This package serves two overarching purposes:
- To provide an open-source, code-based algorithm to classify type 1 and type 2 diabetes using Danish registers as data sources.
- To inspire discussions within the Danish register-based research space on the openness and ease of use on the existing tooling and registers, and on the need for an official process for updating or contributing to existing data sources.
To read up on the overall design of this package as well as on the
algorithm, check out the vignette("design"). For more
explanation on the motivations, rationale, and needs for this algorithm
and package, check out the vignette("rationale"). To see
the specific data needed for this package and algorithm, see
vignette("data-sources").
Usage
First, let’s load up the package, as well as dplyr.
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(osdc)The core of this package depends on the list of variables within different registers that are needed in order to classify the diabetes status of an individual. This can be found in the dataset:
variable_description
#> # A tibble: 36 × 7
#> register_name register_abbrev variable_name start_year end_year
#> <chr> <chr> <chr> <dbl> <dbl>
#> 1 CPR-registerets befolkning… bef pnr 1968 NA
#> 2 CPR-registerets befolkning… bef koen 1968 NA
#> 3 CPR-registerets befolkning… bef foed_dato 1968 NA
#> 4 Laegemiddelstatistikregist… lmdb pnr 1995 NA
#> 5 Laegemiddelstatistikregist… lmdb eksd 1995 NA
#> 6 Laegemiddelstatistikregist… lmdb atc 1995 NA
#> 7 Laegemiddelstatistikregist… lmdb volume 1995 NA
#> 8 Laegemiddelstatistikregist… lmdb apk 1995 NA
#> 9 Laegemiddelstatistikregist… lmdb indo 1995 NA
#> 10 Landspatientregisterets ad… lpr_adm pnr 1977 2018
#> # ℹ 26 more rows
#> # ℹ 2 more variables: danish_description <chr>, english_description <chr>Let’s convert that to a nicer format to show the list as a table.
variable_description |>
select(register_name, register_abbrev, variable_name, english_description) |>
knitr::kable()| register_name | register_abbrev | variable_name | english_description |
|---|---|---|---|
| CPR-registerets befolkningstabel | bef | pnr | pseudonymised social security number |
| CPR-registerets befolkningstabel | bef | koen | sex |
| CPR-registerets befolkningstabel | bef | foed_dato | date of birth |
| Laegemiddelstatistikregisteret | lmdb | pnr | pseudonymised social security number |
| Laegemiddelstatistikregisteret | lmdb | eksd | date of purchase |
| Laegemiddelstatistikregisteret | lmdb | atc | ATC code (fully specified) |
| Laegemiddelstatistikregisteret | lmdb | volume | number of daily standard doses (DDD) in package |
| Laegemiddelstatistikregisteret | lmdb | apk | number of packages purchased |
| Laegemiddelstatistikregisteret | lmdb | indo | indication code |
| Landspatientregisterets administrationstabel (LPR2) | lpr_adm | pnr | pseudonymised social security number |
| Landspatientregisterets administrationstabel (LPR2) | lpr_adm | recnum | record id number |
| Landspatientregisterets administrationstabel (LPR2) | lpr_adm | d_inddto | date of admission or initial contact |
| Landspatientregisterets administrationstabel (LPR2) | lpr_adm | c_spec | specialty code of department |
| Landspatientregisterets diagnosetabel (LPR2) | lpr_diag | recnum | record id number |
| Landspatientregisterets diagnosetabel (LPR2) | lpr_diag | c_diag | diagnosis code |
| Landspatientregisterets diagnosetabel (LPR2) | lpr_diag | c_diagtype | diagnosis type |
| Landspatientregisterets kontakttabel (LPR3) | kontakter | cpr | pseudonymised social security number |
| Landspatientregisterets kontakttabel (LPR3) | kontakter | dw_ek_kontakt | record id number |
| Landspatientregisterets kontakttabel (LPR3) | kontakter | dato_start | date of admission or initial contact |
| Landspatientregisterets kontakttabel (LPR3) | kontakter | hovedspeciale_ans | specialty of department |
| Landspatientregisterets diagnosetabel (LPR3) | diagnoser | dw_ek_kontakt | record id number |
| Landspatientregisterets diagnosetabel (LPR3) | diagnoser | diagnosekode | diagnosis code |
| Landspatientregisterets diagnosetabel (LPR3) | diagnoser | diagnosetype | diagnosis type |
| Landspatientregisterets diagnosetabel (LPR3) | diagnoser | senere_afkraeftet | was the diagnosis retracted later? |
| Sygesikringsregisteret | sysi | pnr | pseudonymised social security number |
| Sygesikringsregisteret | sysi | barnmak | was the service provided to the patient’s child? |
| Sygesikringsregisteret | sysi | speciale | billing code of the service (fully specified) |
| Sygesikringsregisteret | sysi | honuge | year and week of service |
| Sygesikringsregisteret | sssy | pnr | pseudonymised social security number |
| Sygesikringsregisteret | sssy | barnmak | was the service provided to the patient’s child? |
| Sygesikringsregisteret | sssy | speciale | billing code of the service (fully specified) |
| Sygesikringsregisteret | sssy | honuge | year and week of service |
| Laboratoriedatabasens forskertabel | lab_forsker | patient_cpr | pseudonymised social security number |
| Laboratoriedatabasens forskertabel | lab_forsker | samplingdate | date of sampling |
| Laboratoriedatabasens forskertabel | lab_forsker | analysiscode | NPU code of analysis |
| Laboratoriedatabasens forskertabel | lab_forsker | value | numerical result of analysis |