AndreaBozzo/ceres-open-data-index huggingface dataset:
R script and input data for "ALL-EMA sampling design"

License: GPL-v2
The R script presents an advanced sampling approach for monitoring biodiversity on agricultural land by combining multiple objectives and integrating environmental and geographic space.
The example demonstrates the first-stage selection of squares (km2) in the ALL-EMA sampling design using modern sampling techniques such as unequal probability sampling with fixed sample size, balanced sampling, stratified balancing and geographic spreading. Sampling is done with unequal probabilities and weights defined by power allocation to give equal weight to extrapolations to the total agricultural area of Switzerland and two stratifications of predefined interest (regions and agricultural production zones). Calibration is used to limit the distribution of the sampling weights. The sample sizes are almost fixed within the strata and evenly distributed across the years of a temporal rotation plan, which is favourable for the organisation of the field survey. Sampling also ensures an optimal (annual) distribution across geographic space, including altitude. Despite the complexity of the sampling, estimation based on probability theory is straightforward.
Ecker, K.T., Meier, E.S. & Tillé, Y. 2023. Integrating spatial and ecological information into comprehensive biodiversity monitoring on agricultural land. Environmental Monitoring and Assessment 195.

Tags: balanced-sampling, habitat, multi-stage, unequal-probability, vegetation
Long-term behaviour of timber constructions in torrent control

Research question / purpose
Timber is widely used for protection measures in torrent control. However, life span of woody constructions such as timber check dams is limited mainly due to fungal decay. In practice a controversial discussion has been going on if either Norway spruce (Picea abies) or silver fir (Abies alba) is more enduring and if bark removal increases resistance against fungal decay.
Description
This dataset contains monitoring information on a series of 15 timber check dams built in 1996 in Hergiswil, Switzerland. The constructions were alternatively realised with Norway spruce and silver fir, half of them each with remaining and removed bark, respectively. The data includes the identification of decayed zones with a simple practical approach (i.e. measurement of the penetration depth of a slotted screwdriver No. 3) from a total of 12 repeated surveys from 2001 to 2025. 
The following information is contained (by column and column title):
•	Identification of decayed zone (column title “Decay_Id”)
•	Year of survey (column title “Year”)
•	Identification of check dam (column title “Check dam”)
•	Degree of decay (column title “Degree of decay”): 2 = reduced wood strength (penetration depth 2-10 mm); 3 = low wood strength (penetration depth - 10 mm)
•	Sectors 1 to 7 of check dams (column title “Sector”)
•	Element of check dam (column title “Element”): LH (longitudinal log, German: “Längsholz”), Z (transverse log, German: “Zange”), FH (infill log, German: “Füllholz”)
Plan of check dams and additional information on monitoring surveys: survey information (PDF)

Tags: check-dam, fungal-decay, long-term-behaviour, timber-structure, torrent-control
Data: Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord

This dataset contains the raw environmental DNA data associated with the publication *Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord* in the journal Polar Biology (2023). 
 Methods  
 
**Sampling**
We sampled the Lilliehöök fjord on the west coast of Spitsbergen (Svalbard, Norway) over 3 days from 3 to 5 of August 2021. Samples were taken from the glacier front up to the fjord mouth of the Krossfjorden system, around 30 km long, after the Lilliehöök fjord merged with the mouth of Möller fjord. The fjord’s maximum depth has been recorded at 373 m (Svendsen et al. 2002) and has no sill at its entrance, thereby facilitating water exchange with the open ocean of the West Spitsbergen Current. We used a research vessel to sample 5 sites for a total of 15 samples, sampling 3 depths per site (3-m, chlorophyll a maximum and 85-m, unless sea floor was shallower). Shallow and intermediate samples between 3-m and 12-m represent ~35-L of water filtered in-situ using long tubing and a peristaltic pump, and all other deeper samples were taken from a total of 3 Niskin bottles (General Oceanics), representing 22-L of water sampled per sample. Water was filtered through a VigiDNA filtration capsule (SPYGEN) with a 0.20-µm pore size using an Athena peristaltic pump (Proactive Environmental Products, Bradenton, Florida) with a flow rate of ~1-L/min. Each sample was handled with single use tubing and gloves.  
**Molecular**
To perform the amplification, we used two sets of primers: teleo (forward: ACACCGCCCGTCACTCT, reverse: CTTCCGGTACACTTACCATG; Valentini et al. 2016) and the universal eukaryotic 1389F/1510R primer pair, amplifying the V9-18S rDNA gene (Amaral-Zettler et al. 2009) (forward: TTGTACACACCGCCC, reverse: CCTTCYGCAGGTTCACCTAC). 
 Data content: 
+ Metabarcoding data: This zip file contains the 2 sequencing libraries filtered to only retain the samples used in the present study. 
+ Code, data and figure: This zip file contains all data and code to reproduce the figures and the analysis in the study, with an associated README explaining the content of each folder.   
 Additional informations
For more details, please see the Methods in the associated publication: DOI: 10.1007/s00300-023-03187-9.

