This book is an introduction to the model-based approach to survey sampling. It consists of three parts, with Part I focusing on estimation of population totals. Chapters 1 and 2 introduce survey ...sampling, and the model-based approach, respectively. Chapter 3 considers the simplest possible model, the homogenous population model, which is then extended to stratified populations in Chapter 4. Chapter 5 discusses simple linear regression models for populations, and Chapter 6 considers clustered populations. The general linear population model is then used to integrate these results in Chapter 7. Part II of this book considers the properties of estimators based on incorrectly specified models. Chapter 8 develops robust sample designs that lead to unbiased predictors under model misspecification, and shows how flexible modelling methods like non-parametric regression can be used in survey sampling. Chapter 9 extends this development to misspecfication robust prediction variance
estimators and Chapter 10 completes Part II of the book with an exploration of outlier robust sample survey estimation. Chapters 11 to 17 constitute Part III of the book and show how model-based methods can be used in a variety of problem areas of modern survey sampling. They cover (in order) prediction of non-linear population quantities, sub-sampling approaches to prediction variance estimation, design and estimation for multipurpose surveys, prediction for domains, small area estimation, efficient prediction of population distribution functions and the use of transformations in survey inference. The book is designed to be accessible to undergraduate and graduate level students with a good grounding in statistics and applied survey statisticians seeking an introduction to model-based survey design and estimation.
It is unclear whether weighted or unweighted regression is preferred in the analysis of data derived from respondent driven sampling. Our objective was to evaluate the validity of various regression ...models, with and without weights and with various controls for clustering in the estimation of the risk of group membership from data collected using respondent-driven sampling (RDS).
Twelve networked populations, with varying levels of homophily and prevalence, based on a known distribution of a continuous predictor were simulated using 1000 RDS samples from each population. Weighted and unweighted binomial and Poisson general linear models, with and without various clustering controls and standard error adjustments were modelled for each sample and evaluated with respect to validity, bias and coverage rate. Population prevalence was also estimated.
In the regression analysis, the unweighted log-link (Poisson) models maintained the nominal type-I error rate across all populations. Bias was substantial and type-I error rates unacceptably high for weighted binomial regression. Coverage rates for the estimation of prevalence were highest using RDS-weighted logistic regression, except at low prevalence (10%) where unweighted models are recommended.
Caution is warranted when undertaking regression analysis of RDS data. Even when reported degree is accurate, low reported degree can unduly influence regression estimates. Unweighted Poisson regression is therefore recommended.
False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of ...Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .
Sample size in health research Samaranayaka, Ari; Cameron, Claire; Turner, R. M
New Zealand medical student journal,
20/Apr
32
Journal Article
Recenzirano
Odprti dostop
Explains why sample size is important in health research and when it should be considered in the research process. Delves into the two types of analyses where the sample size estimate is pivotal in ...the design of the study : where the study aims to estimate a quantity with a certain level of precision, and where the study is testing a hypothesis. Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New Zealand Licence.
Evidence regarding whether imaging can be used effectively to select patients for endovascular thrombectomy (EVT) is scarce. We aimed to investigate the association between baseline imaging features ...and safety and efficacy of EVT in acute ischaemic stroke caused by anterior large-vessel occlusion.
In this meta-analysis of individual patient-level data, the HERMES collaboration identified in PubMed seven randomised trials in endovascular stroke that compared EVT with standard medical therapy, published between Jan 1, 2010, and Oct 31, 2017. Only trials that required vessel imaging to identify patients with proximal anterior circulation ischaemic stroke and that used predominantly stent retrievers or second-generation neurothrombectomy devices in the EVT group were included. Risk of bias was assessed with the Cochrane handbook methodology. Central investigators, masked to clinical information other than stroke side, categorised baseline imaging features of ischaemic change with the Alberta Stroke Program Early CT Score (ASPECTS) or according to involvement of more than 33% of middle cerebral artery territory, and by thrombus volume, hyperdensity, and collateral status. The primary endpoint was neurological functional disability scored on the modified Rankin Scale (mRS) score at 90 days after randomisation. Safety outcomes included symptomatic intracranial haemorrhage, parenchymal haematoma type 2 within 5 days of randomisation, and mortality within 90 days. For the primary analysis, we used mixed-methods ordinal logistic regression adjusted for age, sex, National Institutes of Health Stroke Scale score at admission, intravenous alteplase, and time from onset to randomisation, and we used interaction terms to test whether imaging categorisation at baseline modifies the association between treatment and outcome. This meta-analysis was prospectively designed by the HERMES executive committee but has not been registered.
