Thomas Lumley
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View article: Lipoprotein(a) concentrations and secondary outcomes following first-time acute coronary syndrome: The Multi-Ethnic New Zealand Study of Acute Coronary Syndromes (MENZACS)
Lipoprotein(a) concentrations and secondary outcomes following first-time acute coronary syndrome: The Multi-Ethnic New Zealand Study of Acute Coronary Syndromes (MENZACS) Open
Elevated Lp(a) concentrations are associated with secondary events following ACS. Further research is needed to define optimal thresholds for increased risk and explore ethnic-specific implications for secondary prevention.
View article: Neurodegenerative Diseases in Male Former First-Class New Zealand Rugby Players
Neurodegenerative Diseases in Male Former First-Class New Zealand Rugby Players Open
Background Growing concern surrounds the risk of neurodegenerative diseases in high-level collision sports, but research on Rugby Union's connection to these diseases is limited. Objective This study sought to examine the long-term neurode…
View article: The Prognostic Value of Cardiac Troponin in a Revascularized Cohort with First-Time Myocardial Infarction
The Prognostic Value of Cardiac Troponin in a Revascularized Cohort with First-Time Myocardial Infarction Open
Introduction: The prognostic value of cardiac troponins in revascularized patients with myocardial infarction (MI) is uncertain. This study examined the relationship between peak troponin levels and adverse outcomes in a revascularized coh…
View article: A one-shot, lossless algorithm for cross-cohort learning in mixed-outcomes analysis
A one-shot, lossless algorithm for cross-cohort learning in mixed-outcomes analysis Open
In cross-cohort studies, integrating diverse datasets is essential and challenging due to cohort-specific variations, distributed data storage, and privacy concerns. Traditional methods often require data pooling or harmonization, which ca…
View article: Optimal two-phase sampling designs for generalized raking estimators with multiple parameters of interest
Optimal two-phase sampling designs for generalized raking estimators with multiple parameters of interest Open
Large observational datasets compiled from electronic health records are a valuable resource for medical research but are often affected by measurement error and misclassification. Valid statistical inference requires proper adjustment for…
View article: COLA-GLM: collaborative one-shot and lossless algorithms of generalized linear models for decentralized observational healthcare data
COLA-GLM: collaborative one-shot and lossless algorithms of generalized linear models for decentralized observational healthcare data Open
Clinical insights from real-world data often require aggregating information from institutions to ensure sufficient sample sizes and generalizability. However, patient privacy concerns only limit the sharing of patient-level data, and trad…
View article: Ascertainment Conditional Maximum Likelihood for Continuous Outcome Under Two‐Phase Response‐Selective Design
Ascertainment Conditional Maximum Likelihood for Continuous Outcome Under Two‐Phase Response‐Selective Design Open
Data collection procedures are often time‐consuming and expensive. An alternative to collecting full information from all subjects enrolled in a study is a two‐phase design: Variables that are inexpensive or easy to measure are obtained fo…
View article: Using a ‘one strain-many compounds’ (OSMAC) approach to screen a collection of diverse fungi from Aotearoa New Zealand for antibacterial activity against <i>Escherichia coli</i>
Using a ‘one strain-many compounds’ (OSMAC) approach to screen a collection of diverse fungi from Aotearoa New Zealand for antibacterial activity against <i>Escherichia coli</i> Open
There is an urgent need to identify new chemical compounds with novel modes of action to help manage the antimicrobial resistance crisis. Fungi are prolific producers of secondary metabolites, including those with antimicrobial properties,…
View article: Dietary patterns of patients with acute coronary syndrome in the multi-ethnic New Zealand study of acute coronary syndromes (MENZACS)
Dietary patterns of patients with acute coronary syndrome in the multi-ethnic New Zealand study of acute coronary syndromes (MENZACS) Open
Three distinct dietary patterns were found in patients presenting with first-time ACS in NZ and these patterns were associated with various socio-demographic and clinical factors.
View article: Statistical documentation for multi-disease, multi-domain platform trials: our experience with the Staphylococcus aureus Network Adaptive Platform trial
Statistical documentation for multi-disease, multi-domain platform trials: our experience with the Staphylococcus aureus Network Adaptive Platform trial Open
Platform trials have become widely adopted across multiple disease areas over recent years, however, guidelines for operationalising these trials have not kept pace. We outline a series of documents that summarise the statistical component…
View article: Using Days Alive and Out of Hospital to measure inequities and explore pathways through which inequities emerge after coronary artery bypass grafting in Aotearoa New Zealand: a secondary data analysis using a retrospective cohort
Using Days Alive and Out of Hospital to measure inequities and explore pathways through which inequities emerge after coronary artery bypass grafting in Aotearoa New Zealand: a secondary data analysis using a retrospective cohort Open
Objectives To describe the use of days alive and out of hospital (DAOH) as a sensitive measure of equity of outcomes after surgery by comparing outcomes after a coronary artery bypass grafts (CABG) operation between Māori and non-Māori pat…
View article: Optimum Allocation for Adaptive Multi-Wave Sampling in <i>R</i>: The <i>R</i> Package <b>optimall</b>
Optimum Allocation for Adaptive Multi-Wave Sampling in <i>R</i>: The <i>R</i> Package <b>optimall</b> Open
View article: Assessing treatment effects in observational data with missing confounders: A comparative study of practical doubly-robust and traditional missing data methods
Assessing treatment effects in observational data with missing confounders: A comparative study of practical doubly-robust and traditional missing data methods Open
In pharmacoepidemiology, safety and effectiveness are frequently evaluated using readily available administrative and electronic health records data. In these settings, detailed confounder data are often not available in all data sources a…
View article: OrigamiPlot: An R Package and Shiny Web App Enhanced Visualizations for Multivariate Data
OrigamiPlot: An R Package and Shiny Web App Enhanced Visualizations for Multivariate Data Open
We introduce OrigamiPlot, an open-source R package and Shiny web application designed to enhance the visualization of multivariate data. This package implements the origami plot, a novel visualization technique proposed by Duan et al. in 2…
View article: svyVarSel: Variable Selection for Complex Survey Data
svyVarSel: Variable Selection for Complex Survey Data Open
View article: OrigamiPlot: A Visualization Tool Enhancing Radar Plot Visualizations for Multivariate Data
OrigamiPlot: A Visualization Tool Enhancing Radar Plot Visualizations for Multivariate Data Open
Version 0.1.0
View article: Network meta‐analysis: Looping back
Network meta‐analysis: Looping back Open
This discussion contribution provides some subjective early history of network meta‐analysis and also proposes a new bipartite graph structure to better represent multi‐arm trials.