Tags: biodiversity, dna-metabarcoding, environmental-dna, fish, fjord, marine, plankton
Data-set for prediction of natural dry-snow avalanche activity and avalanche size using physics-based snowpack simulations

The data set contained in this repository was used in the analysis by Mayer et al. (2023):
Mayer, S. I., Techel, F., Schweizer, J., and van Herwijnen, A.: Prediction of natural dry-snow avalanche activity using physics-based snowpack simulations, EGUsphere, https://doi.org/10.5194/egusphere-2023-646, 2023.

Tags: avalanche, avalanche-size, machine-learning, natural-avalanches, snowpack-model
Data and Code on Extreme Inflow and Lowflow Analysis for Alpine Reservoirs

Summary
* Dataset of daily inflow to Luzzone reservoir in Ticino, Switzerland
* R scripts used to generate return levels for low reservoir inflow, low precipitation, high inflow, and extreme high precipitation based on various methods from extreme value analysis
 Data
The dataset included here is the "natural" reservoir inflow for the Luzzone reservoir.
Additional analyses were conducted on daily total precipitation of 6 meteorological stations (abbreviations: TIOLI, TIOLV, COM, VRN, VLS, ZEV). These precipitation data are freely available for teaching and research from the MeteoSwiss IDAweb portal (https://www.meteoswiss.admin.ch/services-and-publications/service/weather-and-climate-products/data-portal-for-teaching-and-research.html).
 Codes
R scripts used to determine return levels of the data set are included for both extreme high events and low events. The scripts include the following methods for calculating return levels:
* GEV (Generalized Extreme Value)
* GPD and GPDd (Generalized Pareto Distribution including declustered version)
* eGPD (extended Generalized Pareto Distribution)
* MEV (Metastatistical Extreme Value)

Tags: alpine-precipitation, extreme-values, low-flow, reservoir-inflow, return-periods
Synchrony between spongy moth hatching and leaf phenology of temperate trees

The files correspond to the data and R-script used for the analyses of the following paper "Feasting on the ordinary or starving for the exceptional: phenological synchrony between spongy moth and budburst of European trees in a warmer climate" published in Ecology and Evolution by Vitasse et al. 2023.
There are three zip files corresponding to the Temperature data, phenology/preference/performance tests and R-Scripts for the analyses.
Input data:
'Synchrony_Cuttings_Pheno.txt':

Tags: budburst, chilling, hatch, phenology, spongy-month
Nanoplastics in forests: Exploring the effects of nanoplastics on forest soils and tree physiology (NanoPlast)

The fate of plastic in the environment is of global concern, because its production recently has
increased strongly and it accumulates in terrestrial and aquatic ecosystems. Although some knowledge on
its role in aquatic and terrestrial ecosystems was gained in the recent decade, hitherto very little is known
about the impact of micro and nanoplastics in forest ecosystems.
The aim of this pioneering project was to explore if nanoplastics are taken up by forest trees species
through leaves or roots. In greenhouse experiments, we exposed leaves or roots of seedling of two forest
trees species to solutions with highly 13C-labelled polystyrene nanoparticles (13C-nPS, 99 atom%) and
examined if they were incorporated in different above- and belowground tissues. 
Treated part of the trees for both species showed significant 13C-enrichment, indicating that trees take up nanoparticles. However, the overall 13C signal strength in tissues that were not exposed to the 13C label remained low (Δδ13C-1‰) and was confined to a few seedlings, leaving it ambiguous whether nanoplastic transport occurs or not. 
We acknowledge that the new method developed might be not sensitive enough to unequivocally detect
mechanisms of nanoplastic uptake and transport at environmentally realistic concentrations.

