Add 2026-09-02 MHT exposure to a person-week skeleton
Source:R/lmed-v20260902.R
add_lmed_v20260902.RdWrites the product category columns, `approach1` to `approach3`, the `rd_approach*` columns, and the two person-level exclusion columns.
Arguments
- skeleton
A person-week `data.table` with `id` and `isoyearweek`. Weekly rows only. Where the skeleton comes from `swereg::create_skeleton()`, pass `skeleton[is_isoyear == FALSE]`. See Details.
- 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
The layer differs from `add_lmed_v20260828()` in one respect: a product gets its category from `inst/2023-mht/product_table_20260902.xlsx`, looked up on an exact normalised key, rather than from a prefix ladder. A delivered product with no row is an error.
It adds two columns that no earlier entry point wrote:
`ri_mht_excluded_product`, `TRUE` for every week of a person who ever held a product the table flags for removal
`ri_mht_excluded_reason`, the reason, or `NA`
**The function removes nobody.** It reports. Removing a person changes the cohort, and this layer owns columns of `skeleton`, never its rows.
Everything else is the 2026-08-28 behaviour, reached by calling that layer's own dated helpers rather than by copying them.
**`skeleton` MUST hold weekly rows only.** Each person MUST hold each of its ISO weeks once, consecutively, with no gap. A skeleton from `swereg::create_skeleton()` also carries one annual row per person per year, with `isoyearweek` such as `"1946-**"` and `is_isoyear` set to `TRUE`. An annual row is no ISO week. The function then stops with the error `skeleton$isoyearweek holds a value that is no ISO week: 1946-**`. Pass `skeleton[is_isoyear == FALSE]`, and fill the annual rows in the caller. That subset is a new `data.table`. The function writes its columns there, and the table the caller holds gets none of them.
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 is built from the real deliveries, so it holds no row
# for a name that exists only in a fixture. `Paracetamol` is one: the
# register writes branded spellings such as `Paracetamol Kodein Evolan`.
# Dropping it changes no exposure, because it is not MHT either way.
lmed <- lmed[produkt != "Paracetamol"]
# the fixture holds one negative-duration row, which warns
skeleton <- suppressWarnings(
add_lmed_v20260902(skeleton, lmed, verbose = FALSE)
)
skeleton[, .N, keyby = .(rd_approach1_single)]
#> Key: <rd_approach1_single>
#> rd_approach1_single N
#> <char> <int>
#> 1: exclude 2727
#> 2: local_or_none_mht 2027
#> 3: previous 140
#> 4: systemic_mht 717
#> 5: tibolone 5
skeleton[, .N, keyby = .(ri_mht_excluded_product, ri_mht_excluded_reason)]
#> Key: <ri_mht_excluded_product, ri_mht_excluded_reason>
#> ri_mht_excluded_product ri_mht_excluded_reason N
#> <lgcl> <char> <int>
#> 1: FALSE <NA> 5304
#> 2: TRUE possible gender-affirming therapy 312