largeRCRF-Java

joel/largeRCRF-Java

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044bf08e3d Fix spelling mistake in README master Joel Therrien 2019-11-14 09:04:26 -0800
c4bab39245 Remove the executable component, as the R package component has advanced enough that it can do everything. Joel Therrien 2019-11-14 08:59:27 -0800
f3a4ef01ed Add support for offline forests. v1.0.5 Joel Therrien 2019-11-13 17:08:31 -0800
54af805d4d Fairly significant refactoring; Joel Therrien 2019-10-02 13:54:45 -0700
79a9522ba7 Several changes - Joel Therrien 2019-08-28 18:07:35 -0700
c24626ff61 Upgrade to latest version of Jackson databind. Joel Therrien 2019-08-27 14:53:49 -0700
51696e2546 Fix how variable importance works to be tree based and not forest based Joel Therrien 2019-08-12 14:28:31 -0700
f1c5b292ed Add serialVersionUID to Serializable classes ibs Joel Therrien 2019-08-02 15:10:48 -0700
a56ad4433d Add variable importance methods to library Joel Therrien 2019-07-26 14:59:41 -0700
f23ee21ef3 Add utility function for R package Joel Therrien 2019-07-24 14:26:08 -0700
186de413ed Merge branch 'master' into ibs Joel Therrien 2019-07-22 11:38:15 -0700
aa1f544ea2 Upgrade Jackson in executable project v1.3.0 Joel Therrien 2019-07-22 11:36:29 -0700
86f6c195d7 Fix unused imports Joel Therrien 2019-07-22 11:29:37 -0700
9258f75e4e Add integrated Brier score error measure Joel Therrien 2019-07-22 11:22:07 -0700
7371dab4f1 Fix two bugs on how RightContinuousStepFunction is integrated. Joel Therrien 2019-07-19 14:14:36 -0700
ae9a6b9a3f Add binary and unary operations to RightContinuousStepFunctions Joel Therrien 2019-07-18 15:14:01 -0700
d7cdc9f6e7 Split into two Maven modules Joel Therrien 2019-07-03 09:37:19 -0700
ee4b513298 Remove dependencies from project library Joel Therrien 2019-07-02 16:46:40 -0700
bc2c240823 Update Jackson to 2.9.9 Joel Therrien 2019-07-02 15:39:33 -0700
21ce7ce135 Removed some unnecessary dependencies in a test file. Joel Therrien 2019-06-28 15:25:46 -0700
88dc1c2316 Add README file Joel Therrien 2019-06-28 10:54:42 -0700
78ca8bad73 Update pom to build package with minimal dependencies Joel Therrien 2019-06-27 15:34:09 -0700
22accdb263 Add support for providing an initial forest to add trees to Joel Therrien 2019-06-07 19:55:44 -0700
7da3bd14a5 Add test verifying that CIFs are averaged together in the same way as randomForestSRC Joel Therrien 2019-06-05 15:11:32 -0700
4aac73b868 Improve progress tracking to terminate when all trees are trained Joel Therrien 2019-05-29 15:05:48 -0700
1e40b7ff9b Add missing copyright notices Joel Therrien 2019-05-10 16:02:59 -0700
6f318db79e Add support for seeds to control randomness when training forests Joel Therrien 2019-05-10 16:02:33 -0700
17ae3a9f5a Refactor - rename GroupDifferentiators into SplitFinders Joel Therrien 2019-05-08 16:09:09 -0700
c5c74ad7e9 Fix bug where parallel forests never finish Joel Therrien 2019-04-29 11:02:14 -0700
de3de300cf Change how parallel trees are trained to be more robust to Threads getting terminated. Joel Therrien 2019-04-26 11:04:03 -0700
1e643385ee Adjust MultipleLogRankDifferentiators to use actual implementation found in randomForestSRC Joel Therrien 2019-04-23 14:17:43 -0700
c6a5787975 Use UUIDs to save trees instead of tree number. Joel Therrien 2019-04-16 12:58:23 -0700
