AndreaBozzo/ceres-open-data-index huggingface dataset:
Novel methods to correct for observer and sampling bias in presence-only species distribution models

Aim: While species distribution models (SDMs) are standard tools to predict species distributions, they can suffer from observation and sampling biases, particularly presence-only SDMs that often rely on species observations from non-standardized sampling efforts. To address this issue, sampling background points with a target-group strategy is commonly used, although more robust strategies and refinements could be implemented. Here, we exploited a dataset of plant species from the European Alps to propose and demonstrate efficient ways to correct for observer and sampling bias in presence-only models. 
Innovation: Recent methods correct for observer bias by using covariates related to accessibility in model calibrations (classic bias covariate correction, Classic-BCC). However, depending on how species are sampled, accessibility covariates may not sufficiently capture observer bias. Here, we introduced BCCs more directly related to sampling effort, as well as a novel corrective method based on stratified resampling of the observational dataset before model calibration (environmental bias correction, EBC). We compared, individually and jointly, the effect of EBC and different BCC strategies, when modelling the distributions of 1’900 plant species. We evaluated model performance with spatial block split-sampling and independent test data, and assessed the accuracy of plant diversity predictions across the European Alps.
Main conclusions: Implementing EBC with BCC showed best results for every evaluation method. Particularly, adding the observation density of a target group as bias covariate (Target-BCC) displayed most realistic modelled species distributions, with a clear positive correlation (r≃0.5) found between predicted and expert-based species richness. Although EBC must be carefully implemented in a species-specific manner, such limitations may be addressed via automated diagnostics included in a provided R function. Implementing EBC and bias covariate correction together may allow future studies to address efficiently observer bias in presence-only models, and overcome the standard need of an independent test dataset for model evaluation.

Tags: background-data, cluster, covariate-correction, environmental-stratification, independent-dataset, plant-species, point-process-model, random-stratified-sampling, survey-effort, target-group
Resolution in species distribution models shapes spatial patterns of plant multifaceted diversity

This dataset comprises a large array of ecological data for the European Alps:
    (1) Current soil and climate predictors at various resolutions.
    (2) GBIF observations of the European Alps Flora (~4,000 species).
    (3) Species habitat suitability maps (1,109 species; based on species observations filtered at 40x40-km)
    at various resolutions used in the study to generate (4); except 'expert'...
    (4) Expert, Taxonomic, phylogenetic and functional diversity of the study region at various resolutions
    (from 100-m to 40-km --- 100-m aggregated & mean to km + non-aggregated/predicted) for CLIM,
    SOIL and CLIM-SOIL models.
    (5) Ecological and altitudinal preferences of the European Alps Flora.
    (6) Data outputs of the related published article.
    (7) All scripts used for analyses.
    (8) Additional files used for analyses.
    (9) Improved set of species habitat suitability maps (~2,600 species; based on species observations
    filtered at 1x1-km) and related taxonomic diversity at 100-m resolution (aggregated to km +
    non-aggregated/predicted) for CLIM, SOIL and CLIM-SOIL models ---- not incorporated in the study.

Tags: climate, ecological-indicator-values, functional-diversity, grain-size, phylogenetic-diversity, soil, taxonomic-diversity
Light exposure reshapes photosynthetic thermal tolerance curves, with idiosyncratic responses across 36 species.

Photosynthetic thermal tolerance estimates for 36 tropical species following the static water bath method and measuring maximum quantum yield (Fv/Fm). Thermal tolerance assays were performed once each in near-darkness (~4 μmol photons m^-2 s^-1) and in sub-saturating light (280 μmol photos m^-2 s^-1).

Tags: chlorophyll-fluorescence, irradiance, photoinhibition, photosystem-ii, tcrit, thermal-tolerance, tropical-plants
Niche partitioning between wild bees and honeybees

Cities are socio-ecological systems that filter and select species, thus establishing unique species assemblages and biotic interactions. Urban ecosystems can host richer wild bee communities than highly intensified agricultural areas, specifically in resource-rich urban green spaces such as allotment and family gardens. At the same time, urban beekeeping has boomed in many European cities, raising concerns that the fast addition of a large number of managed bees could deplete the existing floral resources, triggering competition between wild bees and honeybees. The data has been used to investigated the interplay between resource availability and the number of honeybees at local and landscape scales and how this relationship influences wild bee diversity.
This dataset contains the raw and processed data supporting the findings from the paper: "Low resource availability drives feeding niche partitioning between wild bees and honeybees in a European city". 
The data contains:  
1. Bee trait measurements at the species and individual-level  of five functional traits.  
2. The values of the feeding niche partitioning (functional dissimilarity to honeybees)   
3. The predictors of resource availability and beekeeping intensity at local and landscape scales used in the modelling of the paper for the 23 experimental sites.

