docs: 📝 moved logic into algorithm.csv

data-raw/algorithm.csv

@@ -1,10 +1,15 @@
 register,name,title,logic,comments
-lab_forsker,hba1c,HbA1c inclusion,(analysiscode == 'NPU27300' AND value >= 48) OR (analysiscode == 'NPU03835' AND value >= 6.5),Is the IFCC units for NPU27300 and DCCT units for NPU03835
-lmdb,gld,Glucose-lowering drug inclusion,atc =~ '^A10' AND !(atc =~ '^(A10BJ|A10BK01|A10BK03)'),Do not keep GLP-RAs or dapagliflozin/empagliflozin drugs
-lpr_diag,lpr2,Relevant LPR2 diagnoses codes,c_diag =~ '^(DO0[0-6]|DO8[0-4]|DZ3[37]|DE1[0-4]|249|250)' AND (c_diagtype == 'A' OR c_diagtype == 'B'),'A' c_diagtype means primary diagnosis
+lab_forsker,hba1c,HbA1c inclusion,(analysiscode == 'NPU27300' AND value >= 48) OR (analysiscode == 'NPU03835' AND value >= 6.5),Is the IFCC units for NPU27300 and DCCT units for NPU03835.
+lmdb,gld,Glucose-lowering drug inclusion,atc =~ '^A10' AND !(atc =~ '^(A10BJ|A10BK01|A10BK03)'),Do not keep GLP-RAs or dapagliflozin/empagliflozin drugs.
+lpr_diag,lpr2,Relevant LPR2 diagnoses codes,c_diag =~ '^(DO0[0-6]|DO8[0-4]|DZ3[37]|DE1[0-4]|249|250)' AND (c_diagtype == 'A' OR c_diagtype == 'B'),'A' `c_diagtype` means primary diagnosis.
 lpr_diag,lpr2_has_t1d,LPR2 diagnoses codes for T1D,c_diag =~ '^(DE10|249)',
 lpr_diag,lpr2_has_t2d,LPR2 diagnoses codes for T2D,c_diag =~ '^(DE11|250)',
-lpr_diag,lpr2_has_pregnancy_event,LPR2 diagnoses codes for pregnancy-related outcomes,c_diag =~ '^(DO0[0-6]|DO8[0-4]|DZ3[37])',These are recorded pregnancy endings like live births and miscarriages
-lpr_adm,lpr2_is_endocrinology_department,LPR2 endocrinology department,"na_if(c_spec, !(c_spec %in% 8:30)) == 8","True is when the department is endocrinology, false is when it is other medical departments, and missing is all other cases."
-kontakter,lpr3_is_endocrinology_department,LPR3 endocrinology department,"na_if(hovedspeciale_ans, !(hovedspeciale_ans %in% c('medicinsk endokrinologi', 'blandet medicin og kirurgi', 'intern medicin', 'geriatri', 'hepatologi', 'hæmatologi', 'infektionsmedicin', 'kardiologi', 'medicinsk allergologi', 'medicinsk gastroenterologi', 'medicinsk lungesygdomme', 'nefrologi', 'reumatologi', 'palliativ medicin', 'akut medicin', 'dermato-venerologi', 'neurologi', 'onkologi', 'fysiurgi', 'tropemedicin'))) == 'medicinsk endokrinologi'","True is when the department is endocrinology, false is when it is other medical departments, and missing is all other cases."
-,exclude_pregnancy,Remove events within a potential pregnancy period,!(has_pregnancy_event AND has_elevated_hba1c AND (date >= (pregnancy_event_date - weeks(40)) OR date <= (pregnancy_event_date + weeks(12)))),
+lpr_diag,lpr2_has_pregnancy_event,LPR2 diagnoses codes for pregnancy-related outcomes,c_diag =~ '^(DO0[0-6]|DO8[0-4]|DZ3[37])',These are recorded pregnancy endings like live births and miscarriages.
+lpr_adm,lpr2_is_endocrinology_department,LPR2 endocrinology department,"na_if(c_spec, !(c_spec %in% 8:30)) == 8","`TRUE` when the department is endocrinology,`FALSE` when it is other medical departments, and missing is all other cases."
+kontakter,lpr3_is_endocrinology_department,LPR3 endocrinology department,"na_if(hovedspeciale_ans, !(hovedspeciale_ans %in% c('medicinsk endokrinologi', 'blandet medicin og kirurgi', 'intern medicin', 'geriatri', 'hepatologi', 'hæmatologi', 'infektionsmedicin', 'kardiologi', 'medicinsk allergologi', 'medicinsk gastroenterologi', 'medicinsk lungesygdomme', 'nefrologi', 'reumatologi', 'palliativ medicin', 'akut medicin', 'dermato-venerologi', 'neurologi', 'onkologi', 'fysiurgi', 'tropemedicin'))) == 'medicinsk endokrinologi'","`TRUE` when the department is endocrinology, `FALSE` when it is other medical departments, and missing in all other cases."
+diagnoser,lpr3,Relevant LPR3 diagnoses codes,diagnosekode =~ '^(DO0[0-6]|DO8[0-4]|DZ3[37]|DE1[0-4])' AND (diagnosetype == 'A' OR diagnosetype == 'B') AND (senere_afkraeftet == "Nej"),'A' `diagnosekode` means primary diagnosis and `senere_afkraeftet` means diagnosis was later retracted.
+diagnoser,lpr3_has_t1d,LPR3 diagnoses codes for T1D,diagnosekode =~ '^(DE10)',
+diagnoser,lpr3_has_t2d,LPR3 diagnoses codes for T2D,diagnosekode =~ '^(DE11)',
+,no_pregnancy,Remove events within a potential pregnancy period,!(has_pregnancy_event AND has_elevated_hba1c AND (date >= (pregnancy_event_date - weeks(40)) OR date <= (pregnancy_event_date + weeks(12)))),
+,podiatrist_services,speciale =~ '^54' AND barnmak != 0,`barnmak` means the services were provided to a child of the individual.
+,no_potential_pcos,"koen == 2 AND atc =~ '^A10BA02$' AND ((date - foed_dato) < 40 OR indication_code %in% c('0000092', '0000276', '0000781'))",Woman is defined as 2 in `koen`.