Tags: 13c-labelling, forest-trees, nanoplastic, polystyrene, uptake
Seasonal snow data for Switzerland OSHD - FSM2sohd

This dataset includes gridded data on snow depth (m), snow water equivalent (mm), runoff from snow melt (mm) and snow cover fraction for Swtzerland. The data is spanning the water years 2016-2022 at a high spatial resolution of 250 m. Data are stored as daily results.

Tags: oshd, seasonal-snow-data, snow-cover-fraction, snow-depth-distribution, snow-melt
eemma.R, an R script for Ensemble End-Member Mixing Analysis

The R script eemma.R, which implements Ensemble End-Member Mixing Analysis (EEMMA) to estimate source fractions in mixtures, exploiting information contained in time-series correlations among tracer time series.
A brief user's guide, a demonstration script, and a demonstration data set are also provided, to accompany Kirchner, J.W., Mixing models with multiple, overlapping, or incomplete end-members, quantified using time series of a single tracer, Geophysical Research Letters, 2023.
The user's guide is available for public use under Creative Commons CC-BY-SA.  Public use of the scripts is permitted under GNU General Public License 3 (GPL3); for details see https://www.gnu.org/licenses/

Tags: eemma, emma, end-member-mixing-analysis, mixing-models, stable-isotopes, tracers
Fiber Bundle Model for snow failure and concurrent Acoustic Emissions

This dataset contains modeled and experimental results for laboratory snow failure experiments and the concurrent acoustic emissions signatures for different loading rates. For modelling the snow failure we used a fiber bundle model that includes sintering and viscous deformation.
The data underlay the figures in the publication "Modelling Snow Failure Behavior and Concurrent Acoustic Emissions Signatures with a Fiber Bundle Model" submitted for publication to "Geophysical Research Letters".

Tags: acoustic-emissions, fiber-bundle-model, sintering, snow, snow-avalanche, snow-failure, snow-mechanics, viscous-deformation
Raw data-Publication cross-resistance in ash - New Phytologist

What are the research data files about: Raw data on perfomance (dry weight, development and mortality) of emerald ash borer larvae used in published bioassays. Raw data on ash dieback leasion lenghts. Raw data on untargeted and targeted specialized ash metabolites.
Which methods were used: Bioassays in greenhouses and climate chambers to collect data on emerald ash borer and ash dieback perfomance. Phytochemical analyses on ash phloem for quantifiying specialized metabolites.
When and where was the data created / extracted: Summer 2020-2021

Tags: ash-dieback, cross-resistance, defense-chemistry, emerald-ash-borer, fraxinus, intraspecific-variation, invasive-species
SWE2HS model calibration and validation data

The data in this repository was used for the calibration and validation of the 
SWE2HS model in the following publication:
Aschauer, J., Michel, A., Jonas, T., & Marty, C. (2023). An empirical model to calculate snow depth from daily snow water equivalent: SWE2HS 1.0. Geoscientific Model Development Discussions, 1-19. https://doi.org/10.5194/gmd-2022-258
Contains daily snow water equivalent and snow depth timeseries from stations in the European Alps.

Tags: model-calibration-data, model-validation-data, snow-density, snow-depth, snow-water-equivalent
Glide-snow avalanche activity on Dorfberg, Davos, Switzerland

This dataset includes the processed data of the glide-snow avalanche activity and dynamics on Dorfberg (Davos, Switzerland) covering seasons 2008/09 to 2021/22. This dataset was described in the research article:
Fees, A., van Herwijnen A., Altenbach, M., Lombardo, M., Schweizer, J.: Glide-snow avalanche characteristics at different time-scales extracted from time-lapse photography, Annals of Glaciology, 91
We extracted the dynamics of opening glide-cracks and the glide-snow avalanche activity from time-lapse photographs. Glide-snow avalanches were separated into surface and interface events using the liquid water content which was simulated with SNOWPACK at 10 virtual stations on Dorfberg.