Tags: beekeeping, bettergardens, city4bees, gardens, honeybees, pollinator-experiment, resource-availability, urban-biodiversity, urban-ecosystems, urbanization, wild-bees, zurich
3D_Snow_Models

The dataset contains several snow models in the Standard Tesselated Geometry File Format (stl) for 3D visualization, printing and additive manufacturing. Different snow types are available (new snow, rounded snow, depth hoar, buried surface hoar, graupel).

Tags: 3d-model, 3d-print, depth-hoar, new-snow, rounded-snow, snow, snow-cast, weak-layer
Electrodermal Activity (EDA) of Bi-cultural Visitors In Virtual Park Settings

This repository contains data on EDA measurements of visitors with different cultural backgrounds in virtual urban park settings. The parks are a Persian garden (Shiraz, Iran) and a historical park in Zurich, Switzerland. The cultural background of the visitors is Persian and Central European. The repository contains raw data from EDA, processed time series and statistical procedures.

Tags: electrodermal-activity, landscape, place-attachment, sense-of-place, urban-ecology
Arthropod biomass, abundance and species richness trends over 32 years in the agricultural Limpach valley, Switzerland

Recent publications about declines in arthropod biomass, abundance and species diversity
raise concerns and call for measures. Agricultural intensification is likely one cause for the negative trends. But rare long-term arthropod surveys conceal trends in arthropod communities in agricultural land. Here, we report about a standardized sampling of arthropod fauna in a Swiss agricultural landscape, repeated over 32 years (1987, 1997 and 2019). We sampled 8 sites covering 4 semi-natural and agricultural habitat types. Four trap types  were used to capture a wide range of flying and ground dwelling arthropods between May and July. Over the three sampling periods, 58’255 specimens of 1’343 species were analysed. Mean arthropod biomass, abundance and species richness per trap was significantly higher in 2019 than in prior years and gamma diversity of the study area was highest in 2019. Biomass and abundance increased stronger in the flight traps than in the pitfall traps. The implementation of agri-environmental schemes has improved habitat quality since 1993, while landscape composition and pesticide and fertilizer use remained stable over the study period, both contributing to the findings. The results of this study contrast with outcomes of comparable investigations and highlight the importance of further long-term investigations on arthropod dynamics.
Data are provided on request to contact person against bilateral agreement.

Tags: biodiversity, insect-decline, long-term, switzerland, time-series
Observed and simulated snow profile data

This data set includes information on all observed and simulated snow profiles that were used to train and validate the
random forest model described in Mayer et al. (2022). The RF model was trained to assess snow instability from simulated snow stratigraphy. The data set contains observed snow profiles from the region of Davos (DAV subset, 512 profiles) and from all over Switzerland (SWISS subset, 230 profiles). For each observed snow profile, there is a corresponding simulated profile which was obtained using meteorological input data for the numerical snow cover model SNOWPACK. The information on the observed snow profile contains a Rutschblock test result including the depth of the failure interface. As part of the study described in Mayer et al. (2022), each observed snow profile was manually compared to its simulated counterpart and the simulated layer corresponding to the Rutschblock failure layer was identified. 
The data are provided in the following form: one file each per observed and simulated snow profile (2x512 files DAV, 2x230 files SWISS), two files (1 file DAV, 1 file SWISS) containing the observed information on snow instability, the allocation between observed and simulated failure layer, and all features extracted from the simulated weak layers that were used to develop the RF model.

