Find research datasets worth reusing

opencc-by-4.0Jan 2023View details →

Data and code for figures: Kinetic Inductive Electromechanical Transduction for Nanoscale Force Sensing

This directory contains the datasets and code (if applicable) for generating the figures in the research article "Kinetic Inductive Electromechanical Transduction for Nanoscale Force Sensing", Physical Review Applied 20, 024022 (2023).

opencc-by-4.0Feb 2023View details →

Data and code from "Water availability is a stronger driver of soil microbial processing of organic nitrogen than tree species composition"

#### Data description Data from large scale, long-term tree diversity experiment in southwestern France (<a href="https://sites.google.com/view/orpheeexperiment/home">ORPHEE</a>), additionally manipulating water contraint. Variables presented are soil nitrogen cycling rates measured using isotope pool dilutions. Companion paper is found here: Maxwell TL, Augusto L, Tian Y, Wanek W & Fanin N (2023). Water availability is a stronger driver of soil microbial processing of organic nitrogen than tree species composition. European Journal of Soil Science. <a href="https://doi.org/10.1111/ejss.13350">https://doi.org/10.1111/ejss.13350</a> #### Metadata Soil sampling: July 2020 Maxwell_ShortComm_Data.csv data description ID: unique identifier per sample Block: numbered 1-6. Blocks 1,3,6 are control (unirrigated), Blocks, 2,4,5 are irrigated Plot: numbered plot according to the ORPHEE design. Plot 1 = BP, Plot 5 = PP, Plot 9 = BP_PP Espece: species ID. BP = pure birch (Betula pendula), PP = pure pine (Pinus pinaster), BP_PP (50% mixed birch-pine) Rep: sample replicate, 3 replicates per plot Sample name: long unique identifier per sample. Concatenation of Block, Plot, and Espece PD: gross protein depolymerization rates (micrograms nitrogen per grams dry soil per day = µg N g-1 d-1) AAU: gross free amino acid uptake rates (µg N g-1 d-1) Cmicrobial_ug_g: microbial biomass carbon (µg C g-1) Nmicrobial_ug_g: microbial biomass nitrogen (µg N g-1) MRT_FAA_hrs: mean residence time of free amino acids (hours) FAA_ugN_g: free amino acids (µg N g-1) Moisture_percent: soil moisture percent (%) N_nonfumige_ug_g: nitrogen from non fumigated soils, i.e. extractable N (µg N g-1) C_nonfumige_ug_g: nitrogen from non fumigated soils, i.e. extractableC (µg C g-1)

opencc-by-4.0May 2023View details →

Detecting small changes in tropical forests from space... data and code for thesis chapter 4

SAR and UAV-LiDAR data used in chapter 4 of my thesis Detecting small changes in tropical forests from space: experiments using synthetic aperture radar. This content has also been submitted for peer review in Frontiers in Remote Sensing. DEM_timeseries_3m contains phase height and coherence from TanDEM-X InSAR high-resolution spolight images, processed by Jose-Luis Bueso-Bello at DLR. NetCDF format, dimensions latitude, longitude, time. TDX_descending_intensity contains intensity from the same TanDEM-X time series, covering an area of the Madre de Dios region in Peru. These data were processed by Harry Carstairs using ESA's SNAP software. UAV_change_1m_mask is a raster showing the change in canopy height at the study site between June 2019 and July 2021, according to two UAV LiDAR campaigns, with 1m pixels, and with areas with low point density masked out. CODE.zip contains python scripts and notebooks used to collate the data, create change detection metrics, develop SAR models of canopy height, and produce the figures. Funded by European Research Council (ERC) grant to the Tropical Forest Degradation Experiment (FODEX).

opencc-by-4.0May 2023View details →

Figure data and code used in Technical comment on "Fairness considerations in global mitigation investments"

The package contains the data and code to create the figure in the associated technical comment in Science published at <a href="https://www.science.org/doi/10.1126/science.adg5893">https://www.science.org/doi/10.1126/science.adg5893</a>

openCC (other)Nov 2023View details →

Data and code from "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" Kaiser et al. 2023 Behavioral Ecology and Sociobiology

