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Changelog

We use Commitizen to automatically increase the versions, release the package on GitHub (with a tag), and auto-generate this NEWS file. The items listed below are generated based on our commit messages that follow the Conventional Commits standard.

0.9.17 (2025-12-04)

Fix

:bug: split out case data from sim, joining them as one in tests (#456)

0.9.16 (2025-12-01)

Perf

:zap: classification requires DuckDB/SQL (#410)

0.9.15 (2025-11-27)

Refactor

:truck: move ICD8, ICD10, and sim definitions into sysdata (#444)

0.9.14 (2025-11-26)

Perf

:zap: use union_all() for database version of bind_rows() (#439)

0.9.13 (2025-11-21)

Refactor

♻ replace stringr functions with base alternatives in algorithm (#419)

0.9.12 (2025-11-21)

Refactor

:recycle: replace str_detect() with grepl in algorithm (#416)

0.9.11 (2025-11-20)

Refactor

:truck: use from_*() prefix for logical inclusion helper variables (#415)

0.9.10 (2025-11-20)

Refactor

♻ add logical inclusion variables to classification logic (#404)

0.9.9 (2025-11-20)

Perf

:zap: duckplyr doesn’t support lubridate::as_date(), use as.Date() (#408)

0.9.8 (2025-11-20)

Perf

:zap: DuckDB can’t use rename_with(), switch to rename() (#409)

0.9.7 (2025-11-19)

Fix

:bug: Non-cases test filter (#412)

0.9.6 (2025-11-19)

Fix

🐛 convert NAs to FALSE at end in prep for classifying (#379)

0.9.5 (2025-11-19)

Fix

🐛 changes to drop_pregnancies() to support the new refactored logic (#405)

0.9.4 (2025-11-19)

Fix

:bug: don’t use collect() or compute() inside code, only outside (#403)
:bug: convert NAs to FALSE and drop any if TRUE for pregnancy (#398)

0.9.3 (2025-11-19)

Fix

:bug: don’t need to drop indication code after exclusion (#395)

Refactor

♻ add logical helper variables for inclusion events (#400)

0.9.2 (2025-11-17)

Fix

:bug: wrong value in the c_diag of the cases data (#394)

0.9.1 (2025-11-17)

Refactor

:recycle: enhance (non-)case data with sim data and convert to duckdb tibble (#396)

0.9.0 (2025-11-14)

Feat

:sparkles: require using DuckDB in classify_diabetes() (#391)

0.8.8 (2025-10-05)

Fix

:bug: logic around is.na() in pregnancy event isn’t needed (#367)

0.8.7 (2025-10-03)

Refactor

:recycle: deselect columns we don’t need later (#377)

0.8.6 (2025-10-03)

Fix

:bug: use .data$ instead of quotes around is_hba1c (#376)

0.8.5 (2025-10-03)

Fix

:bug: remove HbA1c rows when calculating insulin columns (#371)

0.8.4 (2025-10-03)

Refactor

♻ add separate keep_two_earliest_events() function (#369)

0.8.3 (2025-10-02)

Refactor

:truck: rename cases() to edge_cases() to match file name (#368)

0.8.2 (2025-10-02)

Fix

:bug: use full_join() instead of left_join() (#365)

0.8.1 (2025-10-02)

Fix

:bug: remove rows with NA in both T1 and T2D (#363)

0.8.0 (2025-10-02)

Feat

:sparkles: add non-case of someone with PCOS (#362)

0.7.1 (2025-09-19)

Refactor

:truck: drop_potential_pcos() -> drop_pcos() (#359)

0.7.0 (2025-09-19)

Feat

✨ create_inclusion_dates() (#316)

Refactor

:truck: rename inclusion_ and exclusion_ to keep_ and drop_ (#356)

0.6.3 (2025-09-18)

Refactor

:recycle: convert logic parsing code into its own function (#350)

0.6.2 (2025-09-18)

Refactor

🚚 rename to exclude_pregnancies() (#351)

0.6.1 (2025-09-18)

Refactor

:recycle: “parse, don’t verify”, select correct columns at start (#345)

0.6.0 (2025-09-18)

Feat

:sparkles: classify_t1d() (#309)

0.5.0 (2025-09-18)

Feat

✨ add_t1d_diagnoses_cols() (#288)

0.4.2 (2025-09-18)

Refactor

:truck: rename to keep_, not get_ for pregnancy dates (#346)

0.4.1 (2025-09-18)

Refactor

♻ move add_insulin_purchases_cols() down to after exclusions (#338)

0.4.0 (2025-09-16)

Feat

:sparkles: add_insulin_purchases_cols() (#296)

0.3.4 (2025-08-27)

Refactor

:truck: use _diagnosis for clearer language (#332)

0.3.3 (2025-08-25)

Refactor

:fire: is_non_insulin_gld_code isn’t used, so removing it (#323)

0.3.2 (2025-08-25)

Refactor

:fire: remove most has_ variables, they aren’t needed anymore (#324)

0.3.1 (2025-08-25)

