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Relyea, R. A., and E. E. Werner. 2000. Morphological plasticity of four larval anurans distributed along an environmental gradient. Copeia 2000:178-190.
We investigated morphological plasticity to the presence of predators in the tadpoles of four ranid frog species distributed along a pond hydroperiod gradient in southeast Michigan. We first reared all four species (Wood Frog, Rana sylvatica; Leopard Frog R. pipiens; Green Frog, R. clamitans; and Bullfrog, R. catesbeiana) under identical laboratory conditions in the presence and absence of caged larval dragonflies (Anax spp.). We then reared wood frog and leopard frog in outdoor mesocosms to examine the predator-induced responses during ontogeny. Finally, we reared leopard frog with predators fed either leopard frog or wood frog larvae to determine whether prey responses depended upon predators consuming conspecific prey. All four ranids exhibited some degree of morphological change in the presence of Anax; these differences were species specific and fairly robust to different experimental conditions. The responses over ontogeny indicated that the changes were direct responses to the predator’s presence and not an indirect result of the predator slowing anuran growth or development. Finally, larval leopard frog responded similarly to predators feeding on conspecifics and congenerics. Taken together, these results suggest that morphological responses to predators may be relatively common in larval anurans. Further, because many of the responses are known to be adaptive antipredator strategies, predator-induced morphological plasticity has important evolutionary and ecological implications.
Data and R scripts for analyses of declines in invertebrate species from the Gulf of Maine, USA, 1997 - 2018
Data files and R scripts are for the analyses that are presented in an article that is under revision for Biology Communications. The title of the article is: Declines over the last two decades of five key invertebrate species found on rocky intertidal shores throughout the western North Atlantic. The three data files contain the abundances of four gastropod species and the recruitment of barnacles and mussels from 1997 to 2018, monthly temperature data from three buoys from 2001 to 2018, and pH and aragonite saturation state from 1997 to 2014. R scripts include details of Bayesian estimates for Poisson regressions of species over time, clean-up of environmental data, imputation of missing environmental data and analyses of species versus environmental parameters.
A search index for the ecocomDP R package
This data package contains summary information of datasets in the ecocomDP format published by EDI and NEON. This summary information is formatted in a search index used by the search function of the ecocomDP R package.
Year 2001, 15 minute measurements of stage, water temperature, conductivity, dissolved oxygen, and pH on the Ipswich R. mainstem at North Reading, just upstream of Rt. 28 (~48 km2 drainage area).
Year 2001, continuous measurements, every 15 minutes, were made of stage, water temperature, conductivity, dissolved oxygen, and pH in a small headwater stream draining a moderate sized, mixed land use watershed. Measurements are for part of the ice free season (June – December). Discharge is determined from stage using discharge vs stage regressions. Several day gaps occur periodically due to removal for recalibration.
Year 2002, 15 minute measurements of stage, water temperature, conductivity, dissolved oxygen, and pH on the Ipswich R. mainstem at North Reading, just upstream of Rt. 28 (~48 km2 drainage area).
Year 2002, continuous measurements, every 15 minutes, were made of stage, water temperature, conductivity, dissolved oxygen, and pH in a small headwater stream draining a moderate sized, mixed land use watershed. Measurements are for the ice free season (March – December). No Discharge was determined because beaver activity prevented rating curve estimate. Several day gaps occur periodically due to removal for recalibration.
Year 2003, 15 minute measurements of stage, water temperature, conductivity, dissolved oxygen, and pH on the Ipswich R. mainstem at North Reading, just upstream of Rt. 28 (~48 km2 drainage area).
Year 2003, continuous measurements, every 15 minutes, were made of stage, water temperature, conductivity, dissolved oxygen, and pH in a small headwater stream draining a moderate sized, mixed land use watershed. Measurements are for part of the ice free season (March – December). No Discharge was determined because beaver activity prevented rating curve estimate. Several day gaps occur periodically due to removal for recalibration.
Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments - PDF, datasets and R script
<p><strong>PDF, dataset and R script for the paper:</strong></p> <p>Tariel J, Plénet S, & Luquet E. <em>Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments</em>. </p> <p>Two data sets are provided: one for the analysis of the behavior (dataBehaviour.csv) and one for the analysis of other variables (weight, shell thickness and morphology; dataMorphology.csv). There are analyzed in the same R script (Script_TARIEL-Juliette.R)</p> <p><strong>Signification of variables names:</strong></p> <p>G1: treatment/environment of the grand-parental generation (control C or with predator-cue P)<br> G2: treatment/environment of the parental generation (control C or with predator-cue P)<br> G3: treatment/environment of the offspring generation (control C or with predator-cue P)<br> Family: unique ID for each family<br> Individual: number to identify siblings within a family <br> ID: unique ID for each individual <br> W: snail total weight (g)<br> Th: shell thickness (mm)<br> L: shell length (mm)<br> l: shell width (mm)<br> Lo: aperture length (mm)<br> lo: aperture width (mm)<br> crawlout : position of the snail (0: below the water surface; 1: above/on the water surface)<br> Day : day of measurement (crawling-out behaviour was measured three times through three consecutives days d2, d3 and d4)</p>
Set de datos y códigos en R para DataViz
<p>Set de datos y código en R para el curso de <em>Tratamiento y visualización de datos en la Humanidades Digitales.</em></p> <p><code>stylometry_sample.csv</code> ha sido extraído de Christof Schöch, <em>Bibliography on Stylometry</em>, 2017, dataset (Version v.0.1.3 10.5281), DOI: <a href="https://doi.org/10.5281/zenodo.835190">10.5281/zenodo.835190</a>.</p> <p> </p>
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm
Darwin's naturalization conundrum can be explained by spatial scale: R replication code
<p>1) Code for extracting climatic data:<br> 1_extract_env.R<br> 2_extract_env_county.R<br> 3_relatePlotCounty.R</p> <p>2) Code for generating composite phylogenies:<br> 1_making_sunplin_trees.R</p> <p>3) Code for relatedness analyses:<br> DNH_calculations_PHY_obs.cluster.R<br> DNH_calculations_PHY_random.cluster.R<br> DNH_calculations_TAX.cluster_obs.R<br> DNH_calculations_TAX.cluster_random.R</p> <p> </p> <p> </p>
R code and radiocarbon dates to reproduce figures and results of our paper "Population dynamics ..."
<p>R Codes and dataset to reproduce figures and results of the paper <strong><em>Population dynamics during the Neolithic transition and the onset of megalithism in Portugal according to summed probability distribution of radiocarbon determinations</em>. </strong></p>
Fig. 34. Begonia koelzii R in A revision and one new species of Begonia L. (Begoniaceae, Cucurbitales) in Northeast India
Fig. 34. Begonia koelzii R.Camfield sp. nov. A. Plant habit. B. Leaf. C. Bulbil. D. Young female flowers. E. Fruit. Photographs courtesy of Nick Macer, of a plant in Manipur.
Dataset and R-script for simple mechanistic model of Heracleum sosnowskyi seed dispersal by wind
<p>The dataset contains:</p> <p>- primary data about Heracleum sosnowskyi seeds traits (terminal velocity, mass, area, wing loading) and release heights for <em>H. sosnowskyi</em> populations from two geographically distant Russia regions;</p> <p>- results of experiments of model seeds launches under different wind speeds;</p> <p>- R script for exploratory statistical analysis, linear regressions and mechanistc models testing.</p> <p>The anemochorous seed dispersal was generalized with a number of empirical and mechanistic models of varying complexity. The aim of this work was to develop the simplest possible mechanistic model of <em>Heracleum sosnowskyi</em> that allows to determine the distance of seed dispersal by wind with an accuracy comparable to that of empirical measurements. We measured and compared the characteristics of the seeds (terminal velocity, mass, area, wing loading) as well as the release height for <em>H. sosnowskyi</em> populations from two geographically distant Russia regions. We tested two simplest mechanistic models: a ballistic model and a wind gradient model using identical artificial seeds with characteristics similar to those of real <em>H. sosnowskyi</em> seeds. The wind gradient model gave the best results, despite the fact that uniform in shape, weight and size artificial <em>H. sosnowskyi</em> seeds, when dropped simultaneously from the same height, fly off at different distances. This model provides an estimate of dispersal distances with an accuracy comparable to that of empirical measurements. We plan to use the presented model to develop an individual-based model that will allow us to calculate the flight distances of <em>H. sosnowskyi</em> propagules, taking into account real weather conditions in different years and in different parts of its invasion range. All primary data and R-scripts used are freely available at the Zenodo repository (https://doi.org/10.5281/zenodo.3766035).</p> <p> </p>
Dataset, Survey, and R Notebooks for "Does Surprisal Predict Code Comprehension Difficulty?"