This dataset is published in support of "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" by Kaiser et al. 2023 in Behavioral Ecology and Sociobiology. Data and code to test the assumptions and key predictions of the Trivers-Willard hypothesis, which proposes that females produce more sons or daughters depending on food availability, in the black-throated blue warbler at the Hubbard Brook Experimental Forest, NH, 2007-2012. Datasets support analyses of sex ratio bias at both the nest and nestling levels. Data tables support the comparison of the ratio of variances in the scaled pre-fledging mass of male and female nestlings using an F test and reproduction of Figures 2a and 2b. Figures are those used in the published manuscript. Code supports the calculation of offspring sex ratio bias at the population level, and considering separately both low- and high-quality habitats, using the Neuhäuser test, statistical models testing the assumptions of the Trivers-Willard hypothesis, effects of food availability and parental provisioning on offspring sex ratio, and effects of food availability on pre-fledging nestling mass of sons and daughters, and a power analysis to determine the power to detect an effect of food supplementation on sex ratio. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the US Forest Service, Northern Research Station.

openCC (other)Aug 2025View details →

Data and Code in support of Nitrogen and phosphorus co-limitation of forest growth in northern hardwood forests; Blumenthal et al. 2025

The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation of forest productivity through a series of nutrient manipulations in northern hardwood forests. This data set is published in support of a manuscript titled "Nitrogen and phosphorus co-limitation of forest growth in northern hardwood forests" and includes data and code used in the analysis. The primary diameter breast height dataset can be found in: Fisk, M.C., R.D. Yanai, and T.J. Fahey. 2025. Tree DBH response to nitrogen and phosphorus fertilization in the MELNHE study, Hubbard Brook Experimental Forest, Bartlett Experimental Forest, and Jeffers Brook ver 2. Environmental Data Initiative. https://doi.org/10.6073/pasta/fb8f8d5b903627bee9ad6aa4c32f2289. Additional detail on the MELNHE project, including a datatable of site descriptions and a pdf file with the project description and diagram of plot configuration can be found in this data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=344 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.

openCC (other)Sep 2024View details →

Data and code from "Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability" Kaiser et al. 2024 Ecology and Evolution

Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing ‘green’ season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a two-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons. These data were gathered as part of the Hubbard Brook Ecosystem Study (HB

openCC (other)Dec 2025View details →

Limno run codes, dates, and locations associated with vertical lake profile data collected in the McMurdo Dry Valleys, Antarctica (1991-2025, ongoing)

This data package provides a summary of "limno runs" performed each season in lakes located throughout the McMurdo Dry Valleys of Antarctica as part of the McMurdo Dry Valleys Long Term Ecological Research program. Each limno run is identified by unique code that allows one to compile a complete set of limnological data from a particular lake and location at specific time points. There are usually two or three limno runs performed per lake per austral summer field season, although the number of runs may vary by lake and by season depending on site access, site conditions, and other external factors.

opencc-by-4.0Feb 2020View details →

Data and R Code from "A novel approach to sustainability assessment of food supply chains using networks of ecosystem services"

Data and R code from this paper applying network analysis (iGraph) to two case studies pre and post agroecological transitions in Central America and Tanzania, Africa from the IPES-Food report. Further descriptions of this data and code can be found within the extended manuscript. R Code relies on the data from the scenarios (e.g., Nodes and Relations CSVs) and creates the output network metrics (e.g., Node Metric CSVs).

opencc-by-4.0May 2020View details →

Data and code for the analysis in "Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland"

Data and code used for the analysis in Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland (Lemaitre et al., Swiss Medial Weekly 2020).

opencc-by-4.0May 2020View details →

Data and code to perform the"Target deformation" workflow in R: virtual reconstruction of the Equus stenonis holotype skulll

