Add 2026-10-02 MHT exposure to a person-week skeleton
Source:R/lmed-v20261002.R
add_lmed_v20261002.RdWrites every column that `add_lmed_v20260924()` writes, and adds `approach5`, `rd_approach5_single` and `rd_approach5_multiple`. It reads `inst/2023-mht/product_table_20261002.xlsx` and `inst/2023-mht/dataDictionary20261002.xlsx`, and no other workbook.
Arguments
- skeleton
A person-week `data.table` with `id` and `isoyearweek`. Weekly rows only, as for `add_lmed_v20260924()`.
- lmed
A `data.table` of dispensed prescriptions.
- id_name
The person identifier column of `lmed`.
- create_rd
Logical. If `FALSE`, writes no `rd_approach*` column.
- verbose
Logical. If `TRUE`, report progress with `message()`.
Details
Every column other than the three approach 5 columns equals the output of `add_lmed_v20260924()`. Approach 5 pools the oestrogen routes of approach 4, and gives the hormonal IUD (E1) its own level. The `post_grouping` sheet gives it the levels below, where oestrogen means A1, A2 or A6:
`estrogen_progesterone`: B4 or B11, or oestrogen with C1 or C5.
`estrogen_other_progestogen`: B1, B2, B3, B5 to B10, or B12, or oestrogen with C3, C4, D1, D2, D3, I1 or I2.
`estrogen_iud`: oestrogen with E1.
`estrogen_only`: oestrogen, in a week with no B1 to B12, C1 to C5, D1 to D3, E1, I1 or I2.
`tibolone`: F1.
`local_or_none_mht`: a week that lights no level above.
A week with oestrogen, E1 and one of C3, C4, D1, D2, D3, I1 or I2 lights both `estrogen_iud` and `estrogen_other_progestogen`.
The resolver is that of `add_lmed_v20260924()`. When two levels are lit, `approach5` reports the level that started most recently. Two levels that start in the same week are `clashingprescriptions` until the treated episode ends.
See also
add_lmed_v20260924, which documents the behaviour the
two entry points share. `vignette("lmed-v20261002")` explains approaches 1
to 5.
Examples
library(data.table)
skeleton <- copy(fake_skeleton_mht)
lmed <- copy(fake_lmed_2026)
# Utrogestan takes a codebook rule keyed on strength, so it needs `lnmn`.
lmed[, lnmn := NA_character_]
#> lopnr produkt edatum fddd lnmn
#> <int> <char> <Date> <num> <char>
#> 1: 1 Divigel 2015-01-05 90 <NA>
#> 2: 1 Divigel 2015-03-30 90 <NA>
#> 3: 1 Divigel 2015-06-22 90 <NA>
#> 4: 1 Divigel 2015-09-14 90 <NA>
#> 5: 1 Divigel 2015-12-07 90 <NA>
#> ---
#> 124: 16 Divigel 2016-02-26 90 <NA>
#> 125: 16 Cerazette 2016-03-01 90 <NA>
#> 126: 17 Divigel 2015-01-07 -30 <NA>
#> 127: 17 Divigel 2015-03-31 90 <NA>
#> 128: 18 Paracetamol 2015-01-02 28 <NA>
lmed[produkt == "Utrogestan", lnmn := "Utrogestan, kapsel, mjuk 100 mg"]
#> Index: <produkt>
#> lopnr produkt edatum fddd lnmn
#> <int> <char> <Date> <num> <char>
#> 1: 1 Divigel 2015-01-05 90 <NA>
#> 2: 1 Divigel 2015-03-30 90 <NA>
#> 3: 1 Divigel 2015-06-22 90 <NA>
#> 4: 1 Divigel 2015-09-14 90 <NA>
#> 5: 1 Divigel 2015-12-07 90 <NA>
#> ---
#> 124: 16 Divigel 2016-02-26 90 <NA>
#> 125: 16 Cerazette 2016-03-01 90 <NA>
#> 126: 17 Divigel 2015-01-07 -30 <NA>
#> 127: 17 Divigel 2015-03-31 90 <NA>
#> 128: 18 Paracetamol 2015-01-02 28 <NA>
# The product table holds no row for the fixture-only name `Paracetamol`.
lmed <- lmed[produkt != "Paracetamol"]
# the fixture holds one negative-duration row, which warns
skeleton <- suppressWarnings(
add_lmed_v20261002(skeleton, lmed, verbose = FALSE)
)
skeleton[, .N, keyby = .(approach5)]
#> Key: <approach5>
#> approach5 N
#> <char> <int>
#> 1: estrogen_only 640
#> 2: estrogen_other_progestogen 110
#> 3: estrogen_progesterone 82
#> 4: local_or_none_mht 4779
#> 5: tibolone 5