COSDA-UPC - COmpositional and Spatial Data Analysis
http://hdl.handle.net/2117/79720
2024-03-29T14:59:36ZThe transitivity of the Hardy-Weinberg law
http://hdl.handle.net/2117/367135
The transitivity of the Hardy-Weinberg law
Graffelman, Jan; Weir, B.S.
The Hardy–Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.
2022-05-10T09:40:25ZGraffelman, JanWeir, B.S.The Hardy–Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.Impacto del Green Deal desde un enfoque de sistema alimentario global sostenible
http://hdl.handle.net/2117/365740
Impacto del Green Deal desde un enfoque de sistema alimentario global sostenible
Colomer Xena, Yvonne; Flotats Ripoll, Xavier; Jarauta Bragulat, Eusebio; Gil Martín, Joan Carles; Pío Beltrán, José; Clotet, Ramon; Martin, Rosa María; Romagosa, Ignacio; Savé Montserrat, Robert
El Pacto Verde corre el riesgo de acabar siendo más un cambio de formas que de fondo del sector agroalimentario europeo, si solo se plantea un cambio de sistema productivo, sin que se lleven a cabo valoraciones respecto de lo que este puede representar en aspectos cuantitativos y cualitativos y, por ende, en los agricultores y sectores asociados, más teniendo en cuenta la enorme diferencia edafoclimática y cultural de los diferentes países y regiones de la UE. Europa aspira a convertirse en líder mundial en sostenibilidad y competitividad y para conseguirlo, el sector agroalimentario deberá jugar un papel crucial, pero la Comisión Europea parece excesivamente optimista en sus planteamientos.
Este informe está alineado con la visión de sistema alimentario de Fundación Triptolemos, con la intención de contribuir, como miembro de la sociedad civil, al desarrollo de una política alimentaria integral en la UE siguiendo el dictamen del Comité Económico y Social Europeo. Cada uno de los 6 capítulos contiene al inicio una pequeña introducción. Habida cuenta de la complejidad de los temas tratados y del número de autores (30), puede suceder que un solo hecho influya en varios conceptos y pueda darse por ello, alguna repetición con enfoques diferentes.
2022-04-12T09:58:19ZColomer Xena, YvonneFlotats Ripoll, XavierJarauta Bragulat, EusebioGil Martín, Joan CarlesPío Beltrán, JoséClotet, RamonMartin, Rosa MaríaRomagosa, IgnacioSavé Montserrat, RobertEl Pacto Verde corre el riesgo de acabar siendo más un cambio de formas que de fondo del sector agroalimentario europeo, si solo se plantea un cambio de sistema productivo, sin que se lleven a cabo valoraciones respecto de lo que este puede representar en aspectos cuantitativos y cualitativos y, por ende, en los agricultores y sectores asociados, más teniendo en cuenta la enorme diferencia edafoclimática y cultural de los diferentes países y regiones de la UE. Europa aspira a convertirse en líder mundial en sostenibilidad y competitividad y para conseguirlo, el sector agroalimentario deberá jugar un papel crucial, pero la Comisión Europea parece excesivamente optimista en sus planteamientos.Problem H-888: a Fibonacci-Lucas inequality
http://hdl.handle.net/2117/365277
Problem H-888: a Fibonacci-Lucas inequality
Díaz Barrero, José Luis
(Marta G. - 25/03/2022) enviem a Clara
2022-04-05T09:07:40ZDíaz Barrero, José Luis(Marta G. - 25/03/2022) enviem a ClaraProblem B-1294: polynomials involving Fibonacci and Lucas numbers
http://hdl.handle.net/2117/365276
Problem B-1294: polynomials involving Fibonacci and Lucas numbers
Díaz Barrero, José Luis
2022-04-05T08:54:16ZDíaz Barrero, José LuisAbout a conditional inequality
http://hdl.handle.net/2117/365275
About a conditional inequality
Díaz Barrero, José Luis
2022-04-05T08:47:20ZDíaz Barrero, José LuisUsing compositional mixed-effects models to evaluate responses to amino acid supplementation in milk replacers for calves
http://hdl.handle.net/2117/360598
Using compositional mixed-effects models to evaluate responses to amino acid supplementation in milk replacers for calves
Terré, Marta; Ortuzar Fernández, Iban; Graffelman, Jan; Bassols, A; Vidal, M; Bach, Àlex
The consequences of supplementing Lys, Met, and Thr in milk replacers (MR) for calves have been widely studied, but scarce information exists about potential roles of other AA (whether essential or not). The effects on growth performance of supplementation of 4 different AA combinations in a mixed ration (25.4% crude protein and 20.3% fat) based on skim milk powder and whey protein concentrate were evaluated in 76 Holstein male calves (3 ± 1.7 d old). The 4 MR were as follows: CTRL with no AA supplementation; PG, supplying additional 0.3% Pro and 0.1% Gly; FY, supplying additional 0.2% Phe and 0.2% Tyr; and KMT, providing additional 0.62% Lys, 0.22% Met, and 0.61% Thr. All calves were fed the same milk allowance program and were weaned at 56 d of study. Concentrate intake was limited to minimize interference of potential differences in solid feed intake among treatments. Animals were weighed weekly, intakes recorded daily, and blood samples obtained at 2, 5, and 7 wk of study to determine serum urea and plasma AA concentrations. Plasma AA concentrations were explored using compositional data analysis, and their isometric log-ratio transformations were used to analyze their potential influence on ADG and serum urea concentration using a linear mixed-effects model. We detected no differences in calf performance and feed intake. Plasma relative concentration of the AA supplemented in the KMT and PG treatments increased in their respective treatments, and, in PG calves, a slight increase in the proportion of plasma Gly, Glu, and branched-chain AA was also observed. The proportions of plasma branched-chain AA, His, and Gln increased, and those of Thr, Arg, Lys, and Glu decreased with calves' age. A specific log-contrast balance formed by Arg, Thr, and Lys was found to be the main driver for lowering serum urea concentrations and increasing calf growth. The use of compositional mixed-effects models identified a cluster formed by the combination of Arg, Thr, and Lys, as a potential AA to optimize calf growth.
