Erratum: Variance estimation for effective coverage measures: A simulation study.
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ABSTRACT:
SUBMITTER: Leslie H
PROVIDER: S-EPMC8576354 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
Erratum: Variance estimation for effective coverage measures: A simulation study.
Journal of global health 20211115
[This corrects the article 010506 in vol. 10, PMID: 32257160.]. ...[more]
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Project description:BackgroundEffective coverage research is increasing rapidly in global health and development, as researchers use a range of measures and combine data sources to adjust coverage for the quality of services received. However, most estimates of effective coverage that combine data sources are reported only as point estimates, which may be due to the challenge of calculating the variance for a composite measure. In this paper, we evaluate three methods to quantify the uncertainty in the estimation of effective coverage.MethodsWe conducted a simulation study to evaluate the performance of the exact, delta, and parametric bootstrap methods for constructing confidence intervals around point estimates that are calculated from combined data on coverage and quality. We assessed performance by computing the number of nominally 95% confidence intervals that contain the truth for a range of coverage and quality values and data source sample sizes. To illustrate these approaches, we applied the delta and exact methods to estimates of adjusted coverage of antenatal care (ANC) in Senegal. We used household survey data for coverage and health facility assessments for readiness to provide services.ResultsWith small sample sizes, when the true effective coverage value was close to the boundaries 0 or 1, the exact and parametric bootstrap methods resulted in substantial over or undercoverage and, for the exact method, a high proportion of invalid confidence intervals, while the delta method yielded modest overcoverage. The proportion of confidence intervals containing the truth in all three methods approached the intended 95% with larger sample sizes and as the true effective coverage value moved away from the 0 or 1 boundary. Confidence intervals for adjusted ANC in Senegal were largely overlapping across the delta and exact methods, although at the sub-national level, the exact method produced invalid confidence intervals for estimates near 0 or 1. We provide the code to implement these methods.ConclusionsThe uncertainty around an effective coverage estimate can be characterized; this should become standard practice if effective coverage estimates are to become part of national and global health monitoring. The delta method approach outperformed the other methods in this study; we recommend its use for appropriate inference from effective coverage estimates that combine data sources, particularly when either sample size is small. When used for estimates created from facility type or regional strata, these methods require assumptions of independence that must be considered in each example.
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Project description:The network theory of psychopathology suggests that symptoms in a disorder form a network and that identifying central symptoms within this network might be important for an effective and personalized treatment. However, recent evidence has been inconclusive. We analyzed contemporaneous idiographic networks of depression and anxiety symptoms. Two approaches were compared: a cascade-based attack where symptoms were deactivated in decreasing centrality order, and a normal attack where symptoms were deactivated based on original centrality estimates. Results showed that centrality measures significantly affected the attack's magnitude, particularly the number of components and average path length in both normal and cascade attacks. Degree centrality consistently had the highest impact on the network properties. This study emphasizes the importance of considering centrality measures when identifying treatment targets in psychological networks. Further research is needed to better understand the causal relationships and predictive capabilities of centrality measures in personalized treatments for mental disorders.
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Project description:The efficiency of feed utilization plays an important role in animal breeding. However, measuring feed intake (FI) is costly on an individual basis under practical conditions. Using group measurements to model FI could be practically feasible and cost-effective. The objectives of this study were to develop a random regression model based on repeated group measurements with consideration of missing phenotypes caused by drop out animals. Focus is on variance components (VC) estimation and genetic evaluation, and to investigate the effect of group composition on VC estimation and genetic evaluation using simulated datasets. Data were simulated based on individual FI in a pig population. Each individual had measurement on FI at 6 different time points, reflecting 6 different weeks during the test period. The simulated phenotypes consisted of additive genetic, permanent environment, and random residual effects. Additive genetic and permanent environmental effects were both simulated and modeled by first order Legendre polynomials. Three grouping scenarios based on genetic relationships among the group members were investigated: (1) medium within and across pen genetic relationship; (2) high within group relationship; (3) low within group relationship. To investigate the effect of the drop out animals during test period, a proportion (15%) of animals with individual phenotypes was set as the drop out animals, and two drop out scenarios within each grouping scenario were assessed: (1) animals were randomly dropped out; (2) animals with lower phenotypes were dropped out based on the ranking at each time point. The results show that using group measurements yielded similar VCs estimates but with larger SDs compared with the corresponding scenario of using individual measurements. Compared to scenarios without drop out, similar VC estimates were observed when animals were dropped out randomly, whereas reduced VC estimates were observed when animals were dropped out by the ranking of phenotypes. Different grouping scenarios produced similar VC estimates. Compared to scenarios without drop out, there were no loss of accuracies of genetic evaluation for drop out scenarios. However, dropping out animals by the ranking of phenotypes produced larger bias of estimated breeding values compared to the scenario without dropped out animals and scenario of dropping out animals by random. In conclusion, with an optimized group structure, the developed model can properly handle group measurements with drop out animals, and can achieve comparable accuracy of genetic evaluation for traits measured at the group level.
