v3.0.2

The only change in this release is that the bbi nonmem summary output will now refer to individuals in the data set as "Subjects" instead of "Patients", in accordance with the terminology widely used in scientific and medical literature.

Changelog

ee60eee Merge pull request #211 from metrumresearchgroup/develop
b6be96b Merge pull request #209 from metrumresearchgroup/fix/patients_to_subjects
4a9398a fix:changing patients to subjects in summary output

v3.0.1

Release Notes

Primarily a patch to fix a bug when parsing output from NONMEM 7.5 runs (#205). Also ran gofmt and cleaned up some old files and documentation that had gotten stale and was no longer in use or accurate (#206).

Changelog

8e30805 Merge pull request #208 from metrumresearchgroup/develop
39ae868 Merge pull request #206 from metrumresearchgroup/fmt/proj
d9d592f Merge branch 'develop' into fmt/proj
875ab7c doc: address comments from seth [SKIP CI]
1084064 Merge branch 'master' of github.com:metrumresearchgroup/bbi into develop
7a2285c Merge pull request #205 from metrumresearchgroup/feat/nm75
205e719 doc: cleanup [SKIP CI]
daed428 fmt: go fmt project
d3cf17d test: add note about needing to expand tests
3cd86d3 feat: update for nm75 shrinkage
9ca7e51 update deps and remove server

v3.0.1-rc1

Changelog

39ae868 Merge pull request #206 from metrumresearchgroup/fmt/proj
d9d592f Merge branch 'develop' into fmt/proj
875ab7c doc: address comments from seth [SKIP CI]
1084064 Merge branch 'master' of github.com:metrumresearchgroup/bbi into develop
7a2285c Merge pull request #205 from metrumresearchgroup/feat/nm75
205e719 doc: cleanup [SKIP CI]
daed428 fmt: go fmt project
d3cf17d test: add note about needing to expand tests
3cd86d3 feat: update for nm75 shrinkage
9ca7e51 update deps and remove server

v3.0.0

Rename to bbi

There are no functional changes in this release, but it represents the official rename from babylon to bbi. Previously bbi was used as an alias for the CLI to babylon and by default the built binary was saved as bbi. Going forward it is the name of the entire app. The accompanying R package will now be known as bbr.

Changelog

3ac76a4 fixing goreleaser version path
0f68c43 Merge pull request #204 from metrumresearchgroup/develop
8df424a Merge pull request #203 from metrumresearchgroup/rename_to_bbi
2e4ed8c test: cleaning up references to babylontest
a11a4e0 test: temporarily changed bbitest back to babylontest for drone testing
6992a25 made package path relative instead of github.com...
72bff70 WIP: changing all babylon to bbi, first try. No tests have been run yet.
8b14bb8 Merge pull request #196 from metrumresearchgroup/release/2.3.1
cd72325 Merge pull request #192 from metrumresearchgroup/fix/period-in-model-path

v2.3.1

Release notes

Bug fixes

• Increased buffer size for reading lines from the .ext file to 256k. (#191)

• Changed checks for Bayesian and Non-gradient estimation methods to partial string matching so that more estimation methods are correctly matched. (#191)

• Changed lower-diagonal lookup to a dynamic function instead of a lookup table. This effectively means there is no longer a limit on the number of ETA's that can be parsed from a model. (#189)

• Fixed bug where model files with a period in the name (i.e. 1000.1.ctl) were being parsed incorrectly. (#192)

Changelog

8209f9f fix: need to trim leading . from extension
081b549 fix: use FileAndExt instead of splitting manually (and incorrectly)
c965b95 Merge pull request #191 from metrumresearchgroup/fix/empty-params-timw
cf4d85e fix: surfacing error instead of panicing in ReadParamsAndOutputFromExt
11fa512 fix: increase the max buffer size in ReadParamsAndOutputFromExt to accommodate very wide tables (lots of params)
b060043 fix: Changed CheckIfNotGradientBased and CheckIfBayesian to get all methods that mention relevant strings
54ce915 refactor: made lowerDiagonalLengthToDimension return (0, false) for off-diagonals to conform with previous behavior. Also added documentation comment.
8bc4b7c Merge pull request #189 from metrumresearchgroup/fix/long-etas
96c9bc0 feat: made lowerDiagonalLengthToDimension into a function that calculates dynamically instead of using a lookup table
f93a795 fix: expand number of etas possible to 300
2439917 refactor: generalize Shk and lst parsing

v2.3.0

Release Notes

All user-facing changes for this release only effect the bbi nonmem summary command and its output. There are also some changes to the CI configuration to facilitate rendering updated validation documents with babylontest and goProjectValidator.

