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

PloS One
Oleguer Plana-RipollPer Kragh Andersen

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 interva...Continue Reading

References

May 19, 2011·Circulation. Cardiovascular Quality and Outcomes·Urania Dafni
Jul 11, 2013·Statistics in Medicine·P K Andersen
Dec 10, 2013·Annual Review of Clinical Psychology·Thomas Munk LaursenPreben Bo Mortensen
Jan 7, 2015·JAMA : the Journal of the American Medical Association·Shona J LivingstoneUNKNOWN Scottish Renal Registry
Apr 8, 2015·Bipolar Disorders·Lars Vedel KessingPer Kragh Andersen
May 20, 2015·BMC Cancer·Therese M-L AnderssonPaul C Lambert
Jan 17, 2016·Journal of Affective Disorders·Thomas Munk LaursenTrine Munk-Olsen
Apr 6, 2016·Diabetologia·Dennis PetriePhilip Clarke
Jun 7, 2017·Statistics in Medicine·Per Kragh Andersen
Nov 11, 2017·The Lancet. Psychiatry·Annette ErlangsenVladimir Canudas-Romo
Dec 12, 2017·Statistics in Biosciences·Hein Putter, Hans C van Houwelingen
Nov 18, 2018·Schizophrenia Research·Thomas Munk LaursenAnnette Erlangsen

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Citations

Apr 9, 2020·JAMA Psychiatry·Oleguer Plana-RipollJohn J McGrath
Sep 16, 2020·World Psychiatry : Official Journal of the World Psychiatric Association (WPA)·Oleguer Plana-RipollJohn J McGrath

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Software Mentioned

R
lillies R
ggplot2
R package lillies
simu

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