This function requires that each source of register data is represented as a single DuckDB object in R (e.g. a connection to Parquet files). Each DuckDB object must contain a single table covering all years of that data source, or at least the years you have and are interested in.
Usage
classify_diabetes(
kontakter,
diagnoser,
lpr_diag,
lpr_adm,
sysi,
sssy,
lab_forsker,
bef,
lmdb,
stable_inclusion_start_date = "1998-01-01"
)Arguments
- kontakter
The contacts information table from the LPR3 patient register
- diagnoser
The diagnoses information table from the LPR3 patient register
- lpr_diag
The diagnoses information table from the LPR2 patient register
- lpr_adm
The administrative information table from the LPR2 patient register
- sysi
The SYSI table from the health service register
- sssy
The SSSY table from the health service register
- lab_forsker
The register for laboratory results for research
- bef
The BEF table from the civil register
- lmdb
The LMDB table from the prescription register
- stable_inclusion_start_date
Cutoff date after which inclusion events are considered true incident diabetes cases. Defaults to "1998-01-01", which is one year after the data on pregnancy events from the Patient Register are considered valid for dropping gestational diabetes-related purchases of glucose-lowering drugs. This default assumes that the user is using LPR and LMDB data from at least Jan 1 1997 onward. If the user only has access to LPR and LMDB data from a later date, this parameter should be set to one year after the beginning of the user's data coverage.
Value
The same object type as the input data, which would be a
duckplyr::duckdb_tibble() type object.
See also
See the osdc vignette for a detailed description of the internal implementation of this classification function.
Examples
# Can't run this multiple times, will cause an error as the table
# has already been created in the DuckDB connection.
register_data <- registers() |>
names() |>
simulate_registers() |>
purrr::map(duckplyr::as_duckdb_tibble) |>
purrr::map(duckplyr::as_tbl)
classify_diabetes(
kontakter = register_data$kontakter,
diagnoser = register_data$diagnoser,
lpr_diag = register_data$lpr_diag,
lpr_adm = register_data$lpr_adm,
sysi = register_data$sysi,
sssy = register_data$sssy,
lab_forsker = register_data$lab_forsker,
bef = register_data$bef,
lmdb = register_data$lmdb
)
#> # Source: SQL [?? x 5]
#> # Database: DuckDB 1.4.4 [unknown@Linux 6.14.0-1017-azure:R 4.5.2//tmp/Rtmp7YvlDu/duckplyr/duckplyr1a035401fb90.duckdb]
#> pnr stable_inclusion_date raw_inclusion_date has_t1d has_t2d
#> <chr> <date> <date> <lgl> <lgl>
#> 1 146605139851 2020-11-07 2020-11-07 FALSE TRUE
#> 2 732715981647 2020-08-24 2020-08-24 FALSE TRUE
#> 3 409442575549 2010-05-24 2010-05-24 FALSE TRUE
#> 4 108839343181 2018-08-30 2018-08-30 FALSE TRUE
#> 5 706974528463 2016-08-01 2016-08-01 FALSE TRUE
#> 6 745611946809 2018-10-29 2018-10-29 FALSE TRUE
#> 7 240771768588 2016-11-28 2016-11-28 FALSE TRUE
#> 8 298944792608 2007-11-26 2007-11-26 FALSE TRUE
#> 9 498989088479 2014-11-09 2014-11-09 FALSE TRUE