View article: RARtrials: Response-Adaptive Randomization in Clinical Trials
RARtrials: Response-Adaptive Randomization in Clinical Trials Open
Some response-adaptive randomization methods commonly found in literature are included in this package.These methods include the randomized play-the-winner rule for binary endpoint (Wei and Durham (1978) ), the doubly …
View article: Estimating the risk of SARS-CoV-2 infection in New Zealand border arrivals
Estimating the risk of SARS-CoV-2 infection in New Zealand border arrivals Open
View article: Post‐release mortality of line‐caught snapper <i>Chrysophrys auratus</i> depends on hook site and capture depth
Post‐release mortality of line‐caught snapper <i>Chrysophrys auratus</i> depends on hook site and capture depth Open
Catch‐and‐release angling is common in recreational fisheries, but post‐release mortality (PRM) may be high. We conducted a controlled field experiment to estimate mortality of released snapper Chrysophrys auratus . Recreational fishers ca…
View article: svylme: Linear Mixed Models for Complex Survey Data
svylme: Linear Mixed Models for Complex Survey Data Open
Linear mixed models for complex survey data, by pairwise composite likelihood, as described in Lumley & Huang (2023) . Supports nested and crossed random effects, and correlated random effects as in genetic m…
View article: Kumanu Tāngata: the aftermatch study – protocol to examine the health outcomes of high-level male rugby union players using linked administrative data
Kumanu Tāngata: the aftermatch study – protocol to examine the health outcomes of high-level male rugby union players using linked administrative data Open
There is increasing interest in the potential long-term outcomes of participation in contact and collision sports, driven by evidence of higher rates of neurodegenerative diseases among former athletes. Recent research has capitalised on l…
View article: Detection of IFNAR1 GLU386* loss-of-function variant in dried blood spot cards
Detection of IFNAR1 GLU386* loss-of-function variant in dried blood spot cards Open
View article: A One-Shot Lossless Algorithm for Cross-Cohort Learning in Mixed-Outcomes Analysis
A One-Shot Lossless Algorithm for Cross-Cohort Learning in Mixed-Outcomes Analysis Open
Summary In cross-cohort studies, integrating diverse datasets, such as electronic health records (EHRs), is both essential and challenging due to cohort-specific variations, distributed data storage, and data privacy concerns. Traditional …
View article: Linear mixed models for complex survey data: Implementing and evaluating pairwise likelihood
Linear mixed models for complex survey data: Implementing and evaluating pairwise likelihood Open
Summary As complex‐survey data become more widely used in health and social science research, there is increasing interest in fitting a wider range of regression models. We describe an implementation of two‐level linear mixed models in R u…
View article: Leveraging Error-Prone Algorithm-Derived Phenotypes: Enhancing Association Studies for Risk Factors in Ehr Data
Leveraging Error-Prone Algorithm-Derived Phenotypes: Enhancing Association Studies for Risk Factors in Ehr Data Open
View article: Gaussian Graphical Model Estimations in Multivariate Linear Regression: A method and applications in omics studies
Gaussian Graphical Model Estimations in Multivariate Linear Regression: A method and applications in omics studies Open
Introduction: Regression models for high-dimensional multivariate data curated from high throughput biological assays in omics, brain networks, medical imaging, and psychometric instruments contain network features. Multivariate linear reg…
View article: A blueprint for a multi-disease, multi-domain Bayesian adaptive platform trial incorporating adult and paediatric subgroups: the Staphylococcus aureus Network Adaptive Platform trial
A blueprint for a multi-disease, multi-domain Bayesian adaptive platform trial incorporating adult and paediatric subgroups: the Staphylococcus aureus Network Adaptive Platform trial Open
View article: Practical Considerations for Sandwich Variance Estimation in 2-Stage Regression Settings
Practical Considerations for Sandwich Variance Estimation in 2-Stage Regression Settings Open
In this paper, we present a practical approach for computing the sandwich variance estimator in 2-stage regression model settings. As a motivating example for 2-stage regression, we consider regression calibration, a popular approach for a…
View article: Weighted composite likelihood for linear mixed models in complex samples
Weighted composite likelihood for linear mixed models in complex samples Open
Fitting mixed models to complex survey data is a challenging problem. Most methods in the literature, including the most widely used one, require a close relationship between the model structure and the survey design. In this paper we pres…