fb20b08a23 Add debugging information to RUtils Joel Therrien 2019-04-16 12:55:57 -0700
f1f507d2df Add out-of-bag predict methods for R to use Joel Therrien 2019-04-07 15:11:06 -0700
50b4a3cd89 Fix and optimize how progress is displayed while training trees Joel Therrien 2019-04-05 11:22:59 -0700
ea176cff9a An an evaluateSerial function to Forest Joel Therrien 2019-04-05 11:13:23 -0700
bf168bc2a5 Improve performance of CompetingRiskFunctionCombiner Joel Therrien 2019-03-27 21:06:15 -0700
c8269ae285 Fix bug in test Joel Therrien 2019-03-27 21:06:05 -0700
526a127b9d Change Forest to keep trees in a List instead of a Collection Joel Therrien 2019-03-27 10:57:01 -0700
585d6d3c5b Make SplitRules their own class; independent of their Covariate parents. Joel Therrien 2019-03-25 14:44:31 -0700
76b2cdd3c4 WIP - Some changes to how trees are saved. Joel Therrien 2019-03-25 10:59:55 -0700
76614ee68b Better memory management to help prevent OutOfMemoryExceptions Joel Therrien 2019-03-25 10:59:26 -0700
d65e010c48 Very minor improvement to how tree filenames are saved. Joel Therrien 2019-03-13 11:21:51 -0700
02b7a5cb9a Rebrand project as largeRCRF Joel Therrien 2019-03-13 10:47:37 -0700
cfa3a6f432 Attempting memory optimizations Joel Therrien 2019-03-13 10:39:18 -0700
8014bd4629 Fix bug where NAs cause crash Joel Therrien 2019-03-04 11:36:21 -0800
91cf299362 Add some R utility functions to help data get quickly loaded Joel Therrien 2019-03-04 11:23:31 -0800
29b154110a Fix bug where template.yaml gets replaced whenever user wants to look at help dialog Joel Therrien 2019-02-28 11:12:21 -0800
a7f591c2d3 Add integration capabilities to RightContinuousStepFunction; use it for calculating mortality Joel Therrien 2019-02-18 14:57:26 -0800
e74ba23177 Small changes; more tests. Joel Therrien 2019-02-18 14:57:13 -0800
9f513ab75b Add capabilities to get nodes of a certain type in a forest; used to produce summary statistics Joel Therrien 2019-02-02 09:36:00 -0800
77ec780304 Fix theoretical bug Joel Therrien 2019-01-28 11:45:06 -0800
d8e52ecd82 Add tests around NumericSplitRuleUpdater; fix minor bug. Joel Therrien 2019-01-23 19:37:10 -0800
115c57f829 Improve documentation and add a final to MeanResponseCombiner. Joel Therrien 2019-01-22 11:01:21 -0800
d935fe0bc0 Improve WeightedVarianceGroupDifferentiator to be faster Joel Therrien 2019-01-22 10:56:31 -0800
7a5a8ab0fc Merge branch 'optimizations' of joel/RandomSurvivalForests into master Joel Therrien 2019-01-14 19:08:14 +0000
e709c42da1 Update the competing risk GroupDifferentiators to make efficient use of the SplitRuleUpdater updates Joel Therrien 2019-01-11 22:56:41 -0800
86122fd90d Remove comment that isn't true Joel Therrien 2019-01-10 17:34:52 -0800
31d6ce9b3e Covariates track if they have any NA values, and skip NA handling code if possible Joel Therrien 2019-01-10 14:09:43 -0800
a57741b726 Add PMD rules to pom.xml to enforce higher code quality Joel Therrien 2019-01-10 11:23:55 -0800
a5fe856857 Massive refactor; Use Iterators/Updaters when calculating difference scores for faster calculations. Joel Therrien 2019-01-09 21:31:27 -0800
e892076a05 Add a test for the composite log rank splitting rule. Add some debug toString capabilities on Nodes and Trees Joel Therrien 2019-01-04 11:22:23 -0800
ae40a2e664 Removed naive mortality error measurement Joel Therrien 2018-10-27 19:15:59 -0700
