Updated prevalence for some blood tests (#196)

shared/clinical-code-sets/tests/hba1c/2/README.md

@@ -8,8 +8,17 @@ A patient's HbA1c as recorded via clinical code and value. This code set only in
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `44.93% - 50.88%` suggests that this code set is likely well defined.
 
+_Update **2024/03/01**: prevalence now `50 - 53%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-05-07 | EMIS            | 2605681    | 1170688 (44.93%) |  1170688 (44.93%) |
 | 2021-05-07 | TPP             | 210817     |   98972 (46.95%) |    98972 (46.95%) |
 | 2021-05-07 | Vision          | 334632     |  170245 (50.88%) |   170245 (50.88%) |
+| 2024-03-01 | EMIS            | 2525130    |  1265760 (50.1%) |   1265887 (50.1%) |
+| 2024-03-01 | TPP             | 201782     |   101663 (50.4%) |    101673 (50.4%) |
+| 2024-03-01 | Vision          | 335118     |     177455 (53%) |      177464 (53%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-01

shared/clinical-code-sets/tests/sex-hormone-binding-globulin/1/README.md

@@ -6,8 +6,17 @@ A patient's SHBG level as recorded via clinical code and value. This code set on
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `2.57% - 3.72%` suggests that this code set is perhaps not well defined.
 
+_Update **2024-03-06**: prevalence now `2.6% - 4.6%`._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-05-07 | EMIS            | 2606497    |    87601 (3.36%) |     87601 (3.36%) |
 | 2021-05-07 | TPP             | 210810     |     5424 (2.57%) |      5424 (2.57%) |
 | 2021-05-07 | Vision          | 334784     |    12465 (3.72%) |     12465 (3.72%) |
+| 2024-03-06 | EMIS            | 2525894    |   104472 (4.14%) |    104515 (4.14%) |
+| 2024-03-06 | TPP             | 201753     |     5183 (2.57%) |      5184 (2.57%) |
+| 2024-03-06 | Vision          | 335117     |    15260 (4.55%) |     15259 (4.55%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-06

shared/clinical-code-sets/tests/testosterone/1/README.md

@@ -6,8 +6,17 @@ A patient's testosterone level as recorded via clinical code and value. This cod
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `4.91% - 6.24%` suggests that this code set is likely well defined.
 
+_Update **2024-03-06**: prevalence now `6.1% - 7.4%` for EMIS and VISION._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-05-11 | EMIS            | 2606497    |   137971 (5.29%) |    137971 (5.29%) |
 | 2021-05-11 | TPP             | 210810     |    10359 (4.91%) |     10359 (4.91%) |
 | 2021-05-11 | Vision          | 334784     |    20903 (6.24%) |     20903 (6.24%) |
+| 2024-03-06 | EMIS            | 2525894    |   164555 (6.51%) |    164615 (6.52%) |
+| 2024-03-06 | TPP             | 201753     |    12294 (6.09%) |      12298 (6.1%) |
+| 2024-03-06 | Vision          | 335117     |    24684 (7.37%) |     24687 (7.37%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-06

shared/clinical-code-sets/tests/testosterone/1/testosterone.emis.txt

@@ -0,0 +1,2 @@
+^ESCTSE551843	Serum testosterone measurement
+^ESCTSE551844	Serum testosterone level

shared/clinical-code-sets/tests/vitamin-d/1/README.md

@@ -6,8 +6,17 @@ A patient's vitamin D level as recorded via clinical code and value. This code s
 
 By examining the prevalence of codes (number of patients with the code in their record) broken down by clinical system, we can attempt to validate the clinical code sets and the reporting of the conditions. Here is a log for this code set. The prevalence range `4.30% - 14.10%` suggests that this code set is not well defined and there are TPP codes that are missing.
 
+_Update **2024-03-06**: prevalence now `16% - 18.6%` for EMIS and VISION. TPP much lower at 3.4% suggesting a potential issue._
+
 | Date       | Practice system | Population | Patients from ID | Patient from code |
 | ---------- | --------------- | ---------- | ---------------: | ----------------: |
 | 2021-05-11 | EMIS            | 2606497    |  282971 (10.86%) |   282971 (10.86%) |
 | 2021-05-11 | TPP             | 210810     |     9056 (4.30%) |      9056 (4.30%) |
 | 2021-05-11 | Vision          | 334784     |   47198 (14.10%) |    47198 (14.10%) |
+| 2024-03-06 | EMIS            | 2525894    |     404510 (16%) |      404532 (16%) |
+| 2024-03-06 | TPP             | 201753     |     6837 (3.39%) |      6836 (3.39%) |
+| 2024-03-06 | Vision          | 335117     |    62329 (18.6%) |     62334 (18.6%) |
+
+## Audit log
+
+- Find_missing_codes last run 2024-03-06

shared/clinical-code-sets/tests/vitamin-d/1/vitamin-d.emis.txt

@@ -0,0 +1,4 @@
+^ESCTSE551875	Serum vitamin D measurement
+^ESCTSE551876	Serum vitamin D level
+^ESCTVI269420	Vitamin D, 25-hydroxy measurement
+^ESCTVI386243	Vitamin D measurement