Tags: failure-layer, rutschblock, snow-instability, snow-profiles, snow-stratigraphy, snowpack, snowpack-simulation
Photogrammetric Drone Data Grüenbödeli

We conducted various drone flights at Grüenbödeli near Davos with the Sony RX1R II mounted on a Wingtra drone during 2020/21/22. The data was processed with the Agisoft Metashape Professional Software. 
The following products are available for download: 
- DSM 10cm resolution
- Orthomosaic 3cm/25mm resolution
- Snow Raster 10cm resolution
- original RGB images

Tags: drone-data, dsm, orthophoto, photogrammetry, snow-depth-mapping, uav, wingtra
Impact of non-native tree species in Europe on soil properties and biodiversity: a review

Compiled data on the impacts of seven important NNTs (Acacia dealbata, Ailanthus altissima, Eucalyptus globulus, Prunus serotina, Pseudotsuga menziesii, Quercus rubra, Robinia pseudoacacia) on physical and chemical soil and biodiversity in Europe, and summarise commonalities and differences. A total of 107 publications considered, studies referred to biodiversity attributes and soil properties: 2804 lines and 30 rows.

Tags: biodiversity, biogeography, forest-management, pairwise-stand-comparisons, soil-impacts
intratrait

This data set was used to test whether species specialized to high elevations or with narrow elevational ranges show more conservative (i.e. less variable) trait responses across their elevational distribution, or in response to neighbours, than species from lower elevations or with wider elevational ranges. We did so by studying intraspecific trait variation of 66 species along 40 elevational gradients in four countries (Switzerland, Australia, New Zealand, China) in both hemispheres. As an indication of potential neighbour interactions that could drive trait variation, we also analysed plant species’ height ratio, its height relative to its nearest neighbour.
The following traits and parameters were measured and are available in this data set:
As an indication of plant stature, we measured vegetative and generative height, where vegetative height was distance from soil to highest vegetative leaf and generative height was distance to the highest point on the reproductive shoot. As a measure of reproductive investment, we noted the presence of flowers on the randomly chosen individuals (see below). As a measure of individual and genet basal area, we measured individual plant and patch diameters, in two dimensions (along the largest diameter and perpendicular to it). In clonal plant species, plant diameter was equivalent to an individual rosette, whereas patch diameter referred to the whole genet and could represent the size of a tuft, tussock or cushion. For genera with more singular growth forms (e.g., some Gentiana species) plant and patch diameter were the same. The two diameter measurements were made at right angles, allowing estimates of patch and plant areas to be calculated as an ellipse (i.e., area = 0.5 a 0.5 b Π). All traits were measured on ten randomly selected individuals per site. Flower count data was considered in a binary fashion on a per individual basis (because for some species individuals only produce one flower when flowering) so that the presence or absence of flower(s) was a nominal value between 0 and 10 for each species at each site. We then collected at least three leaves (up to 30 for small and light leaves) from each of the first three individuals selected from each species for determination of leaf dry matter content (LDMC) and specific leaf area (SLA). For calculations of LDMC and SLA, fresh leaves were scanned on a flatbed scanner to determine leaf area. Leaves were then weighed on a balance to a precision of +/- 0.001g, prior to being air dried and reweighed with a balance to a precision of +/- 0.0001g. LDMC was calculated by dividing dry leaf mass by fresh leaf mass. SLA was calculated by dividing leaf area by dry leaf mass. Additionally, within an area of 10 cm diameter around the target individual, we determined the tallest neighbouring species and measured its vegetative and generative height, and estimated the percent cover of the target species, other vegetation, rock, and bare soil. 
For more details see Rixen et al. 2022, Journal of Ecology.

Tags: climate-change, cold-adapted-plants, elevation-gradient, elevation-range, neighbour-interactions, plant-traits
Running COSMO-WRF on very-high resolution over complex terrain

This is a technical documentation of the procedure to run the Weather Research and Forecasting (WRF) model over complex alpine terrain using Consortium for Small-Scale Modeling (COSMO) reanalysis by the Federal Office of Meteorology and Climatology (MeteoSwiss) as initial and boundary conditions (COMSO-WRF). The setup is adapted for very high resolution simulations based on COSMO-2 (2.2 km resolution) reanalysis. This document gives an overview over steps to setup COSMO-WRF and adaptations needed to run COSMO-WRF. Additionally, the calculation of precipitation rate at a horizontal plane and remapping COSMO-WRF output on Swiss coordinates are documented.

