision of Pseudobombax Dugand (Malvaceae- Bombacoideae): typification of names published by E. Hassler and R. Chodat in the related genus Bombax L.". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d75cdcea-4b81-4b1f-ada5-69135a4d7b98">https://bionomia.net/dataset/d75cdcea-4b81-4b1f-ada5-69135a4d7b98</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d75cdcea-4b81-4b1f-ada5-69135a4d7b98">https://gbif.org/dataset/d75cdcea-4b81-4b1f-ada5-69135a4d7b98</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: George Mason University, Ted R. Bradley Herbarium.
Natural history specimen data linked to collectors and determiners held within, "George Mason University, Ted R. Bradley Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/cbd0e918-f98b-41e4-b91f-007dd2ac7414">https://bionomia.net/dataset/cbd0e918-f98b-41e4-b91f-007dd2ac7414</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/cbd0e918-f98b-41e4-b91f-007dd2ac7414">https://gbif.org/dataset/cbd0e918-f98b-41e4-b91f-007dd2ac7414</a>. Formatted as a Frictionless Data package.
Paleoecological Analysis in R
<p>This is a public repo that can be used to learn how to conduct a paleoecological analysis in R. The project methods described here are formally reviewed and cited in the following paper.<br>Bosch, JL., Álvarez-Manzaneda, I., Smol, J.P. et al. Blending census and paleolimnological data allows for tracking the establishment and growth of a major gannet colony over several centuries. Sci Rep 14, 20462 (2024). https://doi.org/10.1038/s41598-024-69860-z</p>
Experiences Applying Lean R&D in Industry-Academia Collaboration Projects
<p>Supplementary materials of the paper Experiences Applying Lean R&D in Industry-Academia Collaboration Projects</p>
Replication Data for the retroharmonize R Package Case Study: Working With Arab Barometer Surveys
<p>Replication datasets for the <a href="https://retroharmonize.dataobservatory.eu/articles/arabbarometer.html">retroharmonize Case Study: Working With Arab Barometer Surveys</a></p>
PLATE IVA. Metioche Stal, 1877. (A–J), Metioche japonica (Ichikawa, 2001): A, Male; B, Inner margin of eyes more brightlyrimmed; C, Male sub-genital plate; D, Fore tibiae without tympanum on both sides; E, Shape of last segment of maxillary palpi-securiform; F, Male genitalia; G, Female; H, Tegmina convex; I, Female ovipositor upturned, shaped; apex sharp with teeth on; J, subgenital plate triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IVA. Metioche Stal, 1877. (A–J), Metioche japonica (Ichikawa, 2001): A, Male; B, Inner margin of eyes more brightlyrimmed; C, Male sub-genital plate; D, Fore tibiae without tympanum on both sides; E, Shape of last segment of maxillary palpi-securiform; F, Male genitalia; G, Female; H, Tegmina convex; I, Female ovipositor upturned, shaped; apex sharp with teeth on; J, subgenital plate triangular.
PLATE III. Trigonidium Rambur, 1839. (A–H), Trigonidium humbertianum (Saussure, 1878): A, Male; B, Female; C, Eyesrounded protruding; D–E, Fifth joint of maxillary palpi large and triangular; F, Anterior tibiae with tympanum on both sides; G, Female ovipositor curved, compressed, acute at apex; H, Male sub-genital plate feebly notched at apex. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE III. Trigonidium Rambur, 1839. (A–H), Trigonidium humbertianum (Saussure, 1878): A, Male; B, Female; C, Eyesrounded protruding; D–E, Fifth joint of maxillary palpi large and triangular; F, Anterior tibiae with tympanum on both sides; G, Female ovipositor curved, compressed, acute at apex; H, Male sub-genital plate feebly notched at apex.
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex.
