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cbd80b8 Create LICENSE 10a90ec Update README.md 0407c45 Tbt/add tutorial back (#129) a354160 Update README.md 1666644 Add thesis link f813308 Fixing the CI failure. (#128) 4c30bba Research folder. 3edfe1d Responsive plotting (#127) 13a1cd4 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) 75c6cf7 Add back fast math routines (#126) 10ba41c Fully revert performance changes (#125) 747d848 Revert some performance changes (#124) 2b41a4a Merge branch 'tbt/vscode_config' 6a86ad2 Upgraded vscode config. 9653991 Add slack alerting for CI pipeline (#120) 2bbc28a Small bug fixes for main branch. (#122) 37aa0c9 We become imprint. (#112) 706901a Additional optimizations for Jax Fast INLA (#111) 662ae4a A Python Grid (#105) a0e87cb Remove obsolete Python dependency management (#110) 14e4923 Update obsolete Github links (#109) 8f91d9c Add CI badge to README (#108) 1dae617 Run INLA in 32-bit floating point (#106) c8d3c54 Add CI caching for Conda, Bazel, Pre-commit (#107) 3ff9393 Implementing a fixed N upper bound calculation in Python (#104) ffa8a59 GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) e858feb Exact binomial type I error for Berry. (#95) 183d284 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) a367bd1 Fix for HyperPlane.intersect. (#100) ec37f47 Optimize typeI error with gradient ascent to find the worst grid points. (#94) ea2ced9 Final Berry notebooks and examples (#93) c5e817e Update README.md 5e6b168 Make colorscale configurable through UI (#92) ff7ae76 Update README.md 5ca3d2c Update README.md 6c08499 Running Berry/INLA accumulation. (#91) 608216f Merge pull request #90 from Confirm-Solutions/james.yang/python-models 6c92ad5 Make example smaller c0a74c5 Revert back to numpy version ab9680c Add jax version 502762a Remove print 8accb2e Fix structure and get simple gaussian model from python workin 0c0647b Add trampoline functionality and small test a3cd67b Add back export for std::mt19937 c8d5a8f Simplify generation of bazelrc (#88) a43c92e Add thompson model (#86) aaee63a Merge pull request #85 from mikesklar/tbt/build_quick_fix edff4ca OpenMP linker flag for Mac. Add clangxx to environment.yml da74604 Merge pull request #83 from mikesklar/tbt/conda 3ceb7af Readme updates: installing conda, clarifying clang/gcc usage. d1e7bd0 Implement inference caching (#79) 2134058 clang-format 13.0.1 is now standard. bf76aa5 clang-format 13.0.1 is now standard. fe82eaa try pinning clang and clang-format. 4d75efb Check CI clang-format version and location. 29d5c7a Fix pre-commit failures from before. a2082ac Don't install bazel from conda. 46af945 Setting up conda-centric dev environment. 30da8b3 Make default build options work for Mac and Linux (#78) baa6c9a Kill boost dependency (#77) dd56149 Fix MCMC parallel evaluation (#76) 3992dba Merge branch 'main' of https://github.com/mikesklar/kevlar into main 890384c Finish docs for grid-range 77560cc Update Python README 96a82de Kevlar Refactor (#59) 792b098 Pre-commit and a very simple CI pipeline (#74) 8a46096 Add direct bayes full grid benchmark (#63) b6158e7 Merge pull request #68 from mikesklar/berry 195104f Merge branch 'main' into berry e214ab4 Alex suggested changes. b2b702f Fast inla. a653241 Revert "cholesky version of c++ inla. not faster." 17287fb cholesky version of c++ inla. not faster. 87d45ce Fast c++ version, faster JAX version. 6f5b8d7 Playing around with Jax optimizations. 168458c Fast JAX implementation. Using vmap productively. b5e39ea Merge pull request #67 from mikesklar/const2 8d075ba A few berry improvements 3401cf9 Merge pull request #66 from mikesklar/berry d9a6849 Alex's comments lead to better code. f376a68 Jupytext notebooks to markdown. fec420d Fast INLA. c44a909 restore direct_bayes folder. 4b4ec71 Lots of comparison between INLA methods. 4bc824e numpyro MCMC working! 034cf40 Berry Figure 2 with quadrature 9cee20d Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. 