Open Access
Evaluating recent methods to overcome spatial confounding
(Springer, 2022) Urdangarin Iztueta, Arantxa; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
The concept of spatial confounding is closely connected to spatial regression, although no general definition has been established. A generally accepted idea of spatial confounding in spatial regression models is the change in fixed effects estimates that may occur when spatially correlated random effects collinear with the covariate are included in the model. Different methods have been proposed to alleviate spatial confounding in spatial linear regression models, but it is not clear if they provide correct fixed effects estimates. In this article, we consider some of those proposals to alleviate spatial confounding such as restricted regression, the spatial+ model, and transformed Gaussian Markov random fields. The objective is to determine which one provides the best estimates of the fixed effects. Dowry death data in Uttar Pradesh in 2001, stomach cancer incidence data in Slovenia in the period 1995–2001 and lip cancer incidence data in Scotland between the years 1975–1980 are analyzed. Several simulation studies are conducted to evaluate the performance of the methods in different scenarios of spatial confounding. Results reflect that the spatial+ method seems to provide fixed effects estimates closest to the true value although standard errors could be inflated
Open Access
Big problems in spatio-temporal disease mapping: methods and software
(Elsevier, 2023) Orozco Acosta, Erick; Adin Urtasun, Aritz; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa, PJUPNA20001
Background and objective: Fitting spatio-temporal models for areal data is crucial in many fields such as cancer epidemiology. However, when data sets are very large, many issues arise. The main objective of this paper is to propose a general procedure to analyze high-dimensional spatio-temporal areal data, with special emphasis on mortality/incidence relative risk estimation. Methods: We present a pragmatic and simple idea that permits hierarchical spatio-temporal models to be fitted when the number of small areas is very large. Model fitting is carried out using integrated nested Laplace approximations over a partition of the spatial domain. We also use parallel and distributed strategies to speed up computations in a setting where Bayesian model fitting is generally prohibitively time-consuming or even unfeasible. Results: Using simulated and real data, we show that our method outperforms classical global models. We implement the methods and algorithms that we develop in the open-source R package bigDM where specific vignettes have been included to facilitate the use of the methodology for non-expert users. Conclusions: Our scalable methodology proposal provides reliable risk estimates when fitting Bayesian hierarchical spatio-temporal models for high-dimensional data.
Open Access
Large-scale unsupervised spatio-temporal semantic analysis of vast regions from satellite images sequences
(Springer, 2024) Echegoyen Arruti, Carlos; Pérez, Aritz; Santafé Rodrigo, Guzmán; Pérez Goya, Unai; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Temporal sequences of satellite images constitute a highly valuable and abundant resource for analyzing regions of interest. However, the automatic acquisition of knowledge on a large scale is a challenging task due to different factors such as the lack of precise labeled data, the definition and variability of the terrain entities, or the inherent complexity of the images and their fusion. In this context, we present a fully unsupervised and general methodology to conduct spatio-temporal taxonomies of large regions from sequences of satellite images. Our approach relies on a combination of deep embeddings and time series clustering to capture the semantic properties of the ground and its evolution over time, providing a comprehensive understanding of the region of interest. The proposed method is enhanced by a novel procedure specifically devised to refine the embedding and exploit the underlying spatio-temporal patterns. We use this methodology to conduct an in-depth analysis of a 220 km region in northern Spain in different settings. The results provide a broad and intuitive perspective of the land where large areas are connected in a compact and well-structured manner, mainly based on climatic, phytological, and hydrological factors.
Open Access
In spatio-temporal disease mapping models, identifiability constraints affect PQL and INLA results
(Springer, 2018) Goicoa Mangado, Tomás; Adin Urtasun, Aritz; Ugarte Martínez, María Dolores; Hodges, James S.; Institute for Advanced Materials and Mathematics - INAMAT2
Disease mapping studies the distribution of relative risks or rates in space and time, and typically relies on generalized linear mixed models (GLMMs) including fixed effects and spatial, temporal, and spatio-temporal random effects. These GLMMs are typically not identifiable and constraints are required to achieve sensible results. However, automatic specification of constraints can sometimes lead to misleading results. In particular, the penalized quasi-likelihood fitting technique automatically centers the random effects even when this is not necessary. In the Bayesian approach, the recently-introduced integrated nested Laplace approximations computing technique can also produce wrong results if constraints are not wellspecified. In this paper the spatial, temporal, and spatiotemporal interaction random effects are reparameterized using the spectral decompositions of their precision matrices to establish the appropriate identifiability constraints. Breast cancer mortality data from Spain is used to illustrate the ideas.