Among 1764 pooled patients, 871 were allocated to the EVT group and 893 to the control group. Risk of bias was low except in the THRACE study, which used unblinded assessment of outcomes 90 days after randomisation and MRI predominantly as the primary baseline imaging tool. The overall treatment effect favoured EVT (adjusted common odds ratio cOR for a shift towards better outcome on the mRS 2·00, 95% CI 1·69–2·38; p<0·0001). EVT achieved better outcomes at 90 days than standard medical therapy alone across a broad range of baseline imaging categories. Mortality at 90 days (14·7% vs 17·3%, p=0·15), symptomatic intracranial haemorrhage (3·8% vs 3·5%, p=0·90), and parenchymal haematoma type 2 (5·6% vs 4·8%, p=0·52) did not differ between the EVT and control groups. No treatment effect modification by baseline imaging features was noted for mortality at 90 days and parenchymal haematoma type 2. Among patients with ASPECTS 0–4, symptomatic intracranial haemorrhage was seen in ten (19%) of 52 patients in the EVT group versus three (5%) of 66 patients in the control group (adjusted cOR 3·94, 95% CI 0·94–16·49; pinteraction=0·025), and among patients with more than 33% involvement of middle cerebral artery territory, symptomatic intracranial haemorrhage was observed in 15 (14%) of 108 patients in the EVT group versus four (4%) of 113 patients in the control group (4·17, 1·30–13·44, pinteraction=0·012).
EVT achieves better outcomes at 90 days than standard medical therapy across a broad range of baseline imaging categories, including infarcts affecting more than 33% of middle cerebral artery territory or ASPECTS less than 6, although in these patients the risk of symptomatic intracranial haemorrhage was higher in the EVT group than the control group. This analysis provides preliminary evidence for potential use of EVT in patients with large infarcts at baseline.
Medtronic.
Matched sampling is often used to help assess the causal effect of some exposure or intervention, typically when randomized experiments are not available or cannot be conducted. This book presents a ...selection of Donald B. Rubin's research articles on matched sampling, from the early 1970s, when the author was one of the major researchers involved in establishing the field, to recent contributions to this now extremely active area. The articles include fundamental theoretical studies that have become classics, important extensions, and real applications that range from breast cancer treatments to tobacco litigation to studies of criminal tendencies. They are organized into seven parts, each with an introduction by the author that provides historical and personal context and discusses the relevance of the work today. A concluding essay offers advice to investigators designing observational studies. The book provides an accessible introduction to the study of matched sampling and will be an indispensable reference for students and researchers.
Multiple primary outcomes may be specified in randomised controlled trials (RCTs). When analysing multiple outcomes it's important to control the family wise error rate (FWER). A popular approach to ...do this is to adjust the p-values corresponding to each statistical test used to investigate the intervention effects by using the Bonferroni correction. It's also important to consider the power of the trial to detect true intervention effects. In the context of multiple outcomes, depending on the clinical objective, the power can be defined as: 'disjunctive power', the probability of detecting at least one true intervention effect across all the outcomes or 'marginal power' the probability of finding a true intervention effect on a nominated outcome. We provide practical recommendations on which method may be used to adjust for multiple comparisons in the sample size calculation and the analysis of RCTs with multiple primary outcomes. We also discuss the implications on the sample size for obtaining 90% disjunctive power and 90% marginal power.
We use simulation studies to investigate the disjunctive power, marginal power and FWER obtained after applying Bonferroni, Holm, Hochberg, Dubey/Armitage-Parmar and Stepdown-minP adjustment methods. Different simulation scenarios were constructed by varying the number of outcomes, degree of correlation between the outcomes, intervention effect sizes and proportion of missing data.
The Bonferroni and Holm methods provide the same disjunctive power. The Hochberg and Hommel methods provide power gains for the analysis, albeit small, in comparison to the Bonferroni method. The Stepdown-minP procedure performs well for complete data. However, it removes participants with missing values prior to the analysis resulting in a loss of power when there are missing data. The sample size requirement to achieve the desired disjunctive power may be smaller than that required to achieve the desired marginal power. The choice between whether to specify a disjunctive or marginal power should depend on the clincial objective.
In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative-or compositional-data, differential expression needs careful ...interpretation, and correlation-a statistical workhorse for analyzing pairwise relationships-is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the strength of proportionality between two variables can be meaningfully and interpretably described by a new statistic ϕ which can be used instead of correlation as the basis of familiar analyses and visualisation methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes.
The methods literature regarding sampling in qualitative research is characterized by important inconsistencies and ambiguities, which can be problematic for students and researchers seeking a clear ...and coherent understanding. In this article we present insights about sampling in qualitative research derived from a systematic methods overview we conducted of the literature from three research traditions: grounded theory, phenomenology, and case study. We identified and selected influential methods literature from each tradition using a purposeful and transparent procedure, abstracted textual data using structured abstraction forms, and used a multistep approach for deriving conclusions from the data. We organize the findings from this review into eight topic sections corresponding to the major domains of sampling identified in the review process: definitions of sampling, usage of the term sampling strategy, purposeful sampling, theoretical sampling, sampling units, saturation, sample size, and the timing of sampling decisions. Within each section we summarize how the topic is characterized in the corresponding literature, present our comparative analysis of important differences among research traditions, and offer analytic comments on the findings for that topic. We identify several specific issues with the available guidance on certain topics, representing opportunities for future methods authors to improve our collective understanding.
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in ...silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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