| 1. |
- Donofrio, Claudio, et al.
(författare)
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Long-term Reproducibility for Jupyter Notebook
- 2023
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Konferensbidrag (refereegranskat)abstract
- Computational notebooks (e.g. Jupyter notebook) are a popular choice for interactive scientific computing to convey descriptive information together with executable source code. The user can annotate the scientific development of the work, the methods applied, describe ancillary data or the analysis of results, with text, illustrations, figures, and equations. Such ‘executable’ documents provide a paradigm shift in scientific writing, where not only the science is described, but the actual computation and source code are openly available and can be reproduced and validated.Therefore, it is of paramount importance to preserve these documents. A unique and persistent identification (PID) is essential together with providing enough information to execute the source code. Generating a PID for a Jupyter notebook is not technically challenging. We can automatically collect system and run-time information and, with a guided workflow for the user, assemble a rich set of metadata. The collected information allows us to recreate the computational environment and run the source code, which in return (theoretically) should produce the same results as published.The importance of providing a rich set of metadata for all digital objects in a human readable and machine actionable form is well understood and widely accepted as necessity for reproducibility, traceability, and provenance. This is reflected in the FAIR principles (Wilkinson, https://doi.org/10.1038/sdata.2016.18) which are regarded as gold standard by many scientific communities.Pimentel et al. (https://doi.org/10.1109/MSR.2019.00077) analysed over 800’000 Jupyter notebooks from GitHub. 24 % executed without errors and only 4 % produced the same results. The likelihood to successfully compile and run a decade old source code is slim. Long term support for well established operating systems varies between 5 to 10 years, user software support is usually shorter and looking at free and open-source repositories there is often no support (or best effort) offered.We present an approach to safely reproduce the computational environment in the future with a focus on long-term availability. Instead of trying to reinstall the computational environment based on the stored metadata, we propose to archive the docker image, the user space (user installed packages) and finally the source code. Recreating the system in this way is more like restoring a backup, where backup is the equivalent of an entire computer system. It does not solve all the problems but removes a great deal of complexity and uncertainty.Though there are shortcomings in our approach, we believe our solution will lower the threshold for scientists to provide rich meta data, code and results attached to a publication that can be reproduced in the far future.
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| 2. |
- Hedefalk, Finn, et al.
(författare)
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Importance of the Geocoding Level for Historical Demographic Analyses : A Case Study of Rural Parishes in Sweden, 1850–1914
- 2018
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Ingår i: Spatial Demography. - : Springer Science and Business Media LLC. - 2164-7070 .- 2364-2289. ; 6:1, s. 35-69
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Tidskriftsartikel (refereegranskat)abstract
- Geocoding longitudinal and individual-level historical demographic databases enables novel analyses of how micro-level geographic factors affected demographic outcomes over long periods. However, such detailed geocoding involves high costs. Additionally, the high spatial resolution cannot be properly utilized if inappropriate methods are used to quantify the geographic factors. We assess how different geocoding levels and methods used to define geographic variables affects the outcome of detailed spatial and historical demographic analyses. Using a longitudinal and individual-level demographic database geocoded at the property unit level, we analyse the effects of population density and proximity to wetlands on all-cause mortality for individuals who lived in five Swedish parishes, 1850–1914. We compare the results from analyses on three detailed geocoding levels using two common quantification methods for each geographic variable. Together with the method selected for quantifying the geographic factors, even small differences in positional accuracy (20–50 m) between the property units and slightly coarser geographic levels heavily affected the results of the demographic analyses. The results also show the importance of accounting for geographic changes over time. Finally, proximity to wetlands and population density affected the mortality of women and children, respectively. However, all possible determinants of mortality were not evaluated in the analyses. In conclusion, for rural historical areas, geocoding to property units is likely necessary for fine-scale analyses at distances within a few hundred metres. We must also carefully consider the quantification methods that are the most logical for the geographic context and the type of analyses.
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| 3. |
- Metcalfe, Daniel B., et al.
