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
Estimación del desempleo por comarcas en Navarra
(Gobierno de Navarra, Departamento de Economía y Hacienda, 2005) Ugarte Martínez, María Dolores; Militino, Ana F.; González Ramajo, Begoña; Goicoa Mangado, Tomás; Sagaseta López, M.; Estadística e Investigación Operativa; Estatistika eta Ikerketa Operatiboa
El conocimiento del desempleo en una región es un indicador potente del ritmo de crecimiento de una economía, ya que de forma indirecta mide su capacidad para generar empleo. El Instituto de Estadística de Navarra está apostando por proporcionar en un futuro cercano estimaciones del desempleo a un nivel cada vez más desagregado. La heterogeneidad de las comarcas navarras y el interés mostrado por administraciones locales y sindicatos, hace necesario tener un conocimiento de la situación de desempleo a nivel comarcal, evitando así descansar únicamente en el resultado global para toda Navarra tal y como lo proporciona la Encuesta de Población Activa (EPA). La tarea es compleja, pero está incardinada además en uno de los objetivos prioritarios del proyecto europeo EURAREA, del cual ha formado parte el Instituto Nacional de Estadística (INE), y por ende, el Instituto de Estadística de Navarra. Es decir, hay un interés real en Europa por proporcionar estimaciones a nivel comarcal. En Navarra esta tarea ya ha comenzado y en este congreso presentamos algunos de los resultados obtenidos. En particular se ilustran las estimaciones preliminares derivadas de la aplicación de diversos estimadores basados en el diseño para obtener la proporción de parados por sexo en las siete comarcas de Navarra. Se compara además el comportamiento de diversos estimadores en términos del sesgo relativo y del error cuadrático medio relativo. Los estimadores ofrecidos permiten calcular además la estimación del número de ocupados e inactivos, así como de sus correspondientes tasas.
Open Access
Temporal evolution of brain cancer incidence in the municipalities of Navarre and the Basque Country, Spain
(BioMed Central, 2015) Ugarte Martínez, María Dolores; Adin Urtasun, Aritz; Goicoa Mangado, Tomás; Casado, Itziar; Ardanaz, Eva; Larrañaga, Nerea; Estatistika eta Ikerketa Operatiboa; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística e Investigación Operativa; Gobierno de Navarra / Nafarroako Gobernua: proyecto 113 Res. 2186/2014
Background: Brain cancer incidence rates in Spain are below the European’s average. However, there are two regions in the north of the country, Navarre and the Basque Country, ranked among the European regions with the highest incidence rates for both males and females. Our objective here was two-fold. Firstly, to describe the temporal evolution of the geographical pattern of brain cancer incidence in Navarre and the Basque Country, and secondly, to look for specific high risk areas (municipalities) within these two regions in the study period (1986–2008). Methods: A mixed Poisson model with two levels of spatial effects is used. The model also included two levels of spatial effects (municipalities and local health areas). Model fitting was carried out using penalized quasi-likelihood. High risk regions were detected using upper one-sided confidence intervals. Results: Results revealed a group of high risk areas surrounding Pamplona, the capital city of Navarre, and a few municipalities with significant high risks in the northern part of the region, specifically in the border between Navarre and the Basque Country (Gipuzkoa). The global temporal trend was found to be increasing. Differences were also observed among specific risk evolutions in certain municipalities. Conclusions: Brain cancer incidence in Navarre and the Basque Country (Spain) is still increasing with time. The number of high risk areas within those two regions is also increasing. Our study highlights the need of continuous surveillance of this cancer in the areas of high risk. However, due to the low percentage of cases explained by the known risk factors, primary prevention should be applied as a general recommendation in these populations.