Data and code to perform the"Target deformation" workflow in R: virtual reconstruction of the Equus stenonis holotype skulll. TargetDeformation.R: R code with for the Target Deformation procedure. IGF560.ply: 3D mesh of the holotype IGF560 in ply extension. IGF560_set.txt: landmark set of the holotype IGF560. Dm. 5/154.3/4.A4.5.ply: 3D mesh of Dm 5/154.3/4.A4.5 in .ply extension. Dm_set.txt: landmark set of the Dm 5/154.3/4.A4.5 sample. IGF11023: 3D mesh of IGF11023 in.ply extension. IGF11023_set.txt: landmark set on the IGF11023 sample. IGF560R: 3D mesh of IGF560R in.ply extension. IGF560W: 3D mesh of IGF560W in.ply extension. IGF560R-s: 3D mesh of IGF560R-s in.ply extension. IGF560W-s: 3D mesh of IGF560W-s in.ply extension. IGF560_IGF560R_IGF560W.html: file that contain WebGL code to reproduce the 3D meshes of IGF560, IGF560R and IGF560W in a browser. IGF560Rs_IGF560Ws.html: file that contain WebGL code to reproduce the 3D meshes of IGF560R-S and IGF560W-S in a browser. IGF560W Mesh area variation.html: file that contain WebGL code to reproduce two 3d meshes of IGF560W using localmeshDist() and meshdist() in a browser.

opengpl-2.0Oct 2020View details →

Code and data for SylvanSeeds, a seed germination database for temperate deciduous forests

This is a version of record of the manuscript's data and code as accepted by the Journal of Vegetation Science.

opengpl-2.0Oct 2020View details →

Code and data for Mire microclimate: groundwater buffers temperature in waterlogged versus dry soils.

Version of record of the manuscript's code and data, as accepted by the International Journal of Climatology.

Data and R Code for 'Domestication via the commensal pathway in a fish-invertebrate mutualism'

This document contains all data and R code required to replicate the analyses in 'Domestication via the commensal pathway in a fish-invertebrate mechanism' as published in Nature Communications. The R Markdown provided includes descriptions of all variables and the code used for the analysis of the following eight datasets: 1. Transects 2. Census of farms 3. Paired choice experiments 4. Predation experiment 1 5. Predation experiment 2 6. Timed observations 7. Farm algae composition 8. Longfin damselfish body condition In addition, the R Markdown also includes descriptions of all variables for two additional datasets: 9. Estimates of mysid swarm density 10. Mysid waste excretion and nutrient availability A PDF version of the R Markdown with all output is also provided. Please see the methods section of the associated manuscript for further information on data collection and analysis procedures. Author contributions to data collection and analysis: RMB, JMC, ZLC, TLS & WEF collected the data; WEF, RMB, JMC, ZLC & AM implemented the analyses.  Correspond with: rohan.m.brooker@gmail.com

Network properties data and code used in "Ecological plasticity governs ecosystem services in multilayer networks".

Code and network properties data used in the analyses presented in "Ecological plasticity governs ecosystem services in multilayer networks". Further information can be requested of the author David A. Bohan (David.Bohan@inrae.fr).

Data and Code Accompanying the Study on "Benefits of reflex prediction: A case study of Western Kho-Bwa"

Cite the source of the dataset as: <blockquote> Timotheus A. Bodt and Johann-Mattis List (to appear): Benefits of reflex prediction: A case study of Western Kho-Bwa. Diachronica. </blockquote>

Data and code from: Insect biomass decline scaled to species diversity: General patterns derived from a hoverfly community