2022-01-25T12:40:52ZTerré, MartaOrtuzar Fernández, IbanGraffelman, JanBassols, AVidal, MBach, ÀlexThe consequences of supplementing Lys, Met, and Thr in milk replacers (MR) for calves have been widely studied, but scarce information exists about potential roles of other AA (whether essential or not). The effects on growth performance of supplementation of 4 different AA combinations in a mixed ration (25.4% crude protein and 20.3% fat) based on skim milk powder and whey protein concentrate were evaluated in 76 Holstein male calves (3 ± 1.7 d old). The 4 MR were as follows: CTRL with no AA supplementation; PG, supplying additional 0.3% Pro and 0.1% Gly; FY, supplying additional 0.2% Phe and 0.2% Tyr; and KMT, providing additional 0.62% Lys, 0.22% Met, and 0.61% Thr. All calves were fed the same milk allowance program and were weaned at 56 d of study. Concentrate intake was limited to minimize interference of potential differences in solid feed intake among treatments. Animals were weighed weekly, intakes recorded daily, and blood samples obtained at 2, 5, and 7 wk of study to determine serum urea and plasma AA concentrations. Plasma AA concentrations were explored using compositional data analysis, and their isometric log-ratio transformations were used to analyze their potential influence on ADG and serum urea concentration using a linear mixed-effects model. We detected no differences in calf performance and feed intake. Plasma relative concentration of the AA supplemented in the KMT and PG treatments increased in their respective treatments, and, in PG calves, a slight increase in the proportion of plasma Gly, Glu, and branched-chain AA was also observed. The proportions of plasma branched-chain AA, His, and Gln increased, and those of Thr, Arg, Lys, and Glu decreased with calves' age. A specific log-contrast balance formed by Arg, Thr, and Lys was found to be the main driver for lowering serum urea concentrations and increasing calf growth. The use of compositional mixed-effects models identified a cluster formed by the combination of Arg, Thr, and Lys, as a potential AA to optimize calf growth.A system for phenotype harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) program
http://hdl.handle.net/2117/359840
A system for phenotype harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) program
Stilp, Adrienne M.; Johnson, W.L.; Greiner, Alexander; Barnett, David M.; Ganesh, Sundar; Graffelman, Jan; Wengrove, Meagan E.; Srinivasan, Rajan
Genotype-phenotype association studies often combine phenotype data from multiple studies to increase statistical power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data-set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data-sharing mechanisms. This system was developed for the National Heart, Lung, and Blood Institute’s Trans-Omics for Precision Medicine (TOPMed) program, which is generating genomic and other -omics data for more than 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants (recruited in 1948–2012) from up to 17 studies per phenotype. Here we discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include 1) the software code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify, or extend these harmonizations to additional studies, and 2) the results of labeling thousands of phenotype variables with controlled vocabulary terms.
2022-01-17T11:45:07ZStilp, Adrienne M.Johnson, W.L.Greiner, AlexanderBarnett, David M.Ganesh, SundarGraffelman, JanWengrove, Meagan E.Srinivasan, RajanGenotype-phenotype association studies often combine phenotype data from multiple studies to increase statistical power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data-set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data-sharing mechanisms. This system was developed for the National Heart, Lung, and Blood Institute’s Trans-Omics for Precision Medicine (TOPMed) program, which is generating genomic and other -omics data for more than 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants (recruited in 1948–2012) from up to 17 studies per phenotype. Here we discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include 1) the software code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify, or extend these harmonizations to additional studies, and 2) the results of labeling thousands of phenotype variables with controlled vocabulary terms.Maximum-likelihood estimation of the geometric niche preemption model
http://hdl.handle.net/2117/359462
Maximum-likelihood estimation of the geometric niche preemption model
Graffelman, Jan
The geometric series or niche preemption model is an elementary ecological model in biodiversity studies. The preemption parameter of this model is usually estimated by regression or iteratively by using May’s equation. This article proposes a maximum-likelihood estimator for the niche preemption model, assuming a known number of species and multinomial sampling. A simulation study shows that the maximum-likelihood estimator outperforms the classical estimators in this context in terms of bias and precision. We obtain the distribution of the maximum-likelihood estimator and use it to obtain confidence intervals for the preemption parameter and to develop a preemption t test that can address the hypothesis of equal geometric decay in two samples. We illustrate the use of the new estimator with some empirical data sets taken from the literature and provide software for its use.
