From 01a1230a00a284172d2067b6e385045c1bafd057 Mon Sep 17 00:00:00 2001 From: Anders Aasted Isaksen Date: Tue, 20 Aug 2024 11:50:21 +0200 Subject: [PATCH 1/2] Added validation metrics for the updated version, including simplied pregnancy definitions and HbA1c de-duplication by date. --- vignettes/changes.Rmd | 43 +++++++++++++++++++++++++++++++++++-------- 1 file changed, 35 insertions(+), 8 deletions(-) diff --git a/vignettes/changes.Rmd b/vignettes/changes.Rmd index 53c2e660..79f3e570 100644 --- a/vignettes/changes.Rmd +++ b/vignettes/changes.Rmd @@ -20,13 +20,19 @@ these validations over the different versions. ## Specific changes -### Since the original published validation (version 1) +### Since the original validation (version from the paper) 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) ## Validity @@ -34,12 +40,35 @@ 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 | T1D | 0.943 | 0.773 | -| 1 | T1D \>40 yrs | 0.708 | 0.378 | -| 1 | T2D | 0.875 | 0.944 | -| 1 | T2D \<40 yrs | 0.471 | 0.863 | +| 1.1 | T1D | 0.943 | 0.789 | +| 1.1 | T1D \>40 yrs | 0.871 | 0.871 | +| 1.1 | T2D | 0.883 | 0.941 | +| 1.1 | T2D \<40 yrs | 0.519 | 0.857 | + +**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 | +|---------|---------------|-------------|-------------|-------|-------| +| 1.1 | T1D | 0.781 | 0.999 | 0.949 | 0.997 | +| 1.1 | T2D | 0.943 | 0.989 | 0.879 | 0.995 | ## Potential future changes @@ -49,9 +78,7 @@ at onset of T1D (after age 40) and T2D (before age 40), respectively. 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. Simplify logic defining pregnancy index dates to remove dependency - on maternal care visits (if performance in validation allows). -3. Limit the historic scope of primary diagnoses used to evaluate +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). From abab3347083d295533cbf7afde652f183ba10adb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Signe=20Kirk=20Br=C3=B8db=C3=A6k?= Date: Wed, 18 Sep 2024 15:47:31 +0200 Subject: [PATCH 2/2] docs: :memo: add version 1.1 header --- vignettes/changes.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/changes.Rmd b/vignettes/changes.Rmd index 79f3e570..d70e6967 100644 --- a/vignettes/changes.Rmd +++ b/vignettes/changes.Rmd @@ -18,9 +18,9 @@ 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 +## Specific changes since the original validation (version from the paper) -### 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