Tags: avalanche, avalanche-activity, glide-snow-avalanche, snowpack-simulation, time-lapse-photography
Tree-ring laser ablation data

This dataset contains the values of several chemical elements (Mg, Al, Si, S, K, Ca, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Sr, Tl, Pb, Bi) measured in the latewood of tree rings of Mongolian oak from Harbin, China, at a 5-year resolution. Due to the lack of a suitable reference material for wood, absolute concentration was not calculated, and the ratio between the chemical element and 13C was taken as proxy for the element signal.
In Harbin, one of the largest cities and most important industrial centers in northeastern China, air quality monitoring systems were built only by the end of 2015 to meet the national requirements. Thus, dendrochemical analyses could be used as a tool to complement for the lack of air quality data over longer periods of time, allowing for the reconstruction of the temporal trend of trace metals. Our main scopes were to: (a) assess the chemical composition of Quercus mongolica Fisch. ex Ledeb. tree rings from Harbin using a recently developed system of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), (b) identify the main chemical elements which
derived from air pollution and may be used as indicators over the period 1965–2020 in Harbin, while excluding those that were controlled by physiological processes in the tree, and (c) reconstruct the history of pollution in Harbin by comparing the tree-ring chemical composition of recent decades with that of previous decades, in trees growing in the highly polluted city of Harbin and in trees growing in a control site 90 km away from major pollution sources.
Briefly, the temporal trend of some elements was influenced by physiological factors, by environmental factors such as pollution, or influenced by both. Mg, K, Zn, Cu, Ni, Pb, As, Sr and Tl showed changes in pollution levels over time.

Tags: air-pollution, dendrochemistry, dendrochronology, laser-ablation, tree-rings
Multi-Scale Prioritization framework for Urban Blue-Green Infrastructure Planning to Support Biodiversity: Data & Codes

This data includes (1) Scripts to aggregate landscape resistance layers into squared and hexagonal grids (i.e., different representations and resolutions), (2) Input resistance layers and focal nodes in .txt format to run in Circuitscape (Python implementation v4.0.5). Circuitscape is a software tool for modeling and analyzing landscape connectivity, which simulates movement of organisms across landscapes by estimating resistance to movement across each point of the landscape. (3) Scripts for the ecological network analysis, and (4) environmental predictors for amphibian whole-life cycle habitats used to describe the local environment for BGI design (i.e. topographic, hydrologic, edaphic, vegetation, land-use derived, movement-ecology related).

Tags: biodiversity, circuit-theory, ecological-corridors, ecosystem-services, network-analysis, urban-planning
Bryophytes of Europe Traits (BET) dataset

The Bryophytes of Europe Traits (BET) dataset includes values for 65 biological and ecological traits and 25 bioclimatic variables for all 1816 bryophytes included in the European Red List (Hodgetts et al. 2019). The traits are compiled from several regional trait datasets and manually complemented using Floras, species-specific literature and expert knowledge. The bioclimatic variables are calculated using the European range of each species. Details regarding the trait compilation and extraction of bioclimatic variables can be found in the corresponding data paper (Van Zuijlen et al. 2023).

Tags: bioclimatic-variables, hornworts, indicator-values, iucn, life-history-traits, liverworts, mosses, red-list
Photogrammetric Drone Data Schürlialp

The data was collected on 16.04.2021 and on 28.05.2021 with a Wingtra Gen II and a Sony RX1 II RGB sensor to obtain snow depth and distribution data. Following the data collection, the data was processed with Agisoft Metashape. A 10cm DSM, a 10cm snow depth raster, a 3mm orthophoto and the original drone images are available for download.