To study changes in flying insect communities, and hoverflies in particular, malaise trap samples from a German site were compared between two years (Hallmann et al. 2020). The data files deposited here contain data obtained from six malaise traps in the Wahnbachtal (North Rhine-Westphalia, Germany, 50.851944N, 7.320833E) that were deployed in 1989 and again in 2014, at the exact same locations. Traps were situated in wet meadows as well as tall perennial meadows, in close proximity to shrub corridors, to forest–grassland borders, and to the Wahnbach River and surrounded by agricultural land, essentially a rather heterogeneous habitat. The Wahnbach River and the greater part of the valley are protected for watershed purposes and are subject to nature conservation management by the Wahnbach Talperrenverband. Hence, several restrictions apply to safeguard against water contamination. Total insect biomass collected with these traps was already included in Hallmann et al. (2017), but here we focus on additional information: the abundance and richness of hoverflies (Syrphidae) in each of the collected samples (pots). Methodologies of collection are described in Sorg (1990), Schwan et al. (1993), Sorg et al. (2013), Hallmann et al. (2017), and Ssymank et al. (2018).  In brief, malaise traps were deployed throughout the growing season and operated continuously (day and night). Malaise trap construction (e.g., size, material, colouring, and ground sealing) and placing (e.g., positioning, orientation, and slope of the locations) were standardised in all aspects. Insect samples were preserved in 80% ethanol solution. Catches of the six traps investigated in the present study were emptied regularly: On average exposure intervals were 7.0 d (SD = 0.5) in 1989 and 16.7 d (SD = 5.6) in 2014. Across the six traps in 2014 the total exposure time (in number of days) was 42% higher compared to 1989. All collected samples (n = 196) were used in the present analysis with in total 19,604 individual hoverflies counted, distributed over 162 species and 59 genera. To assess how environmental conditions have changed over the 25 year, several additional datasets were assembled. Climatic data were obtained from 169 climatic stations and were used to interpolate daily weather variables to each trap location, using spatiotemporal kriging. These steps are described in detail in Hallmann et al. (2017). Our analysis (see R code) consists of three components. First, we considered total abundance, species richness, and species diversity, at two temporal scales: pooled per year, i.e., across the sampling season, and seasonally (i.e., per day), and we compared these metrics between 1989 and 2014. Second, we examined how total flying biomass (i.e., the weight of all trapped insects, of which hoverflies are only a small proportion) related to total abundance as well as species richness of hoverflies. Third, we derived persistence probabilities and population growth rate trends per species, to examine interspecific variation in these parameters. Descriptions of the deposited files: Groups.csv MF_NR = identifier of each of the six malaise trap locations yrf = year of sampling pot = sample identifier dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap mean.daynr = mean day-of-the-year of the sampling period Nspec = number of different hoverfly species found in a pot Nind = number of hoverfly individuals found in a pot Counts.csv A matrix of counts of individual hoverflies per pot per species. The 196 rows represent the pots in the same order as in the file 'Groups.csv'. The columns represent the 162 different hoverfly species found. The scientific species names are indicated in the column headers. PairedData.csv pot = sample identifier JAHR = year of sampling MF_NR = identifier of each of the six malaise trap locations dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap NI = number of hoverfly individuals found in a potbiomass.daily NSP = number of different hoverfly species found in a pot biomass.daily = daily fresh weight [gram] of flying insects: total fresh weight in a pot divided by the number of sampling days. ModelFrame.csv MF_NR = identifier of each of the six malaise trap locations yrf = year of sampling pot = sample identifier dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap mean.daynr = mean day-of-the-year of the sampling period plot = identifier of each of the six malaise trap locations date = date for which the weather variables are interpolated daynr = day-of-the-year for which the weather variables are interpolated altitude = altitude [m] of the malaise trap locations year = year of sampling temperature = interpolated temperature [degrees Celsius] precipitation = interpolated precipitation [mm per day] wind.speed = interpolated wind speed [m/s] Data_Rcode.pdf This pdf provides the R-code behind the analysis of the Hoverfly data. Three datasets are provided along with this R-code document, namely "Counts.csv", "Groups.csv", "PairedData.csv" and "ModelFrame.csv". Additionally, the BUGS-code ""syrphidModel.jag" is required for running the daily-activity model in JAGS. syrphidModel.jag This BUGS-code is required for running the daily-activity model in JAGS.

opencc-by-4.0Dec 2020View details →

Evolutionary coupling range varies widely among enzymes: data and code

Data and code needed to reproduce result of the paper "Evolutionary coupling range varies widely among enzymes", by J. Echave. biorxiv: https://doi.org/10.1101/2020.12.19.423588

opencc-by-4.0Jan 2021View details →

Data and codes for "A cryogenic electro-optic interconnect for superconducting devices"

Here you find all raw data files and processing Python scripts for plots presented in "A cryogenic electro-optic interconnect for superconducting devices" Amir Youssefi, et.al. Nature Electronics 2021