Tags: complex-terrain, cosmo-wrf, high-resolution, meteoswiss, numerical-simulation
Preprocessing Antarctic Weather Station (AWS) data in python

There are many sources providing atmospheric weather station data for the Antarctic continent. However, variable naming, timestamps and data types are highly variable between the different sources. The published python code intends to make processing of different AWS sources from Antarctica easier. For all datasets that are taken into account variables are renamed in a consistent way. Data from different sources can then be handled in one consistent python dictionary.
The following data sources are taken into account:
* AAD: Australian Antarctic Division (https://data.aad.gov.au/aws)
* ACECRC: Antarctic Climate and Ecosystems Cooperative Research Centre by the Australian Antarctic Division
* AMRC: Antarctic Meteorological Research Center (ftp://amrc.ssec.wisc.edu/pub/aws/q1h/)
* BAS: British Antarctic Survey (ftp://ftp.bas.ac.uk/src/ANTARCTIC_METEOROLOGICAL_DATA/AWS/; https://legacy.bas.ac.uk/met/READER/ANTARCTIC_METEOROLOGICAL_DATA/)
* CLIMANTARTIDE: Antarctic Meteo-Climatological Observatory by the italian National Programme of Antarctic Research (https://www.climantartide.it/dataaccess/index.php?lang=en)
* IMAU: Institute for Marine and Atmospheric research Utrecht (Lazzara et al., 2012), https://www.projects.science.uu.nl/iceclimate/aws/antarctica.ph
* JMA: Japan Meteorological Agency (https://www.data.jma.go.jp/antarctic/datareport/index-e.html)
* NOAA: National Oceanic and Atmospheric Administration (https://gml.noaa.gov/aftp/data/meteorology/in-situ/spo/)
* Other/AWS_PE: Princess Elisabeth (PE), KU Leuven, Prof. N. van Lipzig, personal communication
* Other/DDU_transect: Stations D-17 and D-47 (in transect between Dumont d’Urville and Dome C, Amory, 2020)
* PANGAEA: World Data Center (e.g. König-Langlo, 2012)
Important notes 
* Information about data sources is available. Some downloading scripts are included in the provided code. However, users should make sure to comply with the data providers terms and conditions.
* Given changing download options of the differnent institutions the above links may not permanently work and data has to be retrieved by the user of this dataset.
* No quality control is applied in the provided preprocessing software - quality control is up to the user of the datasets. Some dataset are quality controlled by the owner.
Acknowledgements
--------------------------
We thank all the data providers for making the data publicly available or providing them upon request. Full acknowledgements can be found in Gerber et al., submitted.
References
---------------
Amory, C. (2020). “Drifting-snow statistics from multiple-year autonomous measurements in Adélie Land, East
Antarctica”. The Cryosphere, 1713–1725. doi: 10.5194/tc-14-1713-2020
Gerber, F., Sharma, V. and Lehning, M.: CRYOWRF - a validation and the effect of blowing snow on the Antarctic SMB, JGR - Atmospheres, submitted.
König-Langlo, G. (2012). “Continuous meteorological observations at Neumayer station (2011-01)”. Alfred Wegener
Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, PANGAEA, doi: 10.1594/PANGAEA.
775173

Tags: antarctica, aws, consistent, cryowrf, python
RoRCC

The dataset "RoRCC" consists of simulation-based results on climate change impacts on Alpine RoR power production; it is based on 21 Swiss RoR power plants, with a total production of 5.9 TWh a-1. The dataset contains the following information:
1) metadata on the RoR power plants under consideration, 2) annual and seasonal production potential scenarios under into three emission scenarios (RCP2.6, RCP4.5, RCP8.5) and three future periods (T1: 2020–2049, T2: 2045–2074, T3: 2070–2099), 3) annual and seasonal streamflow scenarios, 4) annual and seasonal production loss due to environmental flow requirements, 5) annual and seasonal the technical increase potential (via design discharge optimisation) and 6) annual and seasonal changes in the hydrological cycle.

