Tag data analysis

Analysing Patient-Level Data using HES Workshop

This intensive workshop introduces participants to HES (Hospital Episode Statistics) data and how to handle and manipulate these very large patient-level data sets using computer software. Understanding and interpreting the data is a key first step for using these data in economic evaluation or evaluating health care policy and practice. Participants will engage in lectures and problem-solving exercises, analysing the information in highly interactive sessions. Data manipulation and statistical analysis will be taught and demonstrated using Stata.

This workshop is offered to people in the academic, public and commercial sectors.  It is useful for analysts who wish to harness the power of HES non-randomised episode level patient data to shed further light on such things as patient costs and pathways, re-admissions and outcomes and provider performance.  The workshop is suitable for individuals working in NHS hospitals, commissioning organisations, NHS England, Monitor, and the Department of Health and Social Care, pharmaceutical companies or consultancy companies and for health care researchers and PhD students.  Overseas participants may find the tuition helpful for their own country, but note that the course is heavily oriented towards understanding HES data for England.

The workshop fee is 900GBP for the public sector; 1,400GBP for the commercial sector. This includes all tuition, course materials, lunches, the welcome and drinks reception, the workshop dinner and refreshments, but does not include accommodation.

Online registration is now open; further information and registration is at: https://www.york.ac.uk/che/courses/patient-data/

Subsidised places are available for full-time PhD students. If this is applicable to you, please email the workshop administrators and request an Application Form.

Contact: Gillian or Louise, Workshop Administrators, at: che-apd@york.ac.uk;  tel: +44 (0)1904 321436

Sam Watson’s journal round-up for 29th October 2018

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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.

Researcher Requests for Inappropriate Analysis and Reporting: A U.S. Survey of Consulting Biostatisticians. Annals of Internal Medicine. [PubMed] Published October 2018.

I have spent a fair bit of time masquerading as a statistician. While I frequently try to push for Bayesian analyses where appropriate, I have still had to do Frequentist work including power and sample size calculations. In principle these power calculations serve a good purpose: if the study is likely to produce very uncertain results it won’t contribute much to scientific knowledge and so won’t justify its cost. It can indicate that a two-arm trial would be preferred over a three-arm trial despite losing an important comparison. But many power analyses, I suspect, are purely for show; all that is wanted is the false assurance of some official looking statistics to demonstrate that a particular design is good enough. Now, I’ve never worked on economic evaluation, but I can imagine that the same pressures can sometimes exist to achieve a certain result. This study presents a survey of 400 US-based statisticians, which asks them how frequently they are asked to do some inappropriate analysis or reporting and to rate how egregious the request is. For example, the most severe request is thought to be to falsify statistical significance. But it includes common requests like to not show plots as they don’t reveal an effect as significant as thought, to downplay ‘insignificant’ findings, or to dress up post hoc power calculations as a priori analyses. I would think that those responding to this survey are less likely to be those who comply with such requests and the survey does not ask them if they did. But it wouldn’t be a big leap to suggest that there are those who do comply, career pressures being what they are. We already know that statistics are widely misused and misreported, especially p-values. Whether this is due to ignorance or malfeasance, I’ll let the reader decide.

Many Analysts, One Data Set: Making Transparent How Variations in Analytic Choices Affect Results. Advances in Methods and Practices in Psychological Science. [PsyArXiv] Published August 2018.

Every data analysis requires a large number of decisions. From receiving the raw data, the analyst must decide what to do with missing or outlying values, which observations to include or exclude, whether any transformations of the data are required, how to code and combined categorical variables, how to define the outcome(s), and so forth. The consequence of each of these decisions leads to a different analysis, and if all possible analyses were enumerated there could be a myriad. Gelman and Loken called this the ‘garden of forking paths‘ after the short story by Jorge Luis Borges, who explored this idea. Gelman and Loken identify this as the source of the problem called p-hacking. It’s not that researchers are conducting thousands of analyses and publishing the one with the statistically significant result, but that each decision along the way may be favourable towards finding a statistically significant result. Do the outliers go against what you were hypothesising? Exclude them. Is there a nice long tail of the distribution in the treatment group? Don’t take logs.