Additions and changes

• bbi nonmem summary will no longer parse the .cov and .cor files
  • summary --json output will no longer have covariance_theta or correlation_theta elements
  • --no-cov-file and --no-cor-file flags are deprecated
• bbi nonmem covcor command now returns the json output that was formerly contained in the covariance_theta or correlation_theta elements. The --json flag is not needed for this command. It always returns json.
• The following fields were added or modified in the bbi nonmem summary --json output:
  • ofv -- Previously included the objective function value for only the last estimation method. Now includes all estimation methods.
  • condition_number -- The condition number. This will only be in the .lst file in certain cases (when scientists ask for it in the $COV block PRINT=E). There will be one for each estimation method. If any of them are large, the large_condition_number boolean under run_heuristics will be true.
  • eta_pval_significant -- Added to run_heuristics. true if any shrinkage_details.pval < 0.05. Will be false if no shrinkage file is present.
  • PRDERR -- Added to run_heuristics. Indicates whether a PRDERR file is present in the output directory.

Bug fixes

• Previously, the .shk file was not added to the files_used section of the bbi nonmem summary --json output, even when it was used. This has been fixed.

Changelog

d1dd901 Merge pull request #185 from metrumresearchgroup/develop
0907950 Merge pull request #182 from metrumresearchgroup/release/2.3.0
3fda07d changing to user-stories-230 babylontest branch for docs
550168f fix: reverting version because this is what it has on master
66e5649 fix: updated version to 2.3.0 from develop
8ae846b validation: updating story names in validation.json to match markdown in babylontest
c8057ca fix: pushing update to timeout to see if it will actually take effect
9f0bbae fix: Updating drone to use script to manually check for output that indicates failure
aa5ef72 pointing to babylontest/validation-2.3.0 branch to build validation docs
7ba072c fix: prederr to prderr in bbi summary --json
52193c0 release: added validation docs to validation.json
d15ef96 Merge pull request #176 from metrumresearchgroup/feature/new-summary-fields-2008
4ffd6cf Merge branch 'develop' of github.com:metrumresearchgroup/babylon into feature/new-summary-fields-2008
5292a7e Merge pull request #174 from metrumresearchgroup/refactor/cov-cor-out
430f72c feat: added better help messaging when nonexistent command is issued
3d1e93a fix: added explicit error msg when wrong file extension passed to summary
3433a87 fix: added PRIOR to constant parsing for Bayesian methods
be0d88a fix: fixed missing shrinkage bug in summary table method
4204a00 WIP: cleaning up old print statement
fb1d387 fix: catching empty .ext file when renamed with FILE in Janelles 1001 test model
12f2eea cleanup
855e188 WIP: made condition_number get each estimation method
0ea59f7 fix: changed so Bayesian doesnt expect shrinkage file
f9712d7 feat: added parsing objective function from multiple est methods
5ad8349 WIP: added PRDERR and answered p-value subpop question
7f8db5d WIP: adding eta_pval heuristic
e0253bc WIP: cleanup
cc25aa3 Merge pull request #173 from metrumresearchgroup/feature/add-condition-number
72aa981 WIP: added bbi nonmem covcor command, but still need to add tests
4621c4f Merge branch 'feature/add-condition-number' of github.com:metrumresearchgroup/babylon into refactor/cov-cor-out
7a5b686 fix: added main binary to .gitignore
017665d fix: fixed getConditionNumber to work with multiple lines and added test case
2f1592b cleanup: removing binary
7033041 WIP: fixed current tests
64c439d WIP: debugging testing
9ae1e27 WIP: removed cov and cor from summary and created
bc069ef Merge branch 'develop' of github.com:metrumresearchgroup/babylon into feature/add-condition-number
66fe297 WIP: first shot at condition number
f0962aa Merge pull request #171 from metrumresearchgroup/feature/custom-file-names
5a60341 fix: error if invalid modeloutput config present
21ca590 feat: implement parallel summarization of multiple models
c1d6914 feat: proper custom files and addition of total cpu time
61deae2 wip: first cut at adding custom file names for summary files
a18c7c2 fix: objective function importance sampling is not gradient based causing error due to no shrinkage
2882f34 fix: bad log statement
c607c86 Merge pull request #169 from metrumresearchgroup/fix/hash-equality

v2.3.0-rc5

Changelog

v2.3.0-rc4b

Changelog

v2.3.0-rc4

Changelog

3fda07d changing to user-stories-230 babylontest branch for docs
550168f fix: reverting version because this is what it has on master
66e5649 fix: updated version to 2.3.0 from develop
8ae846b validation: updating story names in validation.json to match markdown in babylontest

v2.3.0-rc3

Changelog

c8057ca fix: pushing update to timeout to see if it will actually take effect
9f0bbae fix: Updating drone to use script to manually check for output that indicates failure