This is the peer reviewed version of the following article: Graffelman, J. Maximum-likelihood estimation of the geometric niche preemption model. "Ecosphere", Desembre 2021, vol. 12, núm. 12, p. e03834:1-e03834:12., which has been published in final form at https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.3834. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
2022-01-12T14:00:51ZGraffelman, JanThe geometric series or niche preemption model is an elementary ecological model in biodiversity studies. The preemption parameter of this model is usually estimated by regression or iteratively by using May’s equation. This article proposes a maximum-likelihood estimator for the niche preemption model, assuming a known number of species and multinomial sampling. A simulation study shows that the maximum-likelihood estimator outperforms the classical estimators in this context in terms of bias and precision. We obtain the distribution of the maximum-likelihood estimator and use it to obtain confidence intervals for the preemption parameter and to develop a preemption t test that can address the hypothesis of equal geometric decay in two samples. We illustrate the use of the new estimator with some empirical data sets taken from the literature and provide software for its use.Characterizing the evolution of the Yangtze River Delta multi-port system using compositional data techniques
http://hdl.handle.net/2117/359408
Characterizing the evolution of the Yangtze River Delta multi-port system using compositional data techniques
Huang, Dong; Grifoll Colls, Manel; Feng, Hongxiang; Ortego Martínez, María Isabel; Zheng, Pengjun
The Yangtze River Delta multi-port system (YMPS) receives increasing attention due to its relevance in world trade and excellent competitiveness in the container traffic market. To insight into the development pattern of YMPS, this paper proposes a method that combines the Hierarchical Clustering with compositional data (CoDa) exploratory tools (i.e., biplot and dendrogram) to explore the temporal and spatial evolution of the YMPS from 1992 to 2019. CoDa describes parts of some whole (i.e., frequency and percentage), conveying relative information in the ratios between its components. Container traffic share in a multi-port region is typical CoDa. Traditional statistical approaches to CoDa could lead to spurious correlations and erroneous conclusions. However, using suitable CoDa techniques, such as the centered log-ratio (clr) transformation, can effectively avoid these misinterpretations. The novel method can simultaneously find the temporal and spatial characteristics. The findings indicate that the development of the YMPS has gone through four stages and the evolution of the YMPS is characterized by a tendency towards a ‘multi-core development’ and faces a differentiated pattern of ‘peripheral port challenges’. The analysis further improves the port system’s evolutionary model and explains the underlying reason for the YMPS development. CoDa techniques also provide a new perspective for the temporal and spatial evolution of the transport discipline.
This is an Accepted Manuscript of an article published by Taylor & Francis Group in Maritime Policy & Management on Published online: 12 Sep 2021, available online at: http://www.tandfonline.com/10.1080/03088839.2021.1972175.
2022-01-12T10:53:53ZHuang, DongGrifoll Colls, ManelFeng, HongxiangOrtego Martínez, María IsabelZheng, PengjunThe Yangtze River Delta multi-port system (YMPS) receives increasing attention due to its relevance in world trade and excellent competitiveness in the container traffic market. To insight into the development pattern of YMPS, this paper proposes a method that combines the Hierarchical Clustering with compositional data (CoDa) exploratory tools (i.e., biplot and dendrogram) to explore the temporal and spatial evolution of the YMPS from 1992 to 2019. CoDa describes parts of some whole (i.e., frequency and percentage), conveying relative information in the ratios between its components. Container traffic share in a multi-port region is typical CoDa. Traditional statistical approaches to CoDa could lead to spurious correlations and erroneous conclusions. However, using suitable CoDa techniques, such as the centered log-ratio (clr) transformation, can effectively avoid these misinterpretations. The novel method can simultaneously find the temporal and spatial characteristics. The findings indicate that the development of the YMPS has gone through four stages and the evolution of the YMPS is characterized by a tendency towards a ‘multi-core development’ and faces a differentiated pattern of ‘peripheral port challenges’. The analysis further improves the port system’s evolutionary model and explains the underlying reason for the YMPS development. CoDa techniques also provide a new perspective for the temporal and spatial evolution of the transport discipline.A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles
http://hdl.handle.net/2117/343817
A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles
Graffelman, Jan; Ortoleva, Leonardo
Statistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.
2021-04-16T09:58:21ZGraffelman, JanOrtoleva, LeonardoStatistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.