9e52736 Improved exact integrator. ef6ca5d Berry with analytical mu integration is working nicely. 3dcba48 INLA is correctly modified for p1 theta offset. a696be4 Dirty bayes is correctly modified for p1 theta offset. 74c31b3 Crap, the theta parameterization from Berry is the right one to use... 2e83def Working on one parameter Berry INLA. 1e53769 Massively simplified the berry_dirty notebook. 6637d50 Add QuadRule structure. bc7c638 log_gauss_rule, run black/isort on research/berry folder. a58656b strip notebooks. f7ed040 Merge branch 'main' of github.com:mikesklar/kevlar into berry 4d0757f Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. aeec5cb Exploring DB vs. INLA issues. bd80a65 Replace quadpy with numpy and clear notebook output (#65) 979c492 Kevlar integration (#61) 286cae6 Compute sigma instead of sigma2 in DB Berry replication. 2934747 Compute sigma instead of sigma2 in DB Berry replication. 7726bcb Ben's INLA notebooks (#60) 347691c Replace direct bayes choleskey with faster sherman-morrison (#56) 50efcda Spring cleaning (#55) d6de183 Direct Bayes Kevlar integration (#31) 4425987 Fix openmp not being used issue (#52) 34551d7 Fix Python build rules (#51) 533cf76 Bazel Mac build fix (#50) 1da0c31 Build Python package with Bazel (#46) b3942ea Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) 6233086 Prelminaries for Direct Bayes (#42) cd35dbd Update all READMEs (#40) 7cac6ca Fix sign warnings 402a17a Fix path grabbing once again 720e3d8 Add external to path 4b312a3 Merge branch 'main' of https://github.com/mikesklar/kevlar into main b315078 Add a more general way to add bazel deps ee93c25 Update c++ engine source (#39) 7c339a7 Clean R Legacy and Revamp build system (#38) 0c3b069 Add binomial fit benchmark (#34) dfeb5ec 0th Order Upper Bound Fix (#33) cab7a49 Add dirty multilevel python and R examples (#20) 18ed8eb Generalized Upper Bound (#32) 3630ddd Don't reload test data on plot state change (#29) 1e2fda8 Update generalized upper-bound writeup (#28) 4ac1667 James.yang/examples csv (#27) 07b9de9 Clang-format everything (#25) ac66eca Direct bayes (#19) b627d65 Kevlar revamp!! (#21) 97882fe Merge pull request #18 from mikesklar/scatter 21e7e1a Add basic React rendering test 965ebc9 Merge pull request #17 from mikesklar/scatter cb7a56a Add file upload buttons for custom data ff3439a Merge pull request #12 from mikesklar/scatter 0ac2d45 Add legend labels to scatter plot b1c5922 Merge pull request #9 from mikesklar/scatter 43e1105 Add layer subvisualization b2a590d Merge pull request #7 from mikesklar/scatter 7ca10e4 Allow choosing between scatter and surface plots aaa9c88 Merge pull request #5 from mikesklar/const2 8a01923 Update kevlar flowcharts b832f19 Update flowchart with clearer vis subgraph 2218d46 Add initial web frontend 887654c Modify slight comment change on diagram 07a2467 Add framework_flowchart.md 4c15174 Fix compilation bugs 946f0fe Fix all R examples that were using incorrect grid radius 2430627 Refactor CRTP base to just free function and add lots of comments eea5572 Add exponential and start adagrid stuff f3cbc70 Add exponential dist with log rank + example f1232dc Add Rcpp header 940268b Add fixes to bckt, and export new version with hypos 47aa629 Work in progress f19d6a6 Update README.md 57c7f9d Add generalizations 6128fe8 Combine and ignore bckt a5af985 Add refactor changes with range style ea1b429 Fix build issues on Mac fef1fde Fix example 9aa608e Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work REVERT: 23ea4fd Responsive plotting (#127) REVERT: cf13926 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) REVERT: 8ec57b7 Add back fast math routines (#126) REVERT: 1d29ca2 Fully revert performance changes (#125) REVERT: 6ca99e2 Revert some performance changes (#124) REVERT: e7db4e6 Merge branch 'tbt/vscode_config' REVERT: 01932df Upgraded vscode config. REVERT: e113636 Add slack alerting for CI pipeline (#120) REVERT: 9f450ad Small bug fixes for main branch. (#122) REVERT: 7014de8 We become imprint. (#112) REVERT: 1125c49 Additional