Refactor

:fire: no longer need atc after excluding pregnancy cases (#320)

0.3.0 (2025-08-22)

Feat

:sparkles: check_data_types() (#304)

0.2.0 (2025-08-22)

Feat

:sparkles: join_inclusions() added as step (#246)
:sparkles: include_diabetes_diagnoses() (#258)
✨ exclude_pregnancy() (#261)
:sparkles: first exclusion step (#243)
:sparkles: add exclude_potential_pcos() (#214)
:sparkles: add simulate_registers() (#208)
:sparkles: skeleton of the core diabetes classification (#142)
✨ add include_podiatrist_services() with tests (#182)
✨ add simulated register data to targets pipeline (#167)
✨ update algorithm logic to include regex in parentheses (#159)
:sparkles: add include_gld_purchases() (#138)
add join_lpr3 with tests (#125)
function to join the LPR2 registers (#118)
add join_lpr3 with tests
:sparkles: add the function to join the LPR2 registers
create function to include HbA1c criteria
add function that join inclusion events
helper functions to insert data into Markdown vignettes
internal function to extract logic from algorithm data. Untested
create (draft) function to include HbA1c criteria
added simulated data
:construction: code to get list of Danish ICD 8 codes
:construction: expand on the fixer functions for the simulation data
add function to convert to lowercase.
internal function to get the required variables for a register.
function to get list of the registers abbreviations
internal function to verify if the dataset has required variables.
:sparkles: workflow that assigns PR author as assignee

Fix

:bug: update algorithm() examples with updated logic names (#302)
:bug: refer to correct workflow in R-CMD-check badge (#299)
algorithm: :bug: barnmak logic in podiatrist_services (#278)
:bug: fixes notes about factors and reading CSV file (#248)
:bug: rename pregnancy event variable in algorithm by removing lpr2_ (#236)
🩹 don’t filter to two first observations in include_hba1c() (#202)
:bug: this function needs to be exported so Arrow can find it (#193)
:bug: this function needs to be exported so Arrow can find it
:memo: commit message auto-generated by document workflow (#183)
:bug: regex works on more than one =~ (#176)
:bug: misc fixes to successfully run r-cmd-check (#168)
🐛 change honuge format to yyww (#165)
:bug: verify function actually throws error (#128)
the logic criteria wasn’t being correctly loaded, need to convert to expression
:art: remove duplicate arrow from function flow puml
remove return since it’s not needed
add “indo” to condition since it’s used in the function
flip the condition so it’s true when both “atc” and “name” is in data
typos
:bug: keep earliest two dates, not samples
diagnosis -> diagnoses in inclusion function
add missing header in output example table
minor text edit to make sentence clearer
specify that we use the primary diagnosis for classification
update classify diabetes type flow chart based on feedback from @Aastedet
describe classifying steps as “filters” with “criteria”
add oxford comma to header
:fire: remove old figure experiments
we don’t have tidyverse as a dependency, it isn’t needed here
add missing bracket
apply suggestions from code review
small fix to the comments and proportion of NPU units inserted
:art: add space before register_abbrev
NPU should be 8 long in total, not 8 integers
add “_status” to the name of the “classify_diabetes” function
minor text edits and change “classification date” to “inclusion date”
typo
remove all mentions of “before index date” since these filters are based on all data
edits from code suggestions
move set.seed up
change pnr to only include 001-100 independent of num_samples
removed leftover man/ file that triggers check warning
DuckDB requires colnames(), not names()
Minor text edits
remove extra starting column
convert the variable list into an exported object, not internal
use the created function for getting the abbrev

Refactor

:recycle: add (non-)insulin drug indicator variables (#298)
:recycle: rename verify_required_variables() to check_required_variables() (#306)
♻ move column name lowercasing to classify_diabetes() (#295)
:recycle: criteria -> logic (#294)
:recycle: move lpr2 primary diagnosis logic to algorithm (#289)
♻ update join_lpr3() to be prepare_lpr3() (#273)
:recycle: make yyww_to_yyyymmdd() internal (#283)
:recycle: update prepare_lpr2() col names to be _dept (#282)
:recycle: align variable names in algorithm (#277)
:recycle: update join_lpr2() to be prepare_lpr2() (#272)
:recycle: remove verifying from internal functions (#259)
:recycle: rename cpr column to pnr in join_lpr3() (#245)
:recycle: moved registers into its own R code (#221)
:recycle: change “!” to “NOT” (#226)
:recycle: move algorithm into R file (#204)
:recycle: add contained_doses variable to output (#187)
:recycle: remove name and vnr (#185)
:recycle: make joinable generated padded integers (#170)
take a dataframe rather than a string name of the register
these functions should only output data
:recycle: convert the data-raw/ scripts into functions
kontakter should come first so cpr is first column, plus use inner join
keep only earliest two dates, might not work with some databases
move ICD8 processing into own section and store only relevant info
completely refactor simulation code since simstudy was not working
:recycle: rewrote and revised the code to add false metformin
create function to make pnr, plus other small edits

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