jomo: A Flexible Package for Two-level Joint Modelling Multiple Imputation

Quartagno, Matteo; Grund, Simon; Carpenter, James

doi:10.32614/rj-2019-028

Cited by 149 publications

(164 citation statements)

References 22 publications

(33 reference statements)

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“…For meta-analysis of participant level data, a joint modelling approach with multiple imputation (R package jomo) 31 was fitted to the colonisation data, to account for 'missing' data as a result of differences in the risk factors being collected by each individual study. Models fitted to the data assumed an initial fixed common variance matrix across all individual studies.…”

Section: Resultsmentioning

confidence: 99%

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

Smith

Wheeler

Adler

et al. 2020

Journal of Infection

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Methods: This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings: Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0-39% by conventional culture methods and 3-23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2 •30, 95% CI 1 •26-4 •21 and OR 7 •72, 95% CI 1 •15-51 •85, respectively), in those who were currently smoking (OR 1 •69, 95% CI 1 •12-2 •53) or those who had regular contact with children (OR 1 •93, 95%CI 1 •27-2 •93). Persons living in urban areas had significantly lower carriage prevalence (OR 0 •43, 95%CI 0 •27-0 •70). Interpretation: Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding: No funding was required.

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Section: Resultsmentioning

confidence: 99%

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

Smith

Wheeler

Adler

et al. 2020

Journal of Infection

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“…We used multilevel multiple imputation to impute missing data using the ‘jomo’ package in R (based on a joint multivariate normal modelling approach). 32 Auxiliary variables were total PA (log-transformed), country of birth, language spoken at home, mental health (squared WEMWBS score), BMI z-score, self-rated health, parental involvement and neighbourhood satisfaction. Our imputation model included two levels (adolescents nested in schools).…”

Section: Methodsmentioning

confidence: 99%

Longitudinal associations between neighbourhood trust, social support and physical activity in adolescents: evidence from the Olympic Regeneration in East London (ORiEL) study

Berger

Lewis

Quartagno

et al. 2020

J Epidemiol Community Health

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BackgroundMost UK adolescents do not achieve recommended levels of physical activity (PA). Previous studies suggest that the social environment could contribute to inequalities in PA behaviours, but longitudinal evidence is limited. We examined whether neighbourhood trust and social support were longitudinally associated with four common forms of PA: walking to school, walking for leisure, outdoor PA and pay and play PA. We further assessed whether gender moderated these associations.MethodsWe used longitudinal data from the Olympic Regeneration in East London (ORiEL) study. In 2012, 3106 adolescents aged 11–12 were enrolled from 25 schools in four deprived boroughs of East London, UK. Adolescents were followed-up in 2013 and 2014. The final sample includes 2664 participants interviewed at waves 2 and 3. We estimated logistic regression models using generalised estimating equations (GEEs) (pooled models) and proportional odds models (models of change) to assess associations between the social environment exposures and the PA outcomes, adjusting for potential confounders. Item non-response was handled using multilevel multiple imputation.ResultsWe found that different aspects of the social environment predict different types of PA. Neighbourhood trust was positively associated with leisure-type PA. Social support from friends and family was positively associated with walking for leisure. There was some evidence that changes in exposures led to changes in the PA outcomes. Associations did not systematically differ by gender.ConclusionThese results confirm the importance of the social environment to predict PA and its change over time in a deprived and ethnically diverse adolescent population.

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“… 78–80 In particular, we will use the R package jomo that uses Markov chain Monte Carlo techniques to draw replacements for the missing values. 81 This procedure is based on a multilevel imputation model that considers associations between continuous and categorical variables both at the level of participants (level 1) and studies (level 2). In addition, it allows for modelling between-study heterogeneity in the covariance matrices, which is especially useful when imputing variables that are completely missing from studies.…”

Section: Methodsmentioning

confidence: 99%

Efficacy and moderators of psychological interventions in treating subclinical symptoms of depression and preventing major depressive disorder onsets: protocol for an individual patient data meta-analysis of randomised controlled trials

et al. 2018

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IntroductionThe long-term effectiveness of psychological interventions for the treatment of subthreshold depression and the prevention of depression is unclear and effects vary among subgroups of patients, indicating that not all patients profit from such interventions. Randomised clinical trials are mostly underpowered to examine adequately subgroups and moderator effects. The aim of the present study is, therefore, to examine the short-term and long-term as well as moderator effects of psychological interventions compared with control groups in adults with subthreshold depression on depressive symptom severity, treatment response, remission, symptom deterioration, quality of life, anxiety and the prevention of major depressive disorder (MDD) onsets on individual patient level and study level using an individual patient data meta-analysis approach.Methods and analysisSystematic searches in PubMed, PsycINFO, Embase and the Cochrane Central Register of Controlled Trials were conducted. We will use the following types of outcome criteria: (A) onset of major depression; (B) time to major depression onset; (C) observer-reported and self-reported depressive symptom severity; (D) response; (E) remission; (F) symptom deterioration; (G) quality of life, (H) anxiety; and (I) suicidal thoughts and behaviours. Multilevel models with participants nested within studies will be used. Missing data will be handled using a joint modelling approach to multiple imputation. A number of sensitivity analyses will be conducted in order test the robustness of our findings.Ethics and disseminationThe investigators of the primary trials have obtained ethical approval for the data used in the present study and for sharing the data, if this was necessary, according to local requirements and was not covered from the initial ethic assessment.This study will summarise the available evidence on the short-term and long-term effectiveness of preventive psychological interventions for the treatment of subthreshold depression and prevention of MDD onset. Identification of subgroups of patients in which those interventions are most effective will guide the development of evidence-based personalised interventions for patients with subthreshold depression.PROSPERO registration numberCRD42017058585.

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jomo: A Flexible Package for Two-level Joint Modelling Multiple Imputation

Cited by 149 publications

References 22 publications

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

Longitudinal associations between neighbourhood trust, social support and physical activity in adolescents: evidence from the Olympic Regeneration in East London (ORiEL) study

Efficacy and moderators of psychological interventions in treating subclinical symptoms of depression and preventing major depressive disorder onsets: protocol for an individual patient data meta-analysis of randomised controlled trials

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