This document describes the sources of data needed by the OSDC algorithm and gives a brief overview of each of these sources and how they might look like. In addition, the final section contains information on how to gain access to these data.
The algorithm uses these Danish registers as input data sources:
Danish registers used in the OSDC algorithm.
| CPR-registerets befolkningstabel |
bef |
1968 - present |
| Laegemiddelstatistikregisteret |
lmdb |
1995 - present |
| Landspatientregisterets administrationstabel (LPR2) |
lpr_adm |
1977 - 2018 |
| Landspatientregisterets diagnosetabel (LPR2) |
lpr_diag |
1977 - 2018 |
| Landspatientregisterets kontakttabel (LPR3) |
kontakter |
2019 - present |
| Landspatientregisterets diagnosetabel (LPR3) |
diagnoser |
2019 - present |
| Sygesikringsregisteret |
sysi |
1990 - 2005 |
| Sygesikringsregisteret |
sssy |
2006 - present |
| Laboratoriedatabasens forskertabel |
lab_forsker |
2011 - present |
In a future revision, the algorithm can also use the Danish Medical Birth Register to extend the period of time of valid inclusions further back in time compared to what is possible using obstetric codes from the National Patient Register.
Data required from registers
The following is a list of the variables required from specific registers in order for the package to classify diabetes status:
CPR-registerets befolkningstabel (bef) |
pnr |
CPR-registerets befolkningstabel (bef) |
koen |
CPR-registerets befolkningstabel (bef) |
foed_dato |
Laegemiddelstatistikregisteret (lmdb) |
pnr |
Laegemiddelstatistikregisteret (lmdb) |
eksd |
Laegemiddelstatistikregisteret (lmdb) |
atc |
Laegemiddelstatistikregisteret (lmdb) |
volume |
Laegemiddelstatistikregisteret (lmdb) |
apk |
Laegemiddelstatistikregisteret (lmdb) |
indo |
Landspatientregisterets administrationstabel (LPR2) (lpr_adm) |
pnr |
Landspatientregisterets administrationstabel (LPR2) (lpr_adm) |
recnum |
Landspatientregisterets administrationstabel (LPR2) (lpr_adm) |
d_inddto |
Landspatientregisterets administrationstabel (LPR2) (lpr_adm) |
c_spec |
Landspatientregisterets diagnosetabel (LPR2) (lpr_diag) |
recnum |
Landspatientregisterets diagnosetabel (LPR2) (lpr_diag) |
c_diag |
Landspatientregisterets diagnosetabel (LPR2) (lpr_diag) |
c_diagtype |
Landspatientregisterets kontakttabel (LPR3) (kontakter) |
cpr |
Landspatientregisterets kontakttabel (LPR3) (kontakter) |
dw_ek_kontakt |
Landspatientregisterets kontakttabel (LPR3) (kontakter) |
dato_start |
Landspatientregisterets kontakttabel (LPR3) (kontakter) |
hovedspeciale_ans |
Landspatientregisterets diagnosetabel (LPR3) (diagnoser) |
dw_ek_kontakt |
Landspatientregisterets diagnosetabel (LPR3) (diagnoser) |
diagnosekode |
Landspatientregisterets diagnosetabel (LPR3) (diagnoser) |
diagnosetype |
Landspatientregisterets diagnosetabel (LPR3) (diagnoser) |
senere_afkraeftet |
Sygesikringsregisteret (sysi) |
pnr |
Sygesikringsregisteret (sysi) |
barnmak |
Sygesikringsregisteret (sysi) |
speciale |
Sygesikringsregisteret (sysi) |
honuge |
Sygesikringsregisteret (sssy) |
pnr |
Sygesikringsregisteret (sssy) |
barnmak |
Sygesikringsregisteret (sssy) |
speciale |
Sygesikringsregisteret (sssy) |
honuge |
Laboratoriedatabasens forskertabel (lab_forsker) |
patient_cpr |
Laboratoriedatabasens forskertabel (lab_forsker) |
samplingdate |
Laboratoriedatabasens forskertabel (lab_forsker) |
analysiscode |
Laboratoriedatabasens forskertabel (lab_forsker) |
value |
Expected data structure
This section describes how the data sources listed from the above table are expected to look like when they are input into the OSDC algorithm. This should mimic the structure of the raw data as it appears within the virtual machines of Statistics Denmark. The package does not support inputs in their raw .sas7bdat format, and these must be converted to .parquet files first, which can then be loaded in as DuckDB objects. The registers2parquet package provides functions to conveniently handle this.