This article explores the garden of forking paths by getting a number of analysts to try to answer the same question with the same data set. The question was, are darker skinned soccer players more likely to receive a red card that their lighter skinned counterparts? The data set provided had information on league, country, position, skin tone (based on subjective rating), and previous cards. Unsurprisingly there were a large range of results, with point estimates ranging from odds ratios of 0.89 to 2.93, with a similar range of standard errors. Looking at the list of analyses, I see a couple that I might have pursued, both producing vastly different results. The authors see this as demonstrating the usefulness of crowdsourcing analyses. At the very least it should be stark warning to any analyst to be transparent with every decision and to consider its consequences.

Front-Door Versus Back-Door Adjustment With Unmeasured Confounding: Bias Formulas for Front-Door and Hybrid Adjustments With Application to a Job Training Program. Journal of the American Statistical Association. Published October 2018.

Econometricians love instrumental variables. Without any supporting evidence, I would be willing to conjecture it is the most widely used type of analysis in empirical economic causal inference. When the assumptions are met it is a great tool, but decent instruments are hard to come by. We’ve covered a number of unconvincing applications on this blog where the instrument might be weak or not exogenous, and some of my own analyses have been criticised (rightfully) on these grounds. But, and we often forget, there are other causal inference techniques. One of these, which I think is unfamiliar to most economists, is the ‘front-door’ adjustment. Consider the following diagram:

frontdoorOn the right is the instrumental variable type causal model. Provided Z satisfies an exclusion restriction. i.e. independent of U, (and some other assumptions) it can be used to estimate the causal effect of A on Y. The front-door approach, on the left, shows a causal diagram where there is a post-treatment variable, M, unrelated to U, and which causes the outcome Y. Pearl showed that under a similar set of assumptions as instrumental variables, that the effect of A on Y was entirely mediated by M, and that there were no common causes of A and M or of M and Y, then M could be used to identify the causal effect of A on Y. This article discusses the front-door approach in the context of estimating the effect of a jobs training program (a favourite of James Heckman). The instrumental variable approach uses random assignment to the program, while the front-door analysis, in the absence of randomisation, uses program enrollment as its mediating variable. The paper considers the effect of the assumptions breaking down, and shows the front-door estimator to be fairly robust.

 

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Method of the month: Coding qualitative data

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Once a month we discuss a particular research method that may be of interest to people working in health economics. We’ll consider widely used key methodologies, as well as more novel approaches. Our reviews are not designed to be comprehensive but provide an introduction to the method, its underlying principles, some applied examples, and where to find out more. If you’d like to write a post for this series, get in touch. This month’s method is coding qualitative data.

Principles

Health economists are increasingly stepping away from quantitative datasets and conducting interviews and focus groups, as well as collecting free text responses. Good qualitative analysis requires thought and rigour. In this blog post, I focus on coding of textual data – a fundamental part of analysis in nearly all qualitative studies. Many textbooks deal with this in detail. I have drawn on three in particular in this blog post (and my research): Coast (2017), Miles and Huberman (1994), and Ritchie and Lewis (2003).

Coding involves tagging segments of the text with salient words or short phrases. This assists the researcher with retrieving the data for further analysis and is, in itself, the first stage of analysing the data. Ultimately, the codes will feed into the final themes or model resulting from the research. So the codes – and the way they are applied – are important!

Implementation

There is no ‘right way’ to code. However, I have increasingly found it useful to think of two phases of coding. First, ‘open coding’, which refers to the initial exploratory process of identifying pertinent phrases and concepts in the data. Second, formal or ‘axial’ coding, involving the application of a clear, pre-specified coding framework consistently across the source material.

Open coding

Any qualitative analysis should start with the researcher being very familiar with both the source material (such as interview transcripts) and the study objectives. This sounds obvious, but it is easy, as a researcher, to get drawn into the narrative of an interview and forget what exactly you are trying to get out of the research and, by extension, the coding. Open coding requires the researcher to go through the text, carefully, line-by-line, tagging segments with a code to denote its meaning. It is important to be inquisitive. What is being said? Does this relate to the research question and, if so, how?

Take, for example, the excerpt below from a speech by the Secretary of State for Health, Jeremy Hunt, on safety and efficiency in the NHS in 2015:

Let’s look at those challenges. And I think we have good news and bad news. If I start with the bad news it is that we face a triple whammy of huge financial pressures because of the deficit that we know we have to tackle as a country, of the ageing population that will mean we have a million more over 70s by 2020, and also of rising consumer expectations, the incredible excitement that people feel when they read about immunotherapy in the newspapers that gives a heart attack to me and Simon Stevens but is very very exciting for the country. The desire for 24/7 access to healthcare. These are expectations that we have to recognise in the NHS but all of these add to a massive pressure on the system.