optimizations for Jax Fast INLA (#111) REVERT: 72a448e A Python Grid (#105) REVERT: 4e95f8d Remove obsolete Python dependency management (#110) REVERT: 40b9d9e Update obsolete Github links (#109) REVERT: 25f2ffe Add CI badge to README (#108) REVERT: f63b569 Run INLA in 32-bit floating point (#106) REVERT: 6ce8096 Add CI caching for Conda, Bazel, Pre-commit (#107) REVERT: ee78c14 Implementing a fixed N upper bound calculation in Python (#104) REVERT: 29ac69a GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) REVERT: 40ced7d Exact binomial type I error for Berry. (#95) REVERT: 475d8a8 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) REVERT: 2d24a96 Fix for HyperPlane.intersect. (#100) REVERT: 4058c75 Optimize typeI error with gradient ascent to find the worst grid points. (#94) REVERT: 3fae2fb Final Berry notebooks and examples (#93) REVERT: d0c7210 Update README.md REVERT: 5938716 Make colorscale configurable through UI (#92) REVERT: 28512e5 Update README.md REVERT: 081e97e Update README.md REVERT: 76004b3 Running Berry/INLA accumulation. (#91) REVERT: fcf2571 Merge pull request #90 from Confirm-Solutions/james.yang/python-models REVERT: b594f95 Make example smaller REVERT: 0fa053c Revert back to numpy version REVERT: 414ba87 Add jax version REVERT: a34cb76 Remove print REVERT: fd26349 Fix structure and get simple gaussian model from python workin REVERT: 99eb755 Add trampoline functionality and small test REVERT: befb51a Add back export for std::mt19937 REVERT: 70e31a4 Simplify generation of bazelrc (#88) REVERT: f3e7d61 Add thompson model (#86) REVERT: 4f7f26c Merge pull request #85 from mikesklar/tbt/build_quick_fix REVERT: cfa86be OpenMP linker flag for Mac. Add clangxx to environment.yml REVERT: 1c9f0aa Merge pull request #83 from mikesklar/tbt/conda REVERT: 9a81474 Readme updates: installing conda, clarifying clang/gcc usage. REVERT: 1b8f2bb Implement inference caching (#79) REVERT: f7177d3 clang-format 13.0.1 is now standard. REVERT: fbbc60e clang-format 13.0.1 is now standard. REVERT: 1f1dbd8 try pinning clang and clang-format. REVERT: 1d98560 Check CI clang-format version and location. REVERT: edfd2cd Fix pre-commit failures from before. REVERT: 7b44836 Don't install bazel from conda. REVERT: 35d947c Setting up conda-centric dev environment. REVERT: 42a40ba Make default build options work for Mac and Linux (#78) REVERT: 90b3343 Kill boost dependency (#77) REVERT: 7183528 Fix MCMC parallel evaluation (#76) REVERT: befa822 Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 1813b65 Finish docs for grid-range REVERT: 07ea72c Update Python README REVERT: 540fbb9 Kevlar Refactor (#59) REVERT: 09ca99e Pre-commit and a very simple CI pipeline (#74) REVERT: 525bca7 Add direct bayes full grid benchmark (#63) REVERT: a2e5881 Merge pull request #68 from mikesklar/berry REVERT: 61d9593 Merge branch 'main' into berry REVERT: 625a519 Alex suggested changes. REVERT: df6e0fe Fast inla. REVERT: 4fafb7e Revert "cholesky version of c++ inla. not faster." REVERT: 457f19b cholesky version of c++ inla. not faster. REVERT: 7cd976b Fast c++ version, faster JAX version. REVERT: c8b4c24 Playing around with Jax optimizations. REVERT: 10ce1fc Fast JAX implementation. Using vmap productively. REVERT: 4b96f49 Merge pull request #67 from mikesklar/const2 REVERT: e773c6c A few berry improvements REVERT: 8d338f0 Merge pull request #66 from mikesklar/berry REVERT: 5d2ff5e Alex's comments lead to better code. REVERT: ee08728 Jupytext notebooks to markdown. REVERT: 380c510 Fast INLA. REVERT: 7f8ee57 restore direct_bayes folder. REVERT: a8f97cc Lots of comparison between INLA methods. REVERT: 596fc7b numpyro MCMC working! REVERT: 0c1ae09 Berry Figure 2 with quadrature REVERT: 658d039 Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. REVERT: 87f0bcb Improved exact integrator. REVERT: b1d6261 Berry with analytical mu integration is working nicely. REVERT: 08d23af INLA is correctly modified for p1 theta offset. REVERT: aba8cab Dirty bayes is correctly