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Project description:Key messageWe developed an improved variance estimation that incorporates prediction error variance as a correction factor, alongside a novel generalized effective sample size to enhance simulations. This approach enables precise control of variance components, accommodating for more flexible and accurate simulations. Phenotypic variation in field trials results from genetic and environmental factors, and understanding this variation is critical for breeding program simulations. Additive genetic variance, a key component, is often estimated using linear mixed models (LMM), but can be biased due to improper scaling of the genomic relationship matrix. Here, we show that this bias can be minimized by incorporating prediction error variance (PEV) as a correction factor. Our results demonstrate that the PEV-based estimation of additive variance significantly improves accuracy, with root mean square errors orders of magnitude lower than traditional methods. This improved accuracy enables more realistic simulations, and we introduce a novel generalized effective sample size (ESS) to further refine simulations by accounting for sampling variation. Our method outperforms standard simulation approaches, allowing flexibility to include complex interactions such as genotype by environment effects. These findings provide a robust framework for variance estimation and simulation in genetic studies, with broad applicability to breeding programs.
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Project description:[This corrects the article on p. 39 in vol. 26.].
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Project description:Error variance estimation plays an important role in statistical inference for high dimensional regression models. This paper concerns with error variance estimation in high dimensional sparse additive model. We study the asymptotic behavior of the traditional mean squared errors, the naive estimate of error variance, and show that it may significantly underestimate the error variance due to spurious correlations which are even higher in nonparametric models than linear models. We further propose an accurate estimate for error variance in ultrahigh dimensional sparse additive model by effectively integrating sure independence screening and refitted cross-validation techniques (Fan, Guo and Hao, 2012). The root n consistency and the asymptotic normality of the resulting estimate are established. We conduct Monte Carlo simulation study to examine the finite sample performance of the newly proposed estimate. A real data example is used to illustrate the proposed methodology.
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Project description:Microarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing to the small number of replications. Various methods have been proposed in the literature to overcome this lack of degrees of freedom problem. In this context, it is commonly observed that the variance increases proportionally with the intensity level, which has led many researchers to assume that the variance is a function of the mean. Here we concentrate on estimation of the variance as a function of an unknown mean in two models: the constant coefficient of variation model and the quadratic variance-mean model. Because the means are unknown and estimated with few degrees of freedom, naive methods that use the sample mean in place of the true mean are generally biased because of the errors-in-variables phenomenon. We propose three methods for overcoming this bias. The first two are variations on the theme of the so-called heteroscedastic simulation-extrapolation estimator, modified to estimate the variance function consistently. The third class of estimators is entirely different, being based on semiparametric information calculations. Simulations show the power of our methods and their lack of bias compared with the naive method that ignores the measurement error. The methodology is illustrated by using microarray data from leukaemia patients.
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Project description:Simulated oral microbiome with human contamination.
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Project description:Linear mixed models are widely used in ecological and biological applications, especially in genetic studies. Reliable estimation of variance components is crucial for using linear mixed models. However, standard methods, such as the restricted maximum likelihood (REML), are computationally inefficient in large samples and may be unstable with small samples. Other commonly used methods, such as the Haseman-Elston (HE) regression, may yield negative estimates of variances. Utilizing regularized estimation strategies, we propose the restricted Haseman-Elston (REHE) regression and REHE with resampling (reREHE) estimators, along with an inference framework for REHE, as fast and robust alternatives that provide nonnegative estimates with comparable accuracy to REML. The merits of REHE are illustrated using real data and benchmark simulation studies.
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