Open Access
Temperature and water availability during maturation affect the cytokinins and auxins profile of radiata pine somatic embryos
(Frontiers Media, 2018) Moncaleán, Paloma; García Mendiguren, Olatz; Novák, Ondrej; Strnad,Miroslav; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Montalbán, Itziar A.; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika
Somatic embryogenesis (SE) provides us a potent biotechnological tool to manipulate the physical and chemical conditions (water availability) along the process and to study their effect in the final success in terms of quantity of somatic embryos produced. In the last years, our research team has been focused on the study of different aspects of the SE in Pinus spp. One of the main aspects affecting SE is the composition of culture media; in this sense, phytohormones play one of the most crucial roles in this propagation system. Many studies in conifers have shown that different stages of SE and somatic embryo development are correlated with distinct endogenous phytohormone profiles under the stress conditions needed for the process (i.e., cytokinins play a regulatory role in stress signaling, which it is essential for radiata pine SE). Based on this knowledge, the aim of this study was to test the effect of different temperatures (18, 23, and 28°C) and gelling agent concentrations (8, 9, and 10 gL-1) during the maturation stage of Pinus radiata SE in maturation and germination rates. Parallel, phytohormone profile of somatic embryos developed was evaluated. In this sense, the highest gellan gum concentration led to significantly lower water availability. At this gellan gum concentration and 23°C a significantly higher number of somatic embryos was obtained and the overall success of the process increased with respect to other treatments assayed. The somatic embryos produced in these conditions showed the highest concentration of iP-type cytokinins and total ribosides. Although, the different conditions applied during maturation of somatic embryos led to different hormonal profiles, they did not affect the ex vitro survival of the resulting somatic plants, where no significant differences were observed.
Open Access
Small area estimation of gender-based violence: rape incidence risks in Uttar Pradesh, India
(Society of Statistics, Computer and Applications, 2018) Vicente Fuenzalida, Gonzalo; Goicoa Mangado, Tomás; Puranik, A; Ugarte Martínez, María Dolores; Estatistika eta Ikerketa Operatiboa; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística e Investigación Operativa
Violence against women is considered an endemic problem in communities and countries around the world, and it has been declared an issue of epidemic proportions by the World Health Organization (WHO). In India, where the patriarchal nature of the country contributes to increasing violence against women, there has been a dramatic increase of this gender-based violence in the past decades. In this paper we focus on analyzing rape incidence risks in the most populous state of India. In particular, small area models including spatial, temporal, and spatio-temporal components are used to estimate rape incidence risks in the districts of Uttar Pradesh during the period 2001-2014. We discover interesting spatio-temporal patterns of rape incidence as well as point out districts with significant high risks.
Open Access
Tendencias en las tasas de incidencia de cáncer colorrectal en Navarra en el periodo 1990-2005
(Gobierno de Navarra, 2012) Etxeberria Andueza, Jaione; Ugarte Martínez, María Dolores; Barricarte Gurrea, Aurelio; Goicoa Mangado, Tomás; Moreno Iribas, Conchi; Azagra, M. J.; San Roman, E.; Burgui, Rosana; Militino, Ana F.; Ardanaz, Eva; Estadística e Investigación Operativa; Estatistika eta Ikerketa Operatiboa
Fundamento. En España, se ha observado un aumento de la incidencia de cáncer colorrectal (CCR) en ambos sexos en los últimos años, posiblemente debido a las mejoras diagnósticas, a la occidentalización de la dieta y al empeoramiento de los niveles de obesidad entre otros. En este trabajo se han estudiado las tendencias de la incidencia de CCR en las diferentes áreas de salud de Navarra (norte de España) durante el período 1990-2005. Métodos. Para cada sexo y área, se obtuvieron las tendencias de las tasas de incidencia y los correspondientes intervalos de confianza mediante modelos de P-splines. Resultados. Se observa una tendencia creciente de la incidencia de CCR en la mayoría de las áreas para ambos sexos, siendo menos pronunciada en las mujeres que en los hombres. En la zona centro de Pamplona (la capital) se observa una tendencia decreciente para los hombres durante el período estudiado. Conclusiones. Para cambiar las tendencias crecientes observadas en la mayoría de las áreas de la provincia, la prevención primaria es la mejor estrategia. Sin embargo, adquirir estilos de vida saludables tiene resultados a largo plazo por lo que un programa de detección temprana serviría como estrategia de prevención a más corto plazo.