(författare)
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Patchy field sampling biases understanding of climate change impacts across the Arctic
- 2018
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Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:9, s. 1443-1448
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Tidskriftsartikel (refereegranskat)abstract
- Effective societal responses to rapid climate change in the Arctic rely on an accurate representation of region-specific ecosystem properties and processes. However, this is limited by the scarcity and patchy distribution of field measurements. Here, we use a comprehensive, geo-referenced database of primary field measurements in 1,840 published studies across the Arctic to identify statistically significant spatial biases in field sampling and study citation across this globally important region. We find that 31% of all study citations are derived from sites located within 50 km of just two research sites: Toolik Lake in the USA and Abisko in Sweden. Furthermore, relatively colder, more rapidly warming and sparsely vegetated sites are under-sampled and under-recognized in terms of citations, particularly among microbiology-related studies. The poorly sampled and cited areas, mainly in the Canadian high-Arctic archipelago and the Arctic coastline of Russia, constitute a large fraction of the Arctic ice-free land area. Our results suggest that the current pattern of sampling and citation may bias the scientific consensuses that underpin attempts to accurately predict and effectively mitigate climate change in the region. Further work is required to increase both the quality and quantity of sampling, and incorporate existing literature from poorly cited areas to generate a more representative picture of Arctic climate change and its environmental impacts.
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| 4. |
- Nickless, Alecia, et al.
(författare)
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Greenhouse gas observation network design for Africa
- 2020
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Ingår i: Tellus. Series B: Chemical and Physical Meteorology. - : Stockholm University Press. - 1600-0889 .- 0280-6509. ; 72:1, s. 1-30
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Tidskriftsartikel (refereegranskat)abstract
- An optimal network design was carried out to prioritise the installation or refurbishment of greenhouse gas (GHG) monitoring stations around Africa. The network was optimised to reduce the uncertainty in emissions across three of the most important GHGs: CO2, CH4, and N2O. Optimal networks were derived using incremental optimisation of the percentage uncertainty reduction achieved by a Gaussian Bayesian atmospheric inversion. The solution for CO2 was driven by seasonality in net primary productivity. The solution for N2O was driven by activity in a small number of soil flux hotspots. The optimal solution for CH4 was consistent over different seasons. All solutions for CO2 and N2O placed sites in central Africa at places such as Kisangani, Kinshasa and Bunia (Democratic Republic of Congo), Dundo and Lubango (Angola), Zoétélé (Cameroon), Am Timan (Chad), and En Nahud (Sudan). Many of these sites appeared in the CH4 solutions, but with a few sites in southern Africa as well, such as Amersfoort (South Africa). The multi-species optimal network design solutions tended to have sites more evenly spread-out, but concentrated the placement of new tall-tower stations in Africa between 10ºN and 25ºS. The uncertainty reduction achieved by the multi-species network of twelve stations reached 47.8% for CO2, 34.3% for CH4, and 32.5% for N2O. The gains in uncertainty reduction diminished as stations were added to the solution, with an expected maximum of less than 60%. A reduction in the absolute uncertainty in African GHG emissions requires these additional measurement stations, as well as additional constraint from an integrated GHG observatory and a reduction in uncertainty in the prior biogenic fluxes in tropical Africa.
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| 5. |
- Pantazatou, Karolina, et al.
(författare)
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Input data requirements for daylight simulations in urban densifications
- 2023
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Ingår i: Urban Informatics. - 2731-6963. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- One of the biggest challenges in urban densifications is securing adequate daylight access. This study examines the potential of using semantic 3D city models as input to daylight simulations. It is focusing on investigating input data requirements to these simulations from a geodata, 3D city model specification and measuring guideline perspective. To achieve this, geodata simulation input requirements for the most common daylight metrics are documented. Next, 3D city model data from two Swedish municipalities along with 3D data constructed by ourselves in CAD- and GIS-environments are utilized to explore the impact of using 3D city models of different levels of detail (LOD) and positional accuracy in daylight simulations linked to Swedish and European laws and recommendations. Similarly, the measuring guidelines and 3D city model specification requirements related to balconies and other façade accessories are also evaluated along with the utilization of façade reflectance properties and colour. It is found that LOD1 is sufficient for the obstruction angle metric for most roof types but for e.g., gabled roofs LOD2 should be used. A positional accuracy on a decimetre-level is accurate enough for the aforementioned metric. Daylight factor simulations require that balconies and façade accessories protruding more than a couple of decimetres must be represented in the 3D city model along with information on façade material and colour. The outcome of the study is expressed in the form of a list of recommendations for the creation of national profiles of 3D city models supporting daylight simulations.
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| 6. |
- Pantazatou, Karolina, et al.