In this document, we present the variable names in lower case, but case may vary between data sources (and even between years in the same data source) in real data. However, the package should be robust to inconsistent casing, as we internally convert all variable names to lower case.
A small note about the National Patient Register: It contains several tables and types of data. The algorithm uses only hospital diagnosis data contained in four registers, which are pairs of two related registers used before 2019 (LPR2) and from 2019 onward (LPR3). So the LPR2 to LPR3 equivalents are lpr_adm to kontakter and lpr_diag to diagnoser. Most variables have direct equivalents between LPR2 and LPR3, but it should be noted that while c_spec is the LPR2 equivalent of hovedspeciale_ans in LPR3, the specialty values in hovedspeciale_ans are coded as strings of the literal specialty names unlike the padded integer codes that c_spec contains (in our experience).
On Statistics Denmark, these tables are provided as a mix of separate files for each calendar year prior to 2019 (in LPR2 format) and a single file containing all the data from 2019 onward (LPR3 format). The two tables can be joined with either the recnum variable (LPR2 data) or the dw_ek_kontakt variable (LPR3 data).
bef: CPR-registerets befolkningstabel
Variables and their descriptions within the bef register. If you want to see what the data should look like, see simulate_registers().
| pnr |
Pseudonymised social security number |
| koen |
Gender/sex |
| foed_dato |
Date of birth |
lmdb: Laegemiddelstatistikregisteret
Variables and their descriptions within the lmdb register. If you want to see what the data should look like, see simulate_registers().
| pnr |
Pseudonymised social security number |
| eksd |
Date of purchase |
| atc |
Atc code (fully specified) |
| volume |
Number of daily standard doses (ddd) in package |
| apk |
Number of packages purchased |
| indo |
Indication code |
lpr_adm: Landspatientregisterets administrationstabel (LPR2)
Variables and their descriptions within the lpr_adm register. If you want to see what the data should look like, see simulate_registers().
| pnr |
Pseudonymised social security number |
| recnum |
Record id number |
| d_inddto |
Date of admission or initial contact |
| c_spec |
Specialty code of department |
lpr_diag: Landspatientregisterets diagnosetabel (LPR2)
Variables and their descriptions within the lpr_diag register. If you want to see what the data should look like, see simulate_registers().
| recnum |
Record id number |
| c_diag |
Diagnosis code |
| c_diagtype |
Diagnosis type |
kontakter: Landspatientregisterets kontakttabel (LPR3)
Variables and their descriptions within the kontakter register. If you want to see what the data should look like, see simulate_registers().
| cpr |
Pseudonymised social security number |
| dw_ek_kontakt |
Record id number |
| dato_start |
Date of admission or initial contact |
| hovedspeciale_ans |
Specialty of department |
diagnoser: Landspatientregisterets diagnosetabel (LPR3)
Variables and their descriptions within the diagnoser register. If you want to see what the data should look like, see simulate_registers().
| dw_ek_kontakt |
Record id number |
| diagnosekode |
Diagnosis code |
| diagnosetype |
Diagnosis type |
| senere_afkraeftet |
Was the diagnosis retracted later? |
sysi: Sygesikringsregisteret
Variables and their descriptions within the sysi register. If you want to see what the data should look like, see simulate_registers().
| pnr |
Pseudonymised social security number |
| barnmak |
Was the service provided to the patient’s child? |
| speciale |
Billing code of the service (fully specified) |
| honuge |
Year and week of service |
sssy: Sygesikringsregisteret
Variables and their descriptions within the sssy register. If you want to see what the data should look like, see simulate_registers().
| pnr |
Pseudonymised social security number |
| barnmak |
Was the service provided to the patient’s child? |
| speciale |
Billing code of the service (fully specified) |
| honuge |
Year and week of service |
lab_forsker: Laboratoriedatabasens forskertabel
Variables and their descriptions within the lab_forsker register. If you want to see what the data should look like, see simulate_registers().
| patient_cpr |
Pseudonymised social security number |
| samplingdate |
Date of sampling |
| analysiscode |
Npu code of analysis |
| value |
Numerical result of analysis |
Getting access to data
The above data is available through Statistics Denmark and the Danish Health Data Authority. Researchers must be affiliated with an approved research institute in Denmark and fees apply. Information on how to gain access to data can be found at www.dst.dk/en/TilSalg/data-til-forskning (URL often changes, so we can’t link directly).