Open Access
Interpolation of the mean anomalies for cloud filling in land surface temperature and normalized difference vegetation index
(IEEE, 2019) Militino, Ana F.; Ugarte Martínez, María Dolores; Pérez Goya, Unai; Genton, Marc G.; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas
When monitoring time series of remote sensing data, it is advisable to fill gaps, i.e., missing or distorted data, caused by atmospheric effects or technical failures. In this paper, a new method for filling these gaps called interpolation of the mean anomalies (IMA) is proposed and compared with some competitors. The method consists of: 1) defining a neighborhood for the target image from previous and subsequent images across previous and subsequent years; 2) computing the mean target image of the neighborhood; 3) estimating the anomalies in the target image by subtracting the mean image from the target image; 4) filtering the anomalies; 5) averaging the anomalies over a predefined window; 6) interpolating the averaged anomalies; and 7) adding the interpolated anomalies to the mean image. To assess the performance of the IMA method, both a real example and a simulation study are conducted with a time series of Moderate Resolution Imaging Spectroradiometer (MODIS) TERRA and MODIS AQUA images captured over the region of Navarre (Spain) from 2011 to 2013. We analyze the land surface temperature (LST) day and night, and the normalized difference vegetation index (NDVI). In the simulation study, seven sizes of artificial clouds are randomly introduced to each image in the studied time series. The square root of the mean-squared prediction error (RMSE) between the original and the filled data is chosen as an indicator of the goodness of fit. The results show that the IMA method outperforms Timesat, Hants, and Gapfill (GF) in filling small, moderate, and big cloud gaps in both the day and night LST and NDVI data, reaching RMSE reductions of up to 23%.
Open Access
Hybrid pine (Pinus attenuata × Pinus radiata) somatic embryogenesis: what do you prefer, mother or nurse?
(MDPI, 2021) Montalbán, Itziar A.; Castander Olarieta, Ander; Hargreaves, Cathy L.; Gough, Keiko; Reeves, Cathie B.; Ballekom, Shaf van; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Moncaleán, Paloma; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Development of hybrid pines of Pinus radiata D. Don for commercial forestry presents an opportunity to diversify the current resource of plant material. Climate change and different land uses pose challenges, making alternative species necessary to guarantee wood and non-wood products in the future. Pinus radiata var. cedrosensis × Pinus attenuata hybrid possesses different attributes, such as tolerance to drought conditions, better growth and resistance to snow damage at higher altitudes, and more importantly, different wood quality characteristics. Embryogenic cell lines were successfully initiated reciprocal hybrids using as initial explants megagametophytes, excised zygotic embryos and excised zygotic embryos plus nurse culture. However, the questions raised were: does the initiation environment affect the conversion to somatic plantlets months later? Does the mother tree or the cross have an effect on the conversion to somatic plantlets? In the present work we analysed the maturation rate, number of somatic embryos, germination rate, and the ex-vitro growth in cell lines derived from different initiation treatments, mother tree species, and crosses. Differences were not observed for in vitro parameters such as maturation and germination. However, significant differences were observed due to the mother tree species in relation with the ex-vitro growth rates observed, being higher those in which P. radiata acted as a mother. Moreover, embryogenic cell lines from these hybrids were stored at −80◦C and regenerated after one and five years.
Open Access
Improving the quality of satellite imagery based on ground-truth data from rain gauge stations
(MDPI, 2018) Militino, Ana F.; Ugarte Martínez, María Dolores; Pérez Goya, Unai; Estatistika eta Ikerketa Operatiboa; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística e Investigación Operativa; Gobierno de Navarra / Nafarroako Gobernua
Multitemporal imagery is by and large geometrically and radiometrically accurate, but the residual noise arising from removal clouds and other atmospheric and electronic effects can produce outliers that must be mitigated to properly exploit the remote sensing information. In this study, we show how ground-truth data from rain gauge stations can improve the quality of satellite imagery. To this end, a simulation study is conducted wherein different sizes of outlier outbreaks are spread and randomly introduced in the normalized difference vegetation index (NDVI) and the day and night land surface temperature (LST) of composite images from Navarre (Spain) between 2011 and 2015. To remove outliers, a new method called thin-plate splines with covariates (TpsWc) is proposed. This method consists of smoothing the median anomalies with a thin-plate spline model, whereby transformed ground-truth data are the external covariates of the model. The performance of the proposed method is measured with the square root of the mean square error (RMSE), calculated as the root of the pixel-by-pixel mean square differences between the original data and the predicted data with the TpsWc model and with a state-space model with and without covariates. The study shows that the use of ground-truth data reduces the RMSE in both the TpsWc model and the state-space model used for comparison purposes. The new method successfully removes the abnormal data while preserving the phenology of the raw data. The RMSE reduction percentage varies according to the derived variables (NDVI or LST), but reductions of up to 20% are achieved with the new proposal.