PLATE IIA. Paratrigonidium Brunner, 1893. (A–K), Paratrigonidium nitidum Brunner, 1893: A–B, Male and female black, shining;the male with membranous elytra, while female elytra corneous, convex with plain, longitudinal veins. Vertex flattened and sloping; C, Head wide and black; antenae yellow with first joint black; D, Pronotum black, pubescent; E, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; F, Tympanum external; G, Male elytra membranous; H, The hind femurwith a feeble brownish band/stripe; I, Legs yellowish; J, Lateral field of tegmina in male blackish, presenting 3 parallel veins andthe fourth incomplete; K, The female ovipositor fulvous at base, darkened in the middle, cerci long. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IIA. Paratrigonidium Brunner, 1893. (A–K), Paratrigonidium nitidum Brunner, 1893: A–B, Male and female black, shining;the male with membranous elytra, while female elytra corneous, convex with plain, longitudinal veins. Vertex flattened and sloping; C, Head wide and black; antenae yellow with first joint black; D, Pronotum black, pubescent; E, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; F, Tympanum external; G, Male elytra membranous; H, The hind femurwith a feeble brownish band/stripe; I, Legs yellowish; J, Lateral field of tegmina in male blackish, presenting 3 parallel veins andthe fourth incomplete; K, The female ovipositor fulvous at base, darkened in the middle, cerci long.
PLATE IVB. Metioche Stal, 1877. (A–G), Metioche japonica (Ichikawa, 2001): A, Eyes rounded, large and widely separated; B,Antennae: Scape and pedicel dark black, flagellum light in colour; C, Shape of last segment of maxillary palpi-securiform; D, Female sub-genital plate triangular; E, Male sub-genital plate; F, Male genitalia; G, Female ovipositor upturned, sabre shaped; apexsharp with teeth on ventre. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IVB. Metioche Stal, 1877. (A–G), Metioche japonica (Ichikawa, 2001): A, Eyes rounded, large and widely separated; B,Antennae: Scape and pedicel dark black, flagellum light in colour; C, Shape of last segment of maxillary palpi-securiform; D, Female sub-genital plate triangular; E, Male sub-genital plate; F, Male genitalia; G, Female ovipositor upturned, sabre shaped; apexsharp with teeth on ventre.
PLATE IB. Natula Gorochov, 1987. (A–K), Natula matsuurai (Sugimoto, 2001): A, Head; B, Maxillary palpi; C, Second tarsal segment; D, Tympanum on fore tibia; E, Forewing lateral view showing longitudinal veins; F, Hind femur without stripe; G, Male Forewing mirror longer than wide; H, Female sub-genital plate triangular; I, Male sub-genital plate longer than wide, hind margin with a small projected median lobe; J, Hind tibial spines (3 pairs) on both sides; K, Ovipositor upcurved with a dorsal groove in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IB. Natula Gorochov, 1987. (A–K), Natula matsuurai (Sugimoto, 2001): A, Head; B, Maxillary palpi; C, Second tarsal segment; D, Tympanum on fore tibia; E, Forewing lateral view showing longitudinal veins; F, Hind femur without stripe; G, Male Forewing mirror longer than wide; H, Female sub-genital plate triangular; I, Male sub-genital plate longer than wide, hind margin with a small projected median lobe; J, Hind tibial spines (3 pairs) on both sides; K, Ovipositor upcurved with a dorsal groove
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular.
Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
<p><b>Background</b> </p> <p>RNA-seq is a widely adopted affordable method for large scale gene expression profiling. However, user-friendly and versatile tools for wet-lab biologists to analyse RNA-seq data beyond standard analyses such as differential expression, are rare. Especially, the analysis of time-series data is difficult for wet-lab biologists lacking advanced computational training. Furthermore, most meta-analysis tools are tailored for model organisms and not easily adaptable to other species.</p> <p><b>Results</b></p> <p>With RNfuzzyApp, we provide a user-friendly, web-based R-shiny app for differential expression analysis, as well as time-series analysis of RNA-seq data. RNfuzzyApp offers several methods for normalization and differential expression analysis of RNA-seq data, providing easy-to-use toolboxes, interactive plots and downloadable results. For time-series analysis, RNfuzzyApp presents the first web-based, automated pipeline for soft clustering with the Mfuzz R package, including methods to aid in cluster number selection, Mfuzz loop computations, cluster overlap analysis, as well as cluster enrichments.</p> <p><b>Conclusion</b></p> <p>RNfuzzyApp is an intuitive, easy to use and interactive R shiny app for RNA-seq differential expression and time-series analysis, offering a rich selection of interactive plots, providing a quick overview of raw data and generating rapid analysis results. Furthermore, its orthology assignment, enrichment analysis, as well as ID conversion functions are accessible to non-model organisms.</p>
R code to accompany 'A novel initialisation technique for decadal climate predictions'
<p>R code for the diagnostic published in 'A novel initialisation technique for decadal climate predictions' <a href="https://doi.org/10.3389/fclim.2021.681127">https://doi.org/10.3389/fclim.2021.681127</a><br> The data loaded follow the cmor standard.</p>
Physiological data and R script for running physiology combined model for Drosophila suzukii
<p>This is the dataset that accompanies an article entitled "The use of insect life tables in optimizing invasive pest distributional models" that would be published in Ecography. The dataset include two R script that used to generate physical model and the physiology combined model respectively. Our paper shows that the physiology combined model show good performance when applying ecological niche model in risk assessment. We addressed this by determining whether incorporating physiological data from life table analyses of an invasive insect, Drosophila suzukii, improved predictions of ecological niche models. The dataset also include the physiology data D. suzukii that we assembled for running our physiology combined model.</p>
Datasets and R Code for native-invasive shrub analysis
<p>Datasets and R code to reproduce statistical analysis comparing functional traits of native and invasive shrub and liana species of North America.</p>
Source code for R tutorials and dataset for empirical case study on Malurus elegans (red-winged fairy wren)
<p>Biological processes exhibit complex temporal dependencies due to the sequential nature of allocation decisions in organisms' life-cycles, feedback loops, and two-way causality. Consequently, longitudinal data often contain cross-lags: the predictor variable depends on the response variable of the previous time-step. Although statisticians have warned that regression models that ignore such covariate endogeneity in time series are likely to be inappropriate, this has received relatively little attention in biology. Furthermore, the resulting degree of estimation bias remains largely unexplored.</p> <p>We use a graphical model and numerical simulations to understand why and how regression models that ignore cross-lags can be biased, and how this bias depends on the length and number of time series. Ecological and evolutionary examples are provided to illustrate that cross-lags may be more common than is typically appreciated and that they occur in functionally different ways.</p> <p>We show that routinely used regression models that ignore cross-lags are asymptotically unbiased. However, this offers little relief, as for most realistically feasible lengths of time series conventional methods are biased. Furthermore, collecting time series on multiple subjects–such as populations, groups or individuals—does not help to overcome this bias when the analysis focusses on within-subject patterns (often the pattern of interest). Simulations (R tutorial 1 & 2), a literature search and a real-world empirical example on fairy wrens (data archived here with analyses presented in R-tutorial 3) together suggest that approaches that ignore cross-lags are likely biased in the direction opposite to the sign of the cross-lag (e.g. towards detecting density-dependence of vital rates and against detecting life history trade-offs and benefits of group living). Next, we show that multivariate (e.g. structural equation) models can dynamically account for cross-lags, and simultaneously address additional bias induced by measurement error, but only if the analysis considers multiple time series.</p> <p>We provide guidance on how to identify a cross-lag and subsequently specify it in a multivariate model, which can be far from trivial. Our tutorials with data and R code of the worked examples provide step‐by‐step instructions on how to perform such analyses.</p> <p>Our study offers insights into situations in which cross-lags can bias analysis of ecological and evolutionary time series and suggests that adopting dynamical models can be important, as this directly affects our understanding of population regulation, the evolution of life histories and cooperation, and possibly many other topics. Determining how strong estimation bias due to ignoring covariate endogeneity has been in the ecological literature requires further study, also because it may interact with other sources of bias.</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.