R for trial and model-based cost-effectiveness analysis: workshop

Background and objectives

It is our pleasure to announce a workshop and training event on the use of R for trial and model-based cost-effectiveness analysis (CEA). This follows our successful workshop on R for CEA in 2018.

Our event will begin with a half-day short course on R for decision trees and Markov models and the use of the BCEA package for graphical and statistical analysis of results; this will be delivered by Gianluca Baio of UCL and Howard Thom of Bristol University.

This will be followed by a one-day workshop in which we will present a wide variety of technical aspects by experts from academia, industry, and government institutions (including NICE). Topics will include decision trees, Markov models, discrete event simulation, integration of network meta-analysis, extrapolation of survival curves, and development of R packages.

We will include a pre-workshop virtual code challenge on a problem set by our scientific committee. This will take place over Github and a Slack channel with participants encouraged to submit final R code solutions for peer review on efficiency, flexibility, elegance and transparency. Prizes will be provided for the best entry.

Participants are also invited to submit abstracts for potential oral presentations. An optional dinner and networking event will be held on the evening of 8th July.

Registration is open until 1 June 2019 at https://onlinestore.ucl.ac.uk/conferences-and-events/faculty-of-mathematical-physical-sciences-c06/department-of-statistical-science-f61/f61-workshop-on-r-for-trial-modelbased-costeffectiveness-analysis

To submit an abstract, please send it to howard.thom@bristol.ac.uk with the subject “R for CEA abstract”. The word limit is 300. Abstract submission deadline is 15 May 2019 and the scientific committee will make decisions on acceptance by 1st June 2018.

Preliminary Programme

Day 2: Workshop. Tuesday 9th July.

  • 9:30-9:45. Howard Thom. Welcome
  • 9:45-10:15. Nathan Green. Imperial College London. _Simple, pain-free decision trees in R for the Excel user
  • 10:15-10:35 Pedro Saramago. Centre for Health Economics, University of York. Using R for Markov modelling: an introduction
  • 10:35-10:55. Alison Smith. University of Leeds. Discrete event simulation models in R
  • 10:55-11:10. Coffee
  • 11:10-12:20. Participants oral presentation session (4 speakers, 15 minutes each)
  • 12:20-13:45. Lunch
  • 13:45-14:00. Gianluca Baio. University College London. Packing up, shacking up’s (going to be) all you wanna do!. Building packages in R and Github
  • 14:00-14:15. Jeroen Jansen. Innovation and Value Initiative. State transition models and integration with network meta-analysis
  • 14:15-14:25. Ash Bullement. Delta Hat Analytics, UK. Fitting and extrapolating survival curves for CEA models
  • 14:25-14:45. Iryna Schlackow. Nuffield Department of Public Health, University of Oxford. Generic R methods to prepare routine healthcare data for disease modelling
  • 14:45-15:00. Coffee
  • 15:00-15:15. Initiatives for the future and challenges in gaining R acceptance (ISPOR Taskforce, ISPOR Special Interest Group, future of the R for CEA workshop)
  • 15:15-16:30. Participant discussion.
  • 16:30-16:45. Anthony Hatswell. Close and conclusions

 

R for trial and model-based cost-effectiveness analysis: short course

Background and objectives

It is our pleasure to announce a workshop and training event on the use of R for trial and model-based cost-effectiveness analysis (CEA). This follows our successful workshop on R for CEA in 2018.

Our event will begin with a half-day short course on R for decision trees and Markov models and the use of the BCEA package for graphical and statistical analysis of results; this will be delivered by Gianluca Baio of UCL and Howard Thom of Bristol University.

This will be followed by a one-day workshop in which we will present a wide variety of technical aspects by experts from academia, industry, and government institutions (including NICE). Topics will include decision trees, Markov models, discrete event simulation, integration of network meta-analysis, extrapolation of survival curves, and development of R packages.

We will include a pre-workshop virtual code challenge on a problem set by our scientific committee. This will take place over Github and a Slack channel with participants encouraged to submit final R code solutions for peer review on efficiency, flexibility, elegance and transparency. Prizes will be provided for the best entry.

Participants are also invited to submit abstracts for potential oral presentations. An optional dinner and networking event will be held on the evening of 8th July.

Registration is open until 1 June 2019 at https://onlinestore.ucl.ac.uk/conferences-and-events/faculty-of-mathematical-physical-sciences-c06/department-of-statistical-science-f61/f61-short-course-on-r-for-decision-trees-markov-models-the-use-of-bcea

 

Preliminary Programme

Day 1: Introduction to R for Cost-Effectiveness Modelling. Monday 8th July.

  • 13:00-13:15. Howard Thom. Welcome and introductions
  • 13:15-13:45. Howard Thom. Building a decision tree in R
  • 13:45-14:15. Gianluca Baio. Using BCEA to summarise outputs of an economic model
  • 14:15-14:45. Practical 1 (Decision trees)
  • 14:45-15:00. Coffee break
  • 15:00-15:45. Howard Thom. R for building Markov models
  • 15:45-16:15. Gianluca Baio. Further use of BCEA
  • 16:15-17:00. Practical 2 (Markov models)

Sam Watson’s journal round-up for 3rd June 2019

Every Monday our authors provide a round-up of some of the most recently published peer reviewed articles from the field. We don’t cover everything, or even what’s most important – just a few papers that have interested the author. Visit our Resources page for links to more journals or follow the HealthEconBot. If you’d like to write one of our weekly journal round-ups, get in touch.