<p>(Version 1.1 Update)</p> <p>- Removed anonymization after reviewing period ended and paper was accepted at Cogsci 2020.</p> <p>- Added Qualtrics Survey in exported form</p> <p>Dataset and R analysis scripts for the paper "Does Surprisal Predict Code Comprehension Difficulty?". For more details, see "ComprehensionREADME.md" in the included zip file.</p>
R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper
<p>This repository contains the R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper.</p>
Data and R code for the revised manuscript "Downscaling digital soil maps using electromagnetic induction and aerial imagery"
<p>Data and R code for the revised manuscript "Downscaling digital soil maps using electromagnetic induction and aerial imagery". This is the code for the revised version of the manuscript, after adressing comments from reviewers. The data and code for the preprint, before submission to peer review (Møller et al., 2020), is available at <a href="https://doi.org/10.5281/zenodo.3699130">https://doi.org/10.5281/zenodo.3699130</a>.</p> <p>The R code was written for R version 3.6.3.</p> <p>References<br> Møller, A.B., Koganti, T., Beucher, A., Iversen, B.V. and Greve, M.H., 2020. Downscaling digital soil maps using electromagnetic induction and aerial imagery. EarthArXiv. <a href="http://dx.doi.org/10.31223/osf.io/a7xz6">http://dx.doi.org/10.31223/osf.io/a7xz6</a>. [preprint]</p>
Polish is quantitatively different on quartzite flakes used on different worked materials [R analysis]
<p>This upload includes the following files related to the R analysis:</p> <p>- Raw data as a CSV table (processing-quartzite-final.csv), i.e. results from the ConfoMap analysis (see <a href="https://doi.org/10.5281/zenodo.3979116">https://doi.org/10.5281/zenodo.3979116</a>)</p> <p>- RStudio project (Quantification quartzite final.Rproj)</p> <p>- R scripts as R Markdown files (*.Rmd)</p> <p>- R scripts knitted to HTML files (*.html)</p> <p>- An R script (RStudioVersion.R) to write the used version of RStudio to a text file (RStudioVersion.txt)</p> <p>- Output from script #1: processing-quartzite-final.Rbin and processing-quartzite-final.xlsx</p> <p>- Output from script #2: processing-quartzite-final_summary-stats.xlsx</p> <p>- Output from script #3: all plots as PDF files.</p> <p>Note that for running the scripts, the raw data files (processing-quartzite-final.csv, .Rbin and .xlsx) should be stored in a "Data" folder within the working directory.<br> Output (processing-quartzite-final_summary-stats.xlsx and PDF plots) were saved into "Summary-stats" and "Plots" folders, respectively.</p> <p>Zenodo does not allow sub-folders, so this folder structure had to be removed.</p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Figs 1-6 in On Hypnogyra laevissima (R , 1898) (Coleoptera: Staphylinidae: Staphylininae: Xantholinini)
Figs 1-6: Hypnogyra laevissima (1-4) and H. angularis (5-6): (1) head and pronotum; (2-3) aedeagus; (4-6) internal structures of aedeagus in squeeze preparation. Scale bars: 1: 1.0 mm; 2-6: 0.5 mm.
Data and R-script for a tutorial that explains how to convert spreadsheet data to tidy data.
<p>Data and R-script for a tutorial that explains how to convert spreadsheet data to tidy data. The tutorial is published in a blog for The Node (https://thenode.biologists.com/converting-excellent-spreadsheets-tidy-data/education/)</p>
Data and R code from: Pollination interactions reveal direct costs and indirect benefits of plant–plant facilitation for ecosystem engineers
Ecosystem engineers substantially modify the environment via their impact on abiotic conditions and the biota, resulting in facilitation of associated species that would not otherwise grow. Yet, reciprocal effects are poorly understood as studies of plant–plant interactions usually estimate only benefits for associated species while hardly considering how another trophic level may mediate direct and indirect effects for ecosystem engineers. We run a field experiment with ecosystem engineers blooming either alone or with associated plants to decompose net effects and to test the hypothesis that pollinator-mediated interactions provide benefits which balance costs of facilitation by ecosystem engineers. We found that net costs of facilitation are accompanied by pollinator-mediated benefits. Despite ecosystem engineers producing less flowers per plant, they were visited by more and more diverse pollinators per flower when blooming with associated plants than when blooming alone. However, fruit set was unaffected by the presence of associated plants and seed production per plant was higher when ecosystem engineers bloomed alone. Our findings suggest that besides experiencing direct costs, ecosystem engineers can also benefit from facilitating other species via increasing their own visibility to pollinators. This study illuminates how the outcome of direct plant–plant interactions might be mediated by indirect interactions including third players.
ScienceDex guides
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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.