Add 2026-09-24 MHT exposure to a person-week skeleton
Source:R/lmed-v20260924.R
add_lmed_v20260924.RdWrites every column that `add_lmed_v20260922()` writes, and adds `approach4`, `rd_approach4_single` and `rd_approach4_multiple`. It reads `inst/2023-mht/product_table_20260924.xlsx` and `inst/2023-mht/dataDictionary20260924.xlsx`, and no other workbook.
Arguments
- skeleton
A person-week `data.table` with `id` and `isoyearweek`. Weekly rows only, as for `add_lmed_v20260922()`.
- 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 4 columns equals the output of `add_lmed_v20260922()`. Approach 4 splits systemic oestrogen by route and by progestogen type. The `post_grouping` sheet gives it these levels:
`oral_estrogen_progesterone`: B4 or B11, or oral oestrogen (A2 or A6) with C1 or C5.
`oral_estrogen_other_progestogen`: B2, B3, B5, B6, B8, B9, B10 or B12, or A2 or A6 with C3, C4, D1, D2, D3, E1, I1 or I2.
`transdermal_estrogen_progesterone`: transdermal oestrogen (A1) with C1 or C5.
`transdermal_estrogen_other_progestogen`: B1 or B7, or A1 with C3, C4, D1, D2, D3, E1, I1 or I2.
`estrogen_only`: A1, A2 or A6, 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.
The resolver is that of `add_lmed_v20260922()`. When two levels are lit, `approach4` 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_v20260922, which documents the behaviour the
two entry points share. `vignette("lmed-v20260924")` explains approach 4,
and checks each of its worked cases when it builds.
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_v20260924(skeleton, lmed, verbose = FALSE)
)
skeleton[, .N, keyby = .(approach4)]
#> Key: <approach4>
#> approach4 N
#> <char> <int>
#> 1: estrogen_only 640
#> 2: local_or_none_mht 4779
#> 3: oral_estrogen_other_progestogen 28
#> 4: oral_estrogen_progesterone 10
#> 5: tibolone 5
#> 6: transdermal_estrogen_other_progestogen 82
#> 7: transdermal_estrogen_progesterone 72