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Changes to algorithm

Source: vignettes/changes.Rmd
changes.Rmd

In this vignette, you’ll find a description of the changes that have been made to the OSDC algorithm since its original validation. The osdc package uses the latest changes to the algorithm. Potential changes to the algorithm, rather than the specific implementation and code details, that we might in the future will also be described in this vignette. We will also provide validation metrics here whenever we make a change, and track these validations over the different versions.

Specific changes since the original validation (version from the paper)

Version 1.1

  1. We don’t use purchases of semaglutid, dapagliflozin or empagliflozin, neither for inclusion events nor classification of diabetes type (due to increasing use in treatment of non-diabetes).
  2. We no longer use diabetes type reclassification based on insulin purchases in the previous year.
  3. The logic defining pregnancy index dates has been simplified to only use diagnoses of pregnancy endings (no longer uses data on maternal care visits).
  4. De-duplicates subsequent HbA1c samples taken on the same date (originally, if a sampling time was available in the lab data, only samples taken at the same time were de-duplicated)

Version 1.2

  1. No longer uses any GLP1-RAs for inclusion or type-specification.

Validity

Algorithm validity across versions. Reports PPV (positive predictive value) and sensitivity for typical cases and cases with atypical age at onset of T1D (after age 40) and T2D (before age 40), respectively.

On pre-2019 data (as in the paper)

Overall and age at onset-stratified (paper table 1 & 2):

Version Diabetes type PPV Sensitivity
Paper T1D 0.943 0.773
Paper T1D >40 yrs 0.708 0.378
Paper T2D 0.875 0.944
Paper T2D <40 yrs 0.471 0.863
Version Diabetes type PPV Sensitivity
1.2 T1D 0.944 0.783
1.2 T1D >40 yrs 0.708 0.378
1.2 T2D 0.879 0.944
1.2 T2D <40 yrs 0.480 0.863

Bootstrapped metrics (paper S3):

Version Diabetes type Sensitivity Specificity PPV NPV
Paper T1D 0.774 0.999 0.951 0.997
Paper T2D 0.943 0.989 0.878 0.995
Version Diabetes type Sensitivity Specificity PPV NPV
1.2 T1D 0.788 0.999 0.947 0.997
1.2 T2D 0.940 0.990 0.881 0.995

Potential future changes

  1. Add support for using medical birth register to define pregnancies to censor gestational diabetes (GDM). This will allow for the censoring of glucose-lowering drug (GLD) purchases all the way back to 1995 (rather than 1997 onward, as the obstetric codes are limited to), and enable the extension of the window of valid dates of diagnosis to 1996 onward.
  2. Limit the historic scope of primary diagnoses used to evaluate majority of diabetes-specific diagnoses in type classification (e.g. only evaluate majority among the last five type-specific diabetes diagnoses).