Open Access
Online relative risks/rates estimation in spatial and spatio-temporal disease mapping
(Elsevier, 2019) Adin Urtasun, Aritz; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas
Background and objective: Spatial and spatio-temporal analyses of count data are crucial in epidemiology and other fields to unveil spatial and spatio-temporal patterns of incidence and/or mortality risks. However, fitting spatial and spatio-temporal models is not easy for non-expert users. The objective of this paper is to present an interactive and user-friendly web application (named SSTCDapp) for the analysis of spatial and spatio-temporal mortality or incidence data. Although SSTCDapp is simple to use, the underlying statistical theory is well founded and all key issues such as model identifiability, model selection, and several spatial priors and hyperpriors for sensitivity analyses are properly addressed. Methods: The web application is designed to fit an extensive range of fairly complex spatio-temporal models to smooth the very often extremely variable standardized incidence/mortality risks or crude rates. The application is built with the R package shiny and relies on the well founded integrated nested Laplace approximation technique for model fitting and inference. Results: The use of the web application is shown through the analysis of Spanish spatio-temporal breast cancer data. Different possibilities for the analysis regarding the type of model, model selection criteria, and a range of graphical as well as numerical outputs are provided. Conclusions: Unlike other software used in disease mapping, SSTCDapp facilitates the fit of complex statistical models to non-experts users without the need of installing any software in their own computers, since all the analyses and computations are made in a powerful remote server. In addition, a desktop version is also available to run the application locally in those cases in which data confidentiality is a serious issue.
Open Access
A two-stage approach to estimate spatial and spatio-temporal disease risks in the presence of local discontinuities and clusters
(SAGE, 2018-04-13) Adin Urtasun, Aritz; Lee, Duncan; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Disease risk maps for areal unit data are often estimated from Poisson mixed models with local spatial smoothing, for example by incorporating random effects with a conditional autoregressive prior distribution. However, one of the limitations is that local discontinuities in the spatial pattern are not usually modelled, leading to over-smoothing of the risk maps and a masking of clusters of hot/coldspot areas. In this paper, we propose a novel two-stage approach to estimate and map disease risk in the presence of such local discontinuities and clusters. We propose approaches in both spatial and spatio-temporal domains, where for the latter the clusters can either be fixed or allowed to vary over time. In the first stage, we apply an agglomerative hierarchical clustering algorithm to training data to provide sets of potential clusters, and in the second stage, a two-level spatial or spatio-temporal model is applied to each potential cluster configuration. The superiority of the proposed approach with regard to a previous proposal is shown by simulation, and the methodology is applied to two important public health problems in Spain, namely stomach cancer mortality across Spain and brain cancer incidence in the Navarre and Basque Country regions of Spain.
Open Access
The effect of changing temperature and agar concentration at proliferation stage in the final success of Aleppo pine somatic embryogenesis
(Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), 2017) Pereira, Catia; Montalbán, Itziar A.; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Correia, Sandra; Canhoto, Jorge M.; Moncaleán, Paloma; Estadística e Investigación Operativa; Estatistika eta Ikerketa Operatiboa
Aim of the study: The effect of physical and chemical conditions at proliferation stage was evaluated in order to elucidate if this stage is the determinant phase to induce a marked effect in Pinus halepensis somatic embryogenesis. Area of study: The study was conducted in research laboratories of Neiker (Arkaute, Spain). Material and methods: Pinus halepensis embryonal masses from ten embryogenic cell lines subjected to nine treatments (tissues cultured at three temperatures on media supplemented with three agar concentrations) at proliferation stage. Main results: Significant differences were observed among different proliferation conditions months later at the end of maturation, germination and acclimatization stages. Research highlights: Aleppo pine embryonal masses are cultured under standard conditions on a culture medium supplemented with 4.5 g/L Gelrite® at 23ºC. However, better results in terms of plantlet production can be obtained proliferating the embryonal masses at 18ºC in a culture media with significantly lower water availability.
Open Access
Comments on: Modular regression - a Lego system for building structured additive distributional regression models with tensor product interactions
(Springer, 2019) Goicoa Mangado, Tomás; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas
This paper comments the article 'Modular regression - a Lego system for building structured additive distributional regression models with tensor product interactions', where the authors address the important topic of building very general models with interaction terms facing the relevant issue of identifiability.