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