Open Access
Unpaired spatio-temporal fusion of image patches (USTFIP) from cloud covered images
(Elsevier, 2023) Goyena Baroja, Harkaitz; Pérez Goya, Unai; Montesino San Martín, Manuel; Militino, Ana F.; Wang, Qunming; Atkinson, Peter M.; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Spatio-temporal image fusion aims to increase the frequency and resolution of multispectral satellite sensor images in a cost-effective manner. However, practical constraints on input data requirements and computational cost prevent a wider adoption of these methods in real case-studies. We propose an ensemble of strategies to eliminate the need for cloud-free matching pairs of satellite sensor images. The new methodology called Unpaired Spatio-Temporal Fusion of Image Patches (USTFIP) is tested in situations where classical requirements are progressively difficult to meet. Overall, the study shows that USTFIP reduces the root mean square error by 2-to-13% relative to the state-of-the-art Fit-FC fusion method, due to an efficient use of the available information. Implementation of USTFIP through parallel computing saves up to 40% of the computational time required for Fit-FC.
Open Access
Machine learning procedures for daily interpolation of rainfall in Navarre (Spain)
(Springer, 2023) Militino, Ana F.; Ugarte Martínez, María Dolores; Pérez Goya, Unai; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Kriging is by far the most well known and widely used statistical method for interpolating data in spatial random fields. The main reason is that it provides the best linear unbiased predictor and it is an exact interpolator when normality is assumed. The robustness of this method allows small departures from normality, however, many meteorological, pollutant and environmental variables have extremely asymmetrical distributions and Kriging cannot be used. Machine learning techniques such as neural networks, random forest, and k-nearest neighbor can be used instead, because they do not require specific distributional assumptions. The drawback is that they do not take account of the spatial dependence, and for an optimal performance in spatial random fields more complex machine learning techniques could be considered. These techniques also require a relatively large amount of training data and they are computationally challenging to implement. For a reduced number of observations, we illustrate the performance of the aforementioned procedures using daily rainfall data of manual meteorological gauge stations in Navarre, where the only auxiliary variables available are the spatial coordinates and the altitude. The quality of the predictions is carefully checked through three versions of the relative root mean squared error (RRMSE). The conclusion is that when we cannot use Kriging, random forest and neural networks outperform k-nearest neighbor technique, and provide reliable predictions of rainfall daily data with scarce auxiliary information.
Open Access
Steering the synthesis of Fe3O4 nanoparticles under sonication by using a fractional factorial design
(Elsevier, 2021) Echeverría Morrás, Jesús; Moriones Jiménez, Paula; Garrido Segovia, Julián José; Ugarte Martínez, María Dolores; Cervera Gabalda, Laura María; Garayo Urabayen, Eneko; Gómez Polo, Cristina; Pérez de Landazábal Berganzo, José Ignacio; Ciencias; Zientziak; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa; Gobierno de Navarra / Nafarroako Gobernua
Superparamagnetic iron oxide nanoparticles (MNPs) have the potential to act as heat sources in magnetic hyperthermia. The key parameter for this application is the specific absorption rate (SAR), which must be as large as possible in order to optimize the hyperthermia treatment. We applied a Plackett-Burman fractional factorial design to investigate the effect of total iron concentration, ammonia concentration, reaction temperature, sonication time and percentage of ethanol in the aqueous media on the properties of iron oxide MNPs. Characterization techniques included total iron content, Fourier Transform Infrared Spectroscopy, X-Ray Diffraction, High Resolution Transmission Electron Microscopy, and Dynamic Magnetization. The reaction pathway in the coprecipitation reaction depended on the initial Fe concentration. Samples synthesized from 0.220 mol L−1 Fe yielded magnetite and metastable precipitates of iron oxyhydroxides. An initial solution made up of 0.110 mol L−1 total Fe and either 0.90 or 1.20 mol L−1 NH3(aq) led to the formation of magnetite nanoparticles. Sonication of the reaction media promoted a phase transformation of metastable oxyhydroxides to crystalline magnetite, the development of crystallinity, and the increase of specific absorption rate under dynamic magnetization.