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00518ec
feat: add BestDose optimization functionality
Siel Feb 12, 2026
04f741b
fix: use devtools::load_all() in bestdose example script
Siel Feb 12, 2026
19b924c
fix: limits from model not applied properly
mnneely Feb 16, 2026
e0a7bd9
Merge remote-tracking branch 'origin/main' into Michael
mnneely Feb 17, 2026
9cf18bb
fix: malformed PM_post
mnneely Feb 17, 2026
3602e9b
fix: plotting post predictions with data; remade data objects
mnneely Feb 17, 2026
76da1a4
fix: inappropriate truncating of long color names in plot.PM_data
mnneely Feb 17, 2026
1f49bbe
wip: update summary.PM_sim
mnneely Feb 19, 2026
44b0d6a
fix: max_cycles are passed correctly, also error model
Siel Mar 4, 2026
377ab05
fix: missing path in PMcheck or misspelled arguments in PM_sim
mnneely Mar 4, 2026
9fc29dd
feat: new bestdose API
Siel Mar 6, 2026
f909cc4
chore: remove old functions
mnneely Mar 6, 2026
7c8e433
fix: using PMcore on gh
Siel Mar 6, 2026
817cfeb
chore: remove optimize-raw
mnneely Mar 6, 2026
e6cf5df
Merge remote-tracking branch 'origin/bestdose' into BD-Michael
mnneely Mar 6, 2026
c884649
chore: simplify function names
mnneely Mar 7, 2026
898200f
Merge remote-tracking branch 'origin/Michael' into BD-Michael
mnneely Mar 7, 2026
3f3910a
chore: update documentation after merge
mnneely Mar 7, 2026
8a44db7
wip: creating simulated past
mnneely Mar 7, 2026
9ff94b5
wip: update example objects
mnneely Mar 7, 2026
0b62a5f
wip: documentation
mnneely Mar 7, 2026
dc79248
wip: compile with silence and only recompile if simulating with covar…
mnneely Mar 7, 2026
fca65d7
feat: add plots
mnneely Mar 7, 2026
c9b06fb
fix: remove unneeded example
mnneely Mar 7, 2026
bd07b05
wip: register S3 plot.bd method
mnneely Mar 7, 2026
47fd9b5
wip: update plot, add inline targets, sort standard data by id, time,…
mnneely Mar 9, 2026
f73ccc4
Redesign bestdose API and fix bugs
Siel Mar 9, 2026
3ac3e99
Merge BD-Michael: integrate inline future API and improved plotting
Siel Mar 9, 2026
c2e20c9
fix: fixed some errors in the model definition of the example, suppre…
Siel Mar 10, 2026
f2fc5df
fix: the bd_new example now has no time_offset
Siel Mar 10, 2026
d2c58f6
fix: plot is not handling properly time_offset = Null, there are stil…
Siel Mar 10, 2026
5558ac9
wip: sorting PM_data
mnneely Mar 10, 2026
962ea95
Merge branch 'BD-Michael' of https://github.com/LAPKB/Pmetrics into B…
mnneely Mar 10, 2026
055b19f
wip: bias_weight -> prior_weight; target -> future. Accept list, PM_d…
mnneely Mar 10, 2026
73879ee
wip: remove include/exclude
mnneely Mar 10, 2026
f9e7a00
feat: add default date format to PMoptions based on user locale
mnneely Mar 10, 2026
07213a5
wip: updating report
mnneely Mar 13, 2026
89d0949
wip: update report try auc example; crash
mnneely Mar 13, 2026
1b295a2
wip: update example
mnneely Mar 13, 2026
70c9fb6
feat: function to download latest version of R
mnneely Mar 14, 2026
34725f2
wip: BD report updates
mnneely Mar 16, 2026
1ba5050
fix: missing path in PMcheck
mnneely Mar 16, 2026
f7cce6c
WIP: remove bestdose for now (developing in other branch)
mnneely Mar 16, 2026
f97dd2e
fix: PM_compare not pulling covergence properly
mnneely Mar 16, 2026
e89f508
fix: update best logic in PM_compare
mnneely Mar 16, 2026
f9be770
fix: remove errors file
mnneely Mar 16, 2026
a288cc6
wip: update documentation for PM_compare
mnneely Mar 16, 2026
132a268
wip: removing bestdose artifacts from this version
mnneely Mar 18, 2026
f31d8f5
fix: notify user cl models not yet supported
mnneely Mar 19, 2026
7fb037d
fix: handle missing analytic models
mnneely Mar 25, 2026
5a5a60a
fix: update across function
mnneely Mar 25, 2026
93df243
wip: cleaning old files
mnneely Mar 25, 2026
2293826
Stop tracking Archived; add to .gitignore
mnneely Mar 25, 2026
ca890b2
Merge remote-tracking branch 'origin/main' into Michael
mnneely Mar 25, 2026
fa21ba3
wip: update objects
mnneely Mar 25, 2026
f6f1a8b
Update R/PM_sim.R
mnneely Mar 25, 2026
906b4b2
fix: typo in help
mnneely Mar 25, 2026
b888476
Merge branch 'Michael' of https://github.com/LAPKB/Pmetrics into Michael
mnneely Mar 25, 2026
133f853
fix: check for updates periodically
mnneely Mar 26, 2026
ab132e5
fix: add check_updates, latestR, downloadR to _pkgdown.yml
mnneely Mar 26, 2026
d9a574e
Initial plan
Copilot Mar 26, 2026
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6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -63,14 +63,17 @@ inst/Learn/_freeze/
data-raw/Runs/
tests/testthat/Runs/
Examples
!inst/Examples/
Experimental
other/
1
2
3
errors.xlsx

# Misc project outputs
*_test.R
!inst/Examples/Rscript/*_test.R
docs/
docs
src/rust/vendor
Expand All @@ -79,3 +82,6 @@ src/Makevars.win

/.quarto/
**/*.quarto_ipynb

# Old files
Archived
1 change: 0 additions & 1 deletion Archived/.gitignore

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891 changes: 0 additions & 891 deletions Archived/ArchivedFunctions.R

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6 changes: 0 additions & 6 deletions Archived/ERRrepScript.R

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674 changes: 0 additions & 674 deletions Archived/LICENSE

This file was deleted.

321 changes: 0 additions & 321 deletions Archived/LegacyPlots.R

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251 changes: 0 additions & 251 deletions Archived/MMopt.R

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