Tag: code

Calculate the Charlson Score in R

It is unlikely that anyone else will have data formatted in the same way as me, but it shouldn’t be too hard to convert this.

You just need a data where the rows represent patients, and there are a series of columns containing indicator variables for the components of the Charlson score[1].

The following function looks for these 20 variables, and uses a quick bit of matrix multiplication to generate the total score.

For reference, here is the table from the original paper containing the weights for the score.

Charlson Score

[1]: Charlson ME, Pompei P, Ales KL, MacKenzie CR. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. Journal of Chronic Diseases. 1987;40:373-383.

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)