Limits to human life span through extreme value theory. Journal of the American Statistical Association [RePEc] Published 2nd April 2019

The oldest verified person to have ever lived was Jeanne Calment who died in 1997 at the superlative age of 122. No-one else has ever been recorded as living longer than 120, but there have been perhaps a few hundred supercentarians over 110. Whenever someone reaches such a stupendous age, some budding reporter will ask them what the secret was. They will reply that they have stuck to a regimen of three boiled eggs and a glass of scotch every day for 80 years. And this information is of course completely meaningless due to survivorship bias. But as public health and health care improves and with it life expectancy, there remains the question of whether people will ever exceed these extreme ages or whether there is actually a limit to human longevity.

Some studies have attempted to address the question of maximum human longevity by looking at how key biological systems, like getting oxygen to the muscles or vasculature, degrade. They suggest that there would be an upper limit as key systems of the body just cannot last, which is not to say medicine might not find a way to fix or replace them in the future. Another way of addressing this question is to take a purely statistical approach and look at the distribution of the ages of the oldest people alive and try to make inferences about its upper limit. Such an analysis relies on extreme value theory.

There are two types of extreme value data. The first type consists of just the series of maximum values from the distribution. The Fisher-Tippett-Gnedenko theorem shows that these maxima can only be distributed according to one of three distributions. The second type of data are all of the most extreme observations above a certain threshold, and wonderfully there is another triple-barrelled theorem that shows that these data are distributed as a generalised Pareto distribution – the Pickand-Balkema-de Haan theorem. This article makes use of this latter type of data and theorem to estimate: (i) is there an upper limit to the distribution of human life spans? (ii) What is it, if so? And (iii) does it change over time?

The authors use a dataset of the ages of death in days of all Dutch residents who died over the age of 92 between 1986 and 2015. Using these data to estimate the parameters of the generalised Pareto distribution, they find strong evidence to suggest that, statistically at least, it has an upper limit and that this limit is probably around 117-124. Over the years of the study there did not appear to be any change in this limit. This is not to say that it couldn’t change in the future if some new miraculous treatment appeared, but for now, we humans must put up with a short and finite existence.

Infant health care and long-term outcomes. Review of Economics and Statistics [RePEc] Published 13th May 2019

I haven’t covered an article on infant health and economic conditions and longer term outcomes for a while. It used to be that there would be one in every round-up I wrote. I could barely keep up with the literature, which I tried to summarise in a different blog post. Given that it has been a while, I thought I would include a new one. This time we are looking at the effect of mother and child health centres in Norway in the 1930s on the outcomes of adults later in the 20th Century.

Fortunately the health centres were built in different municipalities at different times. The authors note that the “key identifying assumption” is that they were not built at a time related to the health of infants in those areas (well, this and that the model is linear and additive, time trends are linear, etc. etc. something that economists often forget). They don’t go into too much detail on this, but it seems plausible. Another gripe of mine with most empirical economic papers, and indeed in medical and public health fields, is that plotting the data is a secondary concern or doesn’t happen at all. It should be the most important thing. Indeed, in this article much of the discussion can be captured by the figure buried two thirds through. The figure shows that the centres likely led to a big reduction in diarrhoeal disease, probably due to increased rates of breast feeding, but on other outcomes effects are more ambiguous and probably quite small if they exist. Some evidence is provided to suggest that these differences were associated with very modest increases in educational attainment and adult wages. However, a cost-benefit calculation suggests that on the basis of these wage increases the intervention had a annualised rate of return of about 5%.

I should say that this study is well-conducted and fairly solid so any gripes with it are fairly minor. It certainly fits neatly into the wide literature on the topic, and I don’t think anyone would doubt that investing in childhood interventions is likely to have a number of short and long term benefits.

Relationship between poor olfaction and mortality among community-dwelling older adults: a cohort study. Annals of Internal Medicine [PubMed] Published 21st May 2019

I included this last study, not because of any ground-breaking economics or statistics, but because it is interesting. This is one of a number of studies to have looked at the relationship between smell ability and risk of death. These studies have generally found a strong direct relationship between poor olfaction and risk of death in the following years (summarised briefly in this editorial). This study examines a cohort of a couple of thousand older people whose smell was rigourously tested at baseline, among other things. If they died then their death was categorised by a medical examiner into one of four categories: dementia or Parkinson disease, cardiovascular disease, cancer, and respiratory illness.

There was a very strong relationship between poor ability to smell and all-cause death. They found that cumulative risk for death was 46% and 30% higher in persons with a loss of smelling ability at 10 and 13 years respectively. Delving into death by cause, they found that this relationship was most important among those who died of dementia or Parkinson disease, which makes sense as smell is one of the oldest limbic structures and linked to many parts of the brain. Some relationship was seen with cardiovascular disease but not cancer or respiratory illness. They then use a ‘mediation analysis’, i.e. conditioning on post-treatment variables to ‘block’ causal pathways, to identify how much variation is explained and conclude that dementia, Parkinson disease, and weight loss account for about 30% of the observed relationship. However, I am usually suspicious of mediation analyses, and standard arguments would suggest that model parameters would be biased.

Interestingly, olfaction is not normally used as a diagnostic test among the elderly despite sense of smell being one of the strongest predictors of mortality. People do not generally notice their sense of smell waning as it is gradual, so would not likely remark on it to a doctor. Perhaps it is time to start testing it routinely?

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