Riinu and I are sitting in Frankfurt airport discussing the paper retracted in JAMA this week. During analysis, the treatment variable coded [1,2] was recoded in error to [1,0]. The results of the analysis were therefore reversed. The lung-disease self-management program actually resulted in more attendances at hospital, rather than fewer as ... [Read more...]

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Data security is paramount and encryptr was written to make this easier for non-experts. Columns of data can be encrypted with a couple of lines of R code, and single cells decrypted as required. But what was missing was an easy way to encrypt the file source of that data. ... [Read more...]

The new finalfit tables gallery vignette is an excellent reference and quick tutorial describing the variety of table outputs available. It focuses on crosstables and regression tables, and demonstrates how to easily generate results in R and expo... [Read more...]

Many of our projects involve getting doctors, nurses, and medical students to collect data on the patients they are looking after. We want to involve many of them in data analysis, without the requirement for coding experience or access to statistical software. To achieve this we have built Shinyfit, a ... [Read more...]

As a journal editor, I often receive studies in which the investigators fail to describe, analyse, or even acknowledge missing data. This is frustrating, as it is often of the utmost importance. Conclusions may (and do) change when missing data is accounted for.  A few seem to not even appreciate ... [Read more...]

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Your favourite package for getting model outputs directly into publication ready tables is now available on CRAN. They make you work for it! Thank you to all that helped. The development version will continue to be available from github. [Read more...]

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I’ve had few enquires about how to install the summarizer package on a server without internet access, such as the NHS Safe Havens. Upload summarizer-master.zip from here to server. Unzip. Run this: library(devtools) source = devtools:::source_pkg("summarizer-master") install(source) [Read more...]

[crayon-5a5ad6bfdb9ea208679487-i/] is a useful frequentist approach to hierarchical/multilevel linear regression modelling. For good reason, the model output only includes t-values and doesn’t include p-values (partly due to the difficulty in estimating the degrees of freedom, as discussed here). Yes, p-values are evil and ... [Read more...]

ProPublica, an independent investigative journalism organisation, have published surgeon-level complications rates based on Medicare data. I have already highlighted problems with the reporting of the data: surgeons are described as having a “high adjusted rate of complications” if they fall in the red-zone, despite there being too little data to ... [Read more...]

Version control has become essential for me keeping track of projects, as well as collaborating. It allows backup of scripts and easy collaboration on complex projects. RStudio works really well with Git, an open source open source distributed version control system, and GitHub, a web-based Git repository hosting service. I ... [Read more...]

Statistical approaches to randomised controlled trial analysis The statistical approach used in the design and analysis of the vast majority of clinical studies is often referred to as classical or frequentist. Conclusions are made on the results of hypothesis tests with generation of p-values and confidence intervals, and require that ... [Read more...]

With geo-tagging enabled, tweets include information on the location of the user when the tweet was sent. Miguel Rios (@miguelrios) has plotted locations of billions of tweets to create maps of the world. This is pretty amazing stuff – a world map rendered just from twitter posts! Maps are created using ... [Read more...]

This post comes with some big health warnings. The recent events in Leeds highlight the difficulties faced in judging the results of surgery by individual hospital. A clear requirement is timely access to data in a form easily digestible by the public. Here I’ve scraped the publically available data ... [Read more...]

Use R to specify factors, recode variables and begin by-group analyses. Video Files This file contains data on pain score after laparoscopic vs. open hernia repair. Age, gender and primary/recurrent hernia also included. The ultimate aim here is to work out which of these factors are associated with more ... [Read more...]

Video Files This file contains data on pain score after laparoscopic vs. open hernia repair. Age, gender and primary/recurrent hernia also included. The ultimate aim here is to work out which of these factors are associated with more pain after this operation. lap_hernia Script [crayon-533f1cc907137087602057/]   [Read more...]