Tags: drone-data, dsm, orthophoto, photogrammetry, uav, wingtra
Drivers of the microbial metabolic quotient across global grasslands

This dataset contains all data on which the following publication below is based.
Paper Citation:
Risch Anita C., Zimmermann, Stefan, Schütz, Martin, Borer, Elizabeth T., Broadbent, Arthur A.D., Caldeira, Maria C., Davies, Kendi F., Eisenhauer, Nico, Eskelinen, Anu, Fay, Philip A., Hagedorn, Frank, Knops, Johannes M.H., Lembrechts, Jonas, J., MacDougall, Andrew S., McCulley, Rebecca L., Melbourne, Brett A., Moore, Joslin L., Power, Sally A., Seabloom, Eric W., Silveira, Maria L., Virtanen, Risto, Yahdjian, Laura, Ochoa-Hueso, Raul (accepted). Drivers of the microbial metabolic quotient across global grasslands. Global Ecology and Biogeography
Please cite this paper together with the citation for the datafile.
The microbial metabolic quotient (MMQ; mg CO2-C mg MBC-1 h-1), defined as the amount of microbial CO2 respired (MR; mg CO2-C kg soil-1 h-1) per unit of microbial biomass C (MBC; mg C kg soil-1), is a key parameter for understanding the microbial regulation of the carbon (C) cycle, including soil C sequestration. Here, we experimentally tested hypotheses about the individual and interactive effects of multiple nutrient addition (NPK+micronutrients) and herbivore exclusion on MR, MBC, and MMQ across 23 sites (5 continents). Our sites encompassed a wide range of edaphoclimatic conditions, thus we assessed which edaphoclimatic variables affected MMQ the most and how they interacted with our treatments. Soils were collected in plots with established experimental treatments. MR was assessed in a five-week laboratory incubation without glucose addition, MBC via substrate-induced respiration. MMQ was calculated as MR/MBC and corrected for soil temperatures (MMQsoil). Using LMMs and SEMs, we analysed how edaphoclimatic characteristics and treatments interactively affected MMQsoil. MMQsoil was higher in locations with higher mean annual temperature, lower water holding capacity, and soil organic C concentration, but did not respond to our treatments across sites as neither MR nor MBC changed. We attributed this relative homeostasis to our treatments to the modulating influence of edaphoclimatic variables. For example, herbivore exclusion, regardless of fertilization, led to greater MMQsoil only at sites with lower soil organic C (-1.7%). Our results pinpoint the main variables related to MMQsoil across grasslands and emphasize the importance of the local edaphoclimatic conditions in controlling the response of the C cycle to anthropogenic stressors. By testing hypotheses about MMQsoil across global edaphoclimatic gradients, this work also helps to align the conflicting results of prior studies.

Tags: anthropogenic-management, climate, herbivore-exclusion, microbial-biomass-carbon, microbial-respiration, nutrient-addition, soil-properties
IceCube_microCT_Snow_grainsize

The specific surface area (SSA) of different snow types were measured with the IceCube instrument and the Scanco Medical microCT 40. In addition, the snow particles created during the preparation of IceCube samples were counted. The difference in SSA between these instruments is explained by the formation of the surface particles. A numerical simulation using TARTES simulation support the observations.

Tags: icecube, intercomparison, microct, snow, specific-surface-area
Ecological properties of urban ecosystems. Biodiversity dataset of Zurich

Richness, site occurrence and abundance data of bees, beetles, birds, hoverflies, net-wingeds, true bugs, snails, spiders, milipides, wasps collected in the city of Zurich using different sampling techniques, and the environmental variables for each sampling site.
Data are provided on request to contact person against bilateral agreement.

Tags: arthropods, birds, diversity, insects, sdms, snails, species-abundance-distributions, species-richness-models, spiders, urban-ecology, urbanization
Flowering Plants (Angiospermae) in Urban Green Areas in five European Cities

Data of a survey of flowering plants in 80 sites in five European cities and urban agglomerations (Antwerp, Belgium; greater Paris, France; Poznan, Poland; Tartu, Estonia; and Zurich, Switzerland) sampled between April and July 2018.

Tags: angiospermae, antwerp, floral-inventories, floral-resources, paris, plants, poznan, tartu, urban, zurich