This excerpt may be analysed, for example, as part of a study into demand pressures on the NHS. And, in this case, codes such as “ageing population” “consumer expectations” “immunotherapy” “24/7 access to healthcare” might initially be identified. However, if the study was investigating the nature of ministerial responsibility for the NHS, one might pull out very different codes, such as “tackle as a country”, “public demands vs. government stewardship” and “minister – chief exec shared responsibility”.

Codes can be anything – attitudes, behaviours, viewpoints – so long as they relate to the research question. It is very useful to get (at least) one other person to also code some of the same source material. Comparing codes will provide new ideas for the coding framework, a different perspective of the meaning of the source material and a check that key sections of the source material have not been missed. Researchers shouldn’t aim to code all (or even most) of the text of a transcript – there is always some redundancy. And, in general, initial codes should be as close to the source text as possible – some interpretation is fine but it is important to not get too abstract too quickly!

Formal or ‘axial’ coding

When the researcher has an initial list of codes, it is a good time to develop a formal coding framework. The aim here is to devise an index of some sort to tag all the data in a logical, systematic and comprehensive way, and in a way that will be useful for further analysis.

One way to start is to chart how the initial codes can be grouped and relate to one another. For example, in analysing NHS demand pressures, a researcher may group “immunotherapy” with other medical innovations mentioned elsewhere in the study. It’s important to avoid having many disconnected codes, and at this stage, many codes will be changed, subdivided, or combined. Much like an index, the resulting codes could be organised into loose chapters (or themes) such as “1. Consumer expectations”, “2. Access” and/or there might be a hierarchical relationship between codes, for example, with codes relating to national and local demand pressures. A proper axial coding framework has categories and sub-categories of codes with interdependencies formally specified.

There is no right number of codes. There could be as few as 10, or as many as 50, or more. It is crucial however that the list of codes are logically organised (not alphabetically listed) and sufficiently concise, so that the researcher can hold them in their head while coding transcripts. Alongside the coding framework itself – which may only be a page – it can be very helpful to put together an explanatory document with more detail on the meaning of each code and possibly some examples.

Software

Once the formal coding framework is finalised it can be applied to the source material. I find this a good stage to use software like Nvivo. While coding in Nvivo takes a similar amount of time to paper-based methods, it can help speed up the process of retrieving and comparing segments of the text later on. Other software packages are available and some researchers prefer to use computer packages earlier in the process or not all – it is a personal choice.

Again, it is a good idea to involve at least one other person. One possibility is for two researchers to apply the framework separately and code the first, say 5 pages of a transcript. Reliability between coders can then be compared, with any discrepancies discussed and used to adjust the coding framework accordingly. The researchers could then repeat the process. Once reliability is at an acceptable level, a researcher should be able to code the transcripts in a much more reproducible way.

Even at this stage, the formal coding framework does not need to be set in stone. If it is based on a subset of interviews, new issues are likely to emerge in subsequent transcripts and these may need to be incorporated. Additionally, analyses may be conducted with sub-samples of participants or the analysis may move from more descriptive to explanatory work, and therefore the coding needs may change.

Applications

Published qualitative studies will often mention that transcript data were coded, with few details to discern how this was done. In the study I worked on to develop the ICECAP-A capability measure, we coded to identify influences on quality of life in the first batch of interviews and dimensions of quality of life in later batches of interviews. A recent study into disinvestment decisions highlights how a second rater can be used in coding. Reporting guidelines for qualitative research papers highlight three important items related to coding – number of coders, description of the coding tree (framework), and derivation of the themes – that ought to be included in study write-ups.

Coding qualitative data can feel quite laborious. However, the real benefit of a well organised coding framework comes when reconstituting transcript data under common codes or themes. Codes that relate clearly to the research question, and one another, allow the researcher to reorganise the data with real purpose. Juxtaposing previously unrelated text and quotes sparks the discovery of exciting new links in the data. In turn, this spawns the interpretative work that is the fundamental value of the qualitative analysis. In economics parlance, good coding can improve both the efficiency of retrieving text for analysis and the quality of the analytical output itself.

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