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Lillies: An R package for the estimation of excess Life Years Lost among patients with a given disease or condition.

ABSTRACT: Life expectancy at a given age is a summary measure of mortality rates present in a population (estimated as the area under the survival curve), and represents the average number of years an individual at that age is expected to live if current age-specific mortality rates apply now and in the future. A complementary metric is the number of Life Years Lost, which is used to measure the reduction in life expectancy for a specific group of persons, for example those diagnosed with a specific disease or condition (e.g. smoking). However, calculation of life expectancy among those with a specific disease is not straightforward for diseases that are not present at birth, and previous studies have considered a fixed age at onset of the disease, e.g. at age 15 or 20 years. In this paper, we present the R package lillies (freely available through the Comprehensive R Archive Network; CRAN) to guide the reader on how to implement a recently-introduced method to estimate excess Life Years Lost associated with a disease or condition that overcomes these limitations. In addition, we show how to decompose the total number of Life Years Lost into specific causes of death through a competing risks model, and how to calculate confidence intervals for the estimates using non-parametric bootstrap. We provide a description on how to use the method when the researcher has access to individual-level data (e.g. electronic healthcare and mortality records) and when only aggregated-level data are available.

SUBMITTER: Plana-Ripoll O

PROVIDER: S-EPMC7059906 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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lillies: An R package for the estimation of excess Life Years Lost among patients with a given disease or condition.

Plana-Ripoll Oleguer O Canudas-Romo Vladimir V Weye Nanna N Laursen Thomas M TM McGrath John J JJ Andersen Per Kragh PK

PloS one 20200306 3

Life expectancy at a given age is a summary measure of mortality rates present in a population (estimated as the area under the survival curve), and represents the average number of years an individual at that age is expected to live if current age-specific mortality rates apply now and in the future. A complementary metric is the number of Life Years Lost, which is used to measure the reduction in life expectancy for a specific group of persons, for example those diagnosed with a specific disea ...[more]

PMID: 32142521

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Project description:BackgroundPeople with liver disease are at increased risk of developing cardiovascular disease (CVD), however, there has yet been an investigation of incidence burden, risk, and premature mortality across a wide range of liver conditions and cardiovascular outcomes.MethodsWe employed population-wide electronic health records (EHRs; from 1998 to 2020) consisting of almost 4 million adults to assess regional variations in disease burden of five liver conditions, alcoholic liver disease (ALD), autoimmune liver disease, chronic hepatitis B infection (HBV), chronic hepatitis C infection (HCV) and NAFLD, in England. We analysed regional differences in incidence rates for 17 manifestations of CVD in people with or without liver disease. The associations between biomarkers and comorbidities and risk of CVD in patients with liver disease were estimated using Cox models. For each liver condition, we estimated excess years of life lost (YLL) attributable to CVD (i.e., difference in YLL between people with or without CVD).ResultsThe age-standardised incidence rate for any liver disease was 114.5 per 100,000 person years. The highest incidence was observed in NAFLD (85.5), followed by ALD (24.7), HCV (6.0), HBV (4.1) and autoimmune liver disease (3.7). Regionally, the North West and North East regions consistently exhibited high incidence burden. Age-specific incidence rate analyses revealed that the peak incidence for liver disease of non-viral aetiology is reached in individuals aged 50-59 years. Patients with liver disease had a two-fold higher incidence burden of CVD (2634.6 per 100,000 persons) compared to individuals without liver disease (1339.7 per 100,000 persons). When comparing across liver diseases, atrial fibrillation was the most common initial CVD presentation while hypertrophic cardiomyopathy was the least common. We noted strong positive associations between body mass index and current smoking and risk of CVD. Patients who also had diabetes, hypertension, proteinuric kidney disease, chronic kidney disease, diverticular disease and gastro-oesophageal reflex disorders had a higher risk of CVD, as do patients with low albumin, raised C-reactive protein and raised International Normalized Ratio levels. All types of CVD were associated with shorter life expectancies. When evaluating excess YLLs by age of CVD onset and by liver disease type, differences in YLLs, when comparing across CVD types, were more pronounced at younger ages.ConclusionsWe developed a public online app ( https://lailab.shinyapps.io/cvd_in_liver_disease/ ) to showcase results interactively. We provide a blueprint that revealed previously underappreciated clinical factors related to the risk of CVD, which differed in the magnitude of effects across liver diseases. We found significant geographical variations in the burden of liver disease and CVD, highlighting the need to devise local solutions. Targeted policies and regional initiatives addressing underserved communities might help improve equity of access to CVD screening and treatment.

Project description:ImportanceUnited States primary school closures during the 2020 coronavirus disease 2019 (COVID-19) pandemic affected millions of children, with little understanding of the potential health outcomes associated with educational disruption.ObjectiveTo estimate the potential years of life lost (YLL) associated with the COVID-19 pandemic conditioned on primary schools being closed or remaining open.Design, setting, and participantsThis decision analytical model estimated the association between school closures and reduced educational attainment and the association between reduced educational attainment and life expectancy using publicly available data sources, including data for 2020 from the US Centers for Disease Control and Prevention, the US Social Security Administration, and the US Census Bureau. Direct COVID-19 mortality and potential increases in mortality that might have resulted if school opening led to increased transmission of COVID-19 were also estimated.Main outcomes and measuresYears of life lost.ResultsA total of 24.2 million children aged 5 to 11 years attended public schools that were closed during the 2020 pandemic, losing a median of 54 (interquartile range, 48-62.5) days of instruction. Missed instruction was associated with a mean loss of 0.31 (95% credible interval [CI], 0.10-0.65) years of final educational attainment for boys and 0.21 (95% CI, 0.06-0.46) years for girls. Summed across the population, an estimated 5.53 million (95% CI, 1.88-10.80) YLL may be associated with school closures. The Centers for Disease Control and Prevention reported a total of 88 241 US deaths from COVID-19 through the end of May 2020, with an estimated 1.50 million (95% CI, 1.23-1.85 million) YLL as a result. Had schools remained open, 1.47 million (95% credible interval, 0.45-2.59) additional YLL could have been expected as a result, based on results of studies associating school closure with decreased pandemic spread. Comparing the full distributions of estimated YLL under both "schools open" and "schools closed" conditions, the analysis observed a 98.1% probability that school opening would have been associated with a lower total YLL than school closure.Conclusions and relevanceIn this decision analytical model of years of life potentially lost under differing conditions of school closure, the analysis favored schools remaining open. Future decisions regarding school closures during the pandemic should consider the association between educational disruption and decreased expected lifespan and give greater weight to the potential outcomes of school closure on children's health.

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Lillies: An R package for the estimation of excess Life Years Lost among patients with a given disease or condition.

Publications

lillies: An R package for the estimation of excess Life Years Lost among patients with a given disease or condition.

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