modified for p1 theta offset. REVERT: ae2755e Crap, the theta parameterization from Berry is the right one to use... REVERT: f772145 Working on one parameter Berry INLA. REVERT: d2ff89e Massively simplified the berry_dirty notebook. REVERT: b8a83fd Add QuadRule structure. REVERT: 8588e91 log_gauss_rule, run black/isort on research/berry folder. REVERT: 163d127 strip notebooks. REVERT: 9b561a1 Merge branch 'main' of github.com:mikesklar/kevlar into berry REVERT: 3800f42 Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. REVERT: 732769f Exploring DB vs. INLA issues. REVERT: f157635 Replace quadpy with numpy and clear notebook output (#65) REVERT: 0f0ae91 Kevlar integration (#61) REVERT: 915b93d Compute sigma instead of sigma2 in DB Berry replication. REVERT: 93dae31 Compute sigma instead of sigma2 in DB Berry replication. REVERT: cb4e23d Ben's INLA notebooks (#60) REVERT: 363d552 Replace direct bayes choleskey with faster sherman-morrison (#56) REVERT: efeef7d Spring cleaning (#55) REVERT: 3340a3b Direct Bayes Kevlar integration (#31) REVERT: 181d5d6 Fix openmp not being used issue (#52) REVERT: ef52e65 Fix Python build rules (#51) REVERT: 1f5c192 Bazel Mac build fix (#50) REVERT: 33902a6 Build Python package with Bazel (#46) REVERT: debfdf7 Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) REVERT: 58e43e8 Prelminaries for Direct Bayes (#42) REVERT: 59b1f3a Update all READMEs (#40) REVERT: 8b45f49 Fix sign warnings REVERT: fb56c82 Fix path grabbing once again REVERT: 3f0404b Add external to path REVERT: 44f869d Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 3b94819 Add a more general way to add bazel deps REVERT: 17c8d61 Update c++ engine source (#39) REVERT: 745b9e3 Clean R Legacy and Revamp build system (#38) REVERT: cf41d43 Add binomial fit benchmark (#34) REVERT: 3b65233 0th Order Upper Bound Fix (#33) REVERT: cb93daf Add dirty multilevel python and R examples (#20) REVERT: c18d1fb Generalized Upper Bound (#32) REVERT: fc26117 Don't reload test data on plot state change (#29) REVERT: 96d599c Update generalized upper-bound writeup (#28) REVERT: 4aa8325 James.yang/examples csv (#27) REVERT: 46c128e Clang-format everything (#25) REVERT: d977e78 Direct bayes (#19) REVERT: 46125f4 Kevlar revamp!! (#21) REVERT: 67b9c31 Merge pull request #18 from mikesklar/scatter REVERT: 5a3a055 Add basic React rendering test REVERT: 688129f Merge pull request #17 from mikesklar/scatter REVERT: fcc2cc4 Add file upload buttons for custom data REVERT: f83435d Merge pull request #12 from mikesklar/scatter REVERT: 89e5576 Add legend labels to scatter plot REVERT: 08bfb68 Merge pull request #9 from mikesklar/scatter REVERT: bbba082 Add layer subvisualization REVERT: df96e44 Merge pull request #7 from mikesklar/scatter REVERT: 1aa7f04 Allow choosing between scatter and surface plots REVERT: 4e209fc Merge pull request #5 from mikesklar/const2 REVERT: dc10f22 Update kevlar flowcharts REVERT: f719197 Update flowchart with clearer vis subgraph REVERT: 32fa045 Add initial web frontend REVERT: e678a6b Modify slight comment change on diagram REVERT: 6fbe5b7 Add framework_flowchart.md REVERT: 4c3a939 Fix compilation bugs REVERT: f4a0aed Fix all R examples that were using incorrect grid radius REVERT: 7126e66 Refactor CRTP base to just free function and add lots of comments REVERT: e4c7447 Add exponential and start adagrid stuff REVERT: 96a6ee6 Add exponential dist with log rank + example REVERT: 2d1cbd7 Add Rcpp header REVERT: f84be87 Add fixes to bckt, and export new version with hypos REVERT: b82fd87 Work in progress REVERT: effeb0b Update README.md REVERT: 5c1b778 Add generalizations REVERT: 97463f3 Combine and ignore bckt REVERT: fad4329 Add refactor changes with range style REVERT: add7e65 Fix build issues on Mac REVERT: 8f9c8d7 Fix example REVERT: b56fdb7 Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work git-subtree-dir: imprint git-subtree-split: cbd80b8c5bd1bea5bbdd45562ca61c340c35d4c1
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