Author: drstevok

March 15, 2019

Calculate the SOFA score in R

A follow on from the Charlson score function previously posted. Here are functions to calculate the SOFA score.

Please note

it’s almost inconceivable that your data will be similar to mine, and you will be able to just use these ‘as is’; however, they might provide a useful skeleton.
there are some add-ons included (e.g. if a blood gas is not available then you can still generate the SOFA respiratory score using oxygen saturations and the S:F ratio via this (slightly flawed) proposal)
there are some arbitrary decisions too (i.e. vasopressin use is considered to assign patients to 4 SOFA points for cardiovascular dysfunction)

March 15, 2019

Stopping rules and regression to the mean — Statistics Done Wrong

Stopping rules and regression to the mean — Statistics Done Wrong:

if the trial is only half complete but there’s already a statistically significant difference in symptoms with the new medication, the researchers may terminate the study, rather than gathering more data to reinforce the conclusion.

When poorly done, however, this can lead to numerous false positives.

March 15, 2019

Bootstrap at the cluster or the unit level

I have been using the bootstrap more often recently, but the data that I use is typically structured with patients nested in hospitals. The wonderful Cross Validated recommends that any sampling that is to be done should respect the structure of the data.

This means first sampling (with replacement) hospitals, and then sampling (with replacement again) within each hospital before re-assembling the data.

There is a better explanation along with a code snippet from the biostats department at Vanderbilt. However, with 48 hospitals and 15,000 patients, this ran very slowly.

I have re-written this using the data.table with a good (great?) improvement in speed (but some loss of flexibility).

March 15, 2019

Science Isn’t Broken | FiveThirtyEight

Science Isn’t Broken | FiveThirtyEight:

The important lesson here is that a single analysis is not sufficient to find a definitive answer. Every result is a temporary truth, one that’s subject to change when someone else comes along to build, test and analyze anew.

March 14, 2019

Get up, git up

I have been using SourceTree as a GUI for git, but just came across GitUp. It starts off just looking like a pretty way to view your repository with a fairly typical graph, but you can in fact work from within the graph.