Tags: climate-change, design-discharge, environmental-flow, hydropower, run-of-river-power-plants
Stumps as a dead wood resource in forests - data based on the Swiss National Forest Inventory

Based on the detailed tree stump inventory implemented in the Swiss NFI5 (https://www.lfi.ch/lfi/lfi.php), a study was conducted to obtain an accurate assessment of the stumps pool in the Swiss NFI over the last 30 years and to identify its significance for the total dead wood (DW) pool. The NFI5 includes a detailed stump inventory to improve accuracy and completeness of the above-ground DW- pool. Based on available data, stump volume estimates were derived at different accuracies to evaluate the contribution to the total DW-pool over time.
The study found that in Swiss Forests the contribution of stumps to total DW-pool is approximately 25%, and that applying simplifying assumptions to estimate stump volume can result in a significant underestimation of the true size of this pool. This study demonstrates that stumps can be a significant proportion of DW in forests, which should be accounted for in order to improve accuracy and completeness of NFI estimates and derived data such as C stocks for greenhouse gas reporting.
The study is published in Annals of Forest Science (2022) 79:34, https://doi.org/10.1186/s13595-022-01155-7 (open access).
The data can be obtained from the authors upon reasonable request.

Tags: biodiversity, biomass, carbon, national-forest-inventory, protection-forest, volume
SnowMicroPen measurements and manual snowpits from Dronning Maud Land, East Antarctica

SnowMicroPen (SMP) measurements and manual snowpits from Dronning Maud Land, East Antarctica. Measurements were taken in the vicinity of the Belgium Princess Elisabeth Station (PEA), in a transect towards the coast, and on the Lokeryggen and Hammarryggen Ice Rises near the coast. Measurements were taken during 3 individual campaigns in the 2016-2017, 2018-2019 and 2019-2020 field seasons.

Tags: antarctica, microstructure, snow-density, snow-density-profile, snowmicropen
Relationship between physical forest characteristics, visual attractiveness and perception of ecosystem services in urban forests

This questionnaire survey was conducted as an online survey and aimed at investigating the relationship between physical forest characteristics, visual attractiveness of forest and the perception of ecological and cultural ecosystem services in urban forests. Each participant was shown 6 photos out of a pool of 50 photos taken from the Swiss National Forest Inventory (NFI) database. Physical forest characteristics were derived from the photos. The study was conducted as part of the "WaMos meets LFI" (WML) project.

Tags: adults-and-teenagers, nfi-photos, online-questionnaire-survey, perception-of-ecosystem-services, visual-attractiveness
Snow depth mapping by lidar station Braemabuel

We developed a monitoring system using low-cost lidar (Livox Avia) and optical sensors, to measure snow depth variations in an avalanche release area at a high spatiotemporal scale (centimeter to low decimeter spatial resolution and hourly temporal resolution). A detailed description of the setup and a first data analysis is published in: 
[Ruttner, P., Voordendag, A., Hartmann, T., Glaus, J., Wieser, A., & Bühler, Y. (2024). Monitoring snow depth variations in an avalanche release area using low cost lidar and optical sensors. EGUsphere, 2024, 1-20.](https://nhess.copernicus.org/articles/25/1315/2025/)
This dataset contains hourly 3D lidar data of the snow surface at the test site Braemabuel in Davos, Switzerland from the winter season 2023-2024 (23.11.2023 - 14.04.2024). Braema1 is installed at 2191 m a.s.l. in the slope, looking up into the avalache release area, and Braema2 is installed at 2255 m a.s.l at the ridge, looking down. Both scans together cover an area of about 15000 m².
The data is in format ".las" and contains the points in XYZ [m], in the scanner own coordinate system
- scalar fields: intensity, return number, timestamp, tag, label
-- tag: binary code from Livox (see [Livox Avia Manual](https://terra-1-g.djicdn.com/65c028cd298f4669a7f0e40e50ba1131/Download/Avia/Livox%20Avia%20User%20Manual%20202204.pdf))
-- label: marking outliers (filtered by distance and SOR to get snow particles in the air)

Tags: avalanche, lidar, low-cost, monitoring, snow, wind-drifted-snow
Disdrometer Data Laret

A laser optical disdrometer (Parsivel&178; , OTT Hydromet) was used to measure hydrometeors by extinction when passing a laser beam. The instrument can classify eight different kinds of precipitation, including rain, hail, snow, drizzle, and hybrid forms. 
The dataset contains information on precipitation amount and type for the period of February 7 to March 29 2019 in Laret.

Tags: disdrometer, hydrometeors, precipitation, raclets, visibility