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.
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 list:
registers()
#> $bef
#> $bef$name
#> [1] "CPR-registerets befolkningstabel"
#>
#> $bef$start_year
#> [1] 1968
#>
#> $bef$end_year
#> [1] NA
#>
#> $bef$variables
#> # A tibble: 3 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <chr>
#> 1 pnr Pseudonymiseret cpr-nummer Pseudonymised social security … character
#> 2 koen Koen Gender/sex integer
#> 3 foed_dato Foedselsdato Date of birth Date
#>
#>
#> $lmdb
#> $lmdb$name
#> [1] "Laegemiddelstatistikregisteret"
#>
#> $lmdb$start_year
#> [1] 1995
#>
#> $lmdb$end_year
#> [1] NA
#>
#> $lmdb$variables
#> # A tibble: 6 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <list>
#> 1 pnr Pseudonymiseret cpr-nummer Pseudonymised social secu… <chr [1]>
#> 2 eksd Ekspeditionsdato Date of purchase <chr [2]>
#> 3 atc ATC-kode (fuldt specificeret) ATC code (fully specified) <chr [1]>
#> 4 volume Antal standarddoser (DDD) i pakken Number of daily standard … <chr [1]>
#> 5 apk Antal pakker koebt Number of packages purcha… <chr [1]>
#> 6 indo Indikationskode for recept Indication code <chr [1]>
#>
#>
#> $lpr_adm
#> $lpr_adm$name
#> [1] "Landspatientregisterets administrationstabel (LPR2)"
#>
#> $lpr_adm$start_year
#> [1] 1977
#>
#> $lpr_adm$end_year
#> [1] 2018
#>
#> $lpr_adm$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <list>
#> 1 pnr Pseudonymiseret cpr-nummer Pseudonymised social… <chr [1]>
#> 2 recnum Kontakt id-nummer Record id number <chr [1]>
#> 3 d_inddto Indlaeggelsesdato (start paa kontakt) Date of admission or… <chr [2]>
#> 4 c_spec Afdelings specialekode Specialty code of de… <chr [1]>
#>
#>
#> $lpr_diag
#> $lpr_diag$name
#> [1] "Landspatientregisterets diagnosetabel (LPR2)"
#>
#> $lpr_diag$start_year
#> [1] 1977
#>
#> $lpr_diag$end_year
#> [1] 2018
#>
#> $lpr_diag$variables
#> # A tibble: 3 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <chr>
#> 1 recnum Kontakt id-nummer Record id number character
#> 2 c_diag Diagnosekode Diagnosis code character
#> 3 c_diagtype Diagnosetype Diagnosis type character
#>
#>
#> $kontakter
#> $kontakter$name
#> [1] "Landspatientregisterets kontakttabel (LPR3)"
#>
#> $kontakter$start_year
#> [1] 2019
#>
#> $kontakter$end_year
#> [1] NA
#>
#> $kontakter$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <list>
#> 1 cpr Pseudonymiseret cpr-nummer Pseudonymised soci… <chr [1]>
#> 2 dw_ek_kontakt Kontakt id-nummer Record id number <chr [1]>
#> 3 dato_start Indlaeggelsesdato (start paa … Date of admission … <chr [2]>
#> 4 hovedspeciale_ans Afdelings speciale Specialty of depar… <chr [1]>
#>
#>
#> $diagnoser
#> $diagnoser$name
#> [1] "Landspatientregisterets diagnosetabel (LPR3)"
#>
#> $diagnoser$start_year
#> [1] 2019
#>
#> $diagnoser$end_year
#> [1] NA
#>
#> $diagnoser$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <chr>
#> 1 dw_ek_kontakt Kontakt id-nummer Record id number character
#> 2 diagnosekode Diagnosekode Diagnosis code character
#> 3 diagnosetype Diagnosetype Diagnosis type character
#> 4 senere_afkraeftet Blev diagnosen senere afkraef… Was the diagnosis … character
#>
#>
#> $sysi
#> $sysi$name
#> [1] "Sygesikringsregisteret"
#>
#> $sysi$start_year
#> [1] 1990
#>
#> $sysi$end_year
#> [1] 2005
#>
#> $sysi$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <chr>
#> 1 pnr Pseudonymiseret cpr-nummer Pseudonymised social… character
#> 2 barnmak Blev ydelse ydet til patientens barn? Was the service prov… integer
#> 3 speciale Ydelsens honoreringskode Billing code of the … character
#> 4 honuge Aar og uge for ydelse Year and week of ser… character
#>
#>
#> $sssy
#> $sssy$name
#> [1] "Sygesikringsregisteret"
#>
#> $sssy$start_year
#> [1] 2006
#>
#> $sssy$end_year
#> [1] NA
#>
#> $sssy$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <chr>
#> 1 pnr Pseudonymiseret cpr-nummer Pseudonymised social… character
#> 2 barnmak Blev ydelse ydet til patientens barn? Was the service prov… integer
#> 3 speciale Ydelsens honoreringskode Billing code of the … character
#> 4 honuge Aar og uge for ydelse Year and week of ser… character
#>
#>
#> $lab_forsker
#> $lab_forsker$name
#> [1] "Laboratoriedatabasens forskertabel"
#>
#> $lab_forsker$start_year
#> [1] 2011
#>
#> $lab_forsker$end_year
#> [1] NA
#>
#> $lab_forsker$variables
#> # A tibble: 4 × 4
#> name danish_description english_description data_type
#> <chr> <chr> <chr> <list>
#> 1 patient_cpr Pseudonymiseret cpr-nummer Pseudonymised social secu… <chr [1]>
#> 2 samplingdate Dato for proevetagning Date of sampling <chr [2]>
#> 3 analysiscode Analysens NPU-kode NPU code of analysis <chr [1]>
#> 4 value Numerisk resultat af analyse Numerical result of analy… <chr [1]>