vignettes/algorithm.Rmd

@@ -9,94 +9,18 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  echo = FALSE
 )
-```
-
-```{r setup}
 library(osdc)
 library(dplyr)
 ```
 
-## `lpr_diag`
-
-```{r, echo=FALSE}
-algorithm |>
-  filter(register == "lpr_diag") |>
-  knitr::kable()
-```
-
-## `lpr_adm`
-
-```{r, echo=FALSE}
-algorithm |>
-  filter(register == "lpr_adm") |>
-  knitr::kable()
-```
-
-## `diagnoser`
-
--   `diagnosekode` starts with "DO0[0-6]", "DO8[0-4]", "DZ3[37]" or
-    "DE1[0-4]".
-    -   Is T1D if `diagnosekode` starts with "DE10".
-    -   Is T2D if `diagnosekode` starts with "DE11".
--   `diagnosetype` is equal to either "A" or "B".
-    -   Is a primary diagnosis if it equals "A".
--   `senere_afkraeftet` (if the diagnosis was later retracted) is equal
-    to "Nej".
-
-## `kontakter`
-
--   `hovedspeciale_ans` (hospital department) is categorized as
-    "endocrinology" if it equals "medicinsk endokrinologi" or as "other
-    medical" if it equals any of "Blandet medicin og kirurgi", "Intern
-    medicin", "Geriatri", "Hepatologi", "Hæmatologi",
-    "Infektionsmedicin", "Kardiologi", "Medicinsk allergologi",
-    "Medicinsk gastroenterologi", "Medicinsk lungesygdomme",
-    "Nefrologi", "Reumatologi", "Palliativ medicin", "Akut medicin",
-    "Dermato-venerologi", "Neurologi", "Onkologi", "Fysiurgi", or
-    "Tropemedicin".
-
-## `lab_forsker`
-
-```{r, echo=FALSE}
-algorithm |>
-  filter(name == "hba1c") |>
-  knitr::kable()
-```
+## General description
 
-## `ssyi` and `sssy`
-
--   `speciale` starts with "54".
--   `barnmark` (services provided to a child of the individual) is not
-    equal to 0.
-
-## `lmdb`
-
-```{r, echo=FALSE}
-algorithm |>
-  filter(name == "gld") |>
-  knitr::kable()
-```
-
-## `bef` and only GLD (via `lmdb`)
-
-To remove those with potential polycystic ovary syndrome:
-
--   `atc` starts with "A10BA02" and `koen` is equal to 2 (woman) and
-    (`date` minus `foed_dato` (birth date) is less than 40 or
-    `indication_code` equals one of "0000092", "0000276" or "0000781")
-
-## Pregnancy events
-
-```{r, echo=FALSE}
-algorithm |>
-  filter(name == "exclude_pregnancy") |>
-  knitr::kable()
-```
 A more complete description of the classifier is found in Anders Aasted
 Isaksen's [PhD Thesis](https://aastedet.github.io/dissertation/) as well
 as the validation paper [@Isaksen2023]. The description of the algorithm
@@ -157,4 +81,83 @@ year prior to the index date.
 
 Individuals not classified as T1D cases are classified as T2D cases.
 
+## Detailed and technical description
+
+Below are the technical, exact implementation of the above description.
+These are the logical conditions and exact variables and registers used
+that results in the classification of diabetes status and types. They are
+shown in the form of tables for each register, as well as for each
+
+### `lpr_diag`
+
+```{r}
+algorithm |>
+  filter(register == "lpr_diag") |>
+  knitr::kable()
+```
+
+### `lpr_adm`
+
+```{r}
+algorithm |>
+  filter(register == "lpr_adm") |>
+  knitr::kable()
+```
+
+### `diagnoser`
+
+```{r}
+algorithm |>
+  filter(register == "diagnoser") |>
+  knitr::kable()
+```
+
+### `kontakter`
+
+```{r}
+algorithm |>
+  filter(register == "kontakter") |>
+  knitr::kable()
+```
+
+### `lab_forsker`
+
+```{r}
+algorithm |>
+  filter(name == "hba1c") |>
+  knitr::kable()
+```
+
+### `ssyi` and `sssy` for podiatrist services
+
+```{r}
+algorithm |>
+  filter(name == "podiatrist_services") |>
+  knitr::kable()
+```
+
+### `lmdb` for glucose lowering drugs
+
+```{r}
+algorithm |>
+  filter(name == "gld") |>
+  knitr::kable()
+```
+
+### `bef` and only GLD (via `lmdb`) for potential polycystic ovary syndrome
+
+```{r}
+algorithm |>
+  filter(name == "no_potential_pcos") |>
+  knitr::kable()
+```
+
+### Pregnancy events
+
+```{r}
+algorithm |>
+  filter(name == "no_pregnancy") |>
+  knitr::kable()
+```
+
 ## References