(författare)
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Recommendation for Vegetation Information in Semantic 3D City Models Used in Urban Planning Applications
- 2024. - 1
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Ingår i: Recent Advances in 3D Geoinformation Science : Proceedings of the 18th 3D GeoInfo Conference - Proceedings of the 18th 3D GeoInfo Conference. - 1863-2351 .- 1863-2246. - 9783031436987 - 9783031436994 ; , s. 3-30
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Bokkapitel (refereegranskat)abstract
- Cities are growing in size and becoming increasingly dense. This situation calls for strategic planning of green infrastructure in the urban planning process. Safeguarding the green infrastructure is important for maintaining urban ecosystem services and increasing the well-being of urban populations. To facilitate appropriate urban planning that enables cities to grow sustainably, it is important that the geospatial community provides adequate vegetation information. In this study, we investigate the need for vegetation information in urban planning applications such as modelling ecosystem services and noise, as well as performing case studies of using vegetation information in daylight and solar energy simulations. Based on these investigations, we formulate a recommendation of how vegetation information should be included in 3D city models. The study is focused on the development of a Swedish national profile of CityGML, but many of the conclusions are general and universally applicable. In short, the recommendations are that: (1) the vegetation theme should follow CityGML 3.0 with some additional attributes (e.g., popular name of tree species) added as an application domain extension, (2) no LOD division is required for the vegetation information stored (but rather derived if necessary), (3) the vegetation theme should only contain 3D vegetation objects while the 2D vegetation is part of the land cover theme, and (4) the building specification (and city furniture specification) must include the possibility to store information on whether building roofs or facades (and walls) are covered with vegetation.
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| 7. |
- Pantazatou, Karolina, et al.
(författare)
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The influence of geocoding level and definition of geographic context variables on historical demographic analyses
- 2016
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Ingår i: ; , s. 1-5
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Konferensbidrag (refereegranskat)abstract
- The quality of spatial analysis is highly dependent on the geo-referencing quality and the definition of the geographic context variables used. However, such information is seldom considered in historical demographic and epidemiological research that includes the geographic context. We investigate a suitable geographic level for geocoding of the population and definition of geographic context variables for historical demographic studies. Using longitudinal demographic data combined with unique historical geographic microdata on residential histories, we compare two geocoding levels (property unit and address unit) and two definitions of distance to wetlands (an indicator of exposure to malaria in the 19th century Sweden). We first statistically compare the differences in the distance to wetlands between the two geocoding levels. Thereafter, by analysing how distance to wetlands affected the mortality of children aged 1-15 living in four rural parishes in Sweden, 1850-1914, we study the effect of different geocoding levels and definitions of context variables on the quality of historical demographic analysis. We find that both the geocoding level and the definition of the geographic context variables strongly influence the results of the analyses. For the distance to wetland variable, decreasing its average positional accuracy by at least 100 meters affects the results. Consequently, the significant differences between the two geocoding levels indicate the importance of considering the geographic level of detail when geocoding
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| 8. |
- Uggla, Maria, et al.
(författare)
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Future Swedish 3D City Models : Specifications, Test Data, and Evaluation
- 2023
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Ingår i: ISPRS International Journal of Geo-Information. - : MDPI AG. - 2220-9964. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional city models are increasingly being used for analyses and simulations. To enable such applications, it is necessary to standardise semantically richer city models and, in some cases, to connect the models with external data sources. In this study, we describe the development of a new Swedish specification for 3D city models, denoted as 3CIM, which is a joint effort between the three largest cities in Sweden—Stockholm, Gothenburg, and Malmö. Technically, 3CIM is an extension of the OGC standard CityGML 2.0, implemented as an application domain extension (ADE). The ADE is semantically thin, mainly extending CityGML 2.0 to harmonise with national standards; in contrast, 3CIM is mainly based on linkages to external databases, registers, and operational systems for the semantic part. The current version, 3CIM 1.0, includes various themes, including Bridge, Building, Utility, City Furniture, Transportation, Tunnel, Vegetation, and Water. Three test areas were created with 3CIM data, one in each city. These data were evaluated in several use-cases, including visualisation as well as daylight, noise, and flooding simulations. The conclusion from these use-cases is that the 3CIM data, together with the linked external data sources, allow for the inclusion of the necessary information for the visualisation and simulations, but extract, transform, and load (ETL) processes are required to tailor the input data. The next step is to implement 3CIM within the three cities, which will entail several challenges, as discussed at the end of the paper.
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