Consistency and asymptotic normality of the maximum likelihood estimator in a zero-inflated generalized Poisson regression

Poisson regression models for count variables have been utilized in many applications. However, in many problems overdispersion and zero-inflation occur. We study in this paper regression models based on the generalized Poisson distribution (Consul (1989)). These regression models which have been used for about 15 years do not belong to the class of generalized linear models considered by (McCullagh and Nelder (1989)) for which an established asymptotic theory is available. Therefore we prove consistency and asymptotic normality of a solution to the maximum likelihood equations for zero-inflated generalized Poisson regression models. Further the accuracy of the asymptotic normality approximation is investigated through a simulation study. This allows to construct asymptotic confidence intervals and likelihood ratio tests

Testing for zero-modification in count regression models

Count data often exhibit overdispersion and/or require an adjustment for zero outcomes with respect to a Poisson model. Zero-modified Poisson (ZMP) and zero-modified generalized Poisson (ZMGP) regression models are useful classes of models for such data. In the literature so far only score tests are used for testing the necessity of this adjustment. For this testing problem we show how poor the performance of the corresponding score test can be in comparison to the performance of Wald and likelihood ratio (LR) tests through a simulation study. In particular, the score test in the ZMP case results in a power loss of 47% compared to the Wald test in the worst case, while in the ZMGP case the worst loss is 87%. Therefore, regardless of the computational advantage of score tests, the loss in power compared to the Wald and LR tests should not be neglected and these much more powerful alternatives should be used instead. We also prove consistency and asymptotic normality of the maximum likelihood estimators in the above mentioned regression models to give a theoretical justification for Wald and likelihood ratio tests

Zero-inflated generalized Poisson models with regression effects on the mean, dispersion and zero-inflation level applied to patent outsourcing rates

This paper focuses on an extension of zero-inflated generalized Poisson (ZIGP) regression models for count data. We discuss generalized Poisson (GP) models where dispersion is modelled by an additional model parameter. Moreover, zero-inflated models in which overdispersion is assumed to be caused by an excessive number of zeros are discussed. In addition to ZIGP regression introduced by Famoye and Singh (2003), we now allow for regression on the overdispersion and zero-inflation parameters. Consequently, we propose tools for an exploratory data analysis on the dispersion and zero-inflation level. An application dealing with outsourcing of patent filing processes will be used to compare these nonnested models. The model parameters are fitted by maximum likelihood. Asymptotic normality of the ML estimates in this non-exponential setting is proven. Standard errors are estimated using the asymptotic normality of the estimates. Appropriate exploratory data analysis tools are developed. Also, a model comparison using AIC statistics and Vuong tests (see Vuong (1989)) is carried out. For the given data, our extended ZIGP regression model will prove to be superior over GP and ZIP models and even ZIGP models with constant overall dispersion and zero-inflation parameters demonstrating the usefulness of our proposed extensions

Validating linear restrictions in linear regression models with general error structure

A new method for testing linear restrictions in linear regression models is suggested. It allows to validate the linear restriction, up to a specified approximation error and with a specified error probability. The test relies on asymptotic normality of the test statistic, and therefore normality of the errors in the regression model is not required. In a simulation study the performance of the suggested method for model selection purposes, as compared to standard model selection criteria and the t-test, is examined. As an illustration we analyze the US college spending data from 1994

Testing for equality between conditional copulas given discretized conditioning events

Several procedures have been recently proposed to test the simplifying assumption for conditional copulas. Instead of considering pointwise conditioning events, we study the constancy of the conditional dependence structure when some covariates belong to general borelian conditioning subsets. Several test statistics based on the equality of conditional Kendall's tau are introduced, and we derive their asymptotic distributions under the null. When such conditioning events are not fixed ex ante, we propose a data-driven procedure to recursively build such relevant subsets. It is based on decision trees that maximize the differences between the conditional Kendall's taus corresponding to the leaves of the trees. The performances of such tests are illustrated in a simulation experiment. Moreover, a study of the conditional dependence between financial stock returns is managed, given some clustering of their past values. The last application deals with the conditional dependence between coverage amounts in an insurance dataset.Comment: 28 pages, 4 figure

The Asian arowana (<i>Scleropages formosus</i>) genome provides new insights into the evolution of an early lineage of teleosts

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas

The Asian Arowana (Scleropages formosus) Genome Provides New Insights into the Evolution of an Early Lineage of Teleosts

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas

Interlaboratory study for coral Sr/Ca and other element/Ca ratio measurements

The Sr/Ca ratio of coral aragonite is used to reconstruct past sea surface temperature (SST). Twentyone laboratories took part in an interlaboratory study of coral Sr/Ca measurements. Results show interlaboratory bias can be significant, and in the extreme case could result in a range in SST estimates of 7°C. However, most of the data fall within a narrower range and the Porites coral reference material JCp- 1 is now characterized well enough to have a certified Sr/Ca value of 8.838 mmol/mol with an expanded uncertainty of 0.089 mmol/mol following International Association of Geoanalysts (IAG) guidelines. This uncertainty, at the 95% confidence level, equates to 1.5°C for SST estimates using Porites, so is approaching fitness for purpose. The comparable median within laboratory error is <0.5°C. This difference in uncertainties illustrates the interlaboratory bias component that should be reduced through the use of reference materials like the JCp-1. There are many potential sources contributing to biases in comparative methods but traces of Sr in Ca standards and uncertainties in reference solution composition can account for half of the combined uncertainty. Consensus values that fulfil the requirements to be certified values were also obtained for Mg/Ca in JCp-1 and for Sr/Ca and Mg/Ca ratios in the JCt-1 giant clam reference material. Reference values with variable fitness for purpose have also been obtained for Li/Ca, B/Ca, Ba/Ca, and U/Ca in both reference materials. In future, studies reporting coral element/Ca data should also report the average value obtained for a reference material such as the JCp-1

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15–17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype–phenotype map than previously anticipated

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

<p>Abstract</p> <p>Background</p> <p>Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, <it>Fagopyrum esculentum </it>and <it>F. tataricum</it>, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. <it>F. esculentum </it>(common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations <it>Fagopyrum </it>species have not been the subject of large-scale sequencing projects.</p> <p>Results</p> <p>Normalized cDNA corresponding to genes expressed in flowers and inflorescences of <it>F. esculentum </it>and <it>F. tataricum </it>was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for <it>F. esculentum</it>) and 229 (<it>F. tataricum</it>) thousands of reads with average length of 341-349 nucleotides. <it>De novo </it>assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences.</p> <p>Conclusions</p> <p>454 transcriptome sequencing and <it>de novo </it>assembly was performed for two congeneric flowering plant species, <it>F. esculentum </it>and <it>F. tataricum</it>. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.</p