a887a3cc15 Fix bug in Utils.binarySearchLessThan Joel Therrien 2018-10-25 11:21:45 -0700
ae91dbe9e7 Explicitly store RightContinuousStepFunction in CompetingRiskFunctions Joel Therrien 2018-10-25 10:49:43 -0700
c68f67e47a Massive optimizations; Joel Therrien 2018-10-25 10:34:27 -0700
cce5ad1e0f Add parameter to decide on whether to check for node purity or not Joel Therrien 2018-10-15 11:03:35 -0700
7fba964af9 Optimize CompetingRiskResponseCombiner Joel Therrien 2018-10-12 11:42:25 -0700
aa733d5eba Switch code to storing Covariate.Value using arrays instead of Maps Joel Therrien 2018-09-18 11:17:15 -0700
de39f60314 Make CovariateRow's serializable; add R utility functions. Joel Therrien 2018-09-14 14:53:01 -0700
7008959999 Add functionality to analyze using validation sets Joel Therrien 2018-09-13 12:09:20 -0700
98cb97a1f1 Improve performance by integrating binary search into MathFunction Joel Therrien 2018-09-11 17:12:27 -0700
6e58122380 Optimize MathFunction Joel Therrien 2018-09-10 17:16:43 -0700
e0681763ef Add convenience methods to improve R interface performance Joel Therrien 2018-09-10 12:31:35 -0700
b8024275a9 Fix a bug where CompetingRiskFunctions returns NaNs when using set times in response combiner Joel Therrien 2018-09-01 09:43:42 -0700
62198f998d Small code cleanup Joel Therrien 2018-09-01 09:42:48 -0700
2fb80df5a5 Add test for CompetingRiskFunctions Joel Therrien 2018-08-31 22:32:54 -0700
8333579a1f Code cleanup; fixed 3 minor bugs in the settings Joel Therrien 2018-08-31 13:10:30 -0700
75f34853ab Migrate to Java 1.8 Joel Therrien 2018-08-31 12:48:39 -0700
949c8789e7 Switch HashMaps in CompetingRiskFunctions for ArrayLists Joel Therrien 2018-08-27 19:15:06 -0700
22944115ee Fix bug where cause specific mortality was using the cumulative hazard functions instead of the CIF Joel Therrien 2018-08-27 13:19:04 -0700
c85cebb59f Broke two methods in CompetingRiskErrorRateCalculator into static methods in a new class. Joel Therrien 2018-08-27 11:18:56 -0700
e92abdab13 Add functionality to restart tree training where previously left off. Joel Therrien 2018-08-09 16:34:10 -0700
6d65d48844 Increased test ntree; making test more stable. Joel Therrien 2018-08-09 16:33:57 -0700
55eab76610 Simplied code. Joel Therrien 2018-08-08 15:41:40 -0700
9d9dc9ef8d Optimize tree training so that the best split is not applied twice Joel Therrien 2018-08-08 11:34:02 -0700
74151b94db Add alternative way where functions are computed only at final step. Joel Therrien 2018-08-07 15:49:55 -0700
d85f4eb099 Refactored competing risk combiners and differentiators into their own packages. Joel Therrien 2018-08-07 10:59:19 -0700
bf56dfb59d Add ability to compute different error rates. Joel Therrien 2018-08-07 10:52:52 -0700
d3994212b6 Fix a bug in naive mortality error measure; implement IPCW concordance measure if you can provide the censoring distribution. Joel Therrien 2018-07-26 12:45:12 -0700
e1caef6d56 Implement naive mortality error measure Joel Therrien 2018-07-25 15:29:09 -0700
650579a430 Implement naive version of concordance index. Joel Therrien 2018-07-25 14:18:50 -0700
7a77851f94 WIP - Add a CompetingRiskErrorRateCalculator. Joel Therrien 2018-07-24 14:34:36 -0700
d4853f5232 Change how trees are saved so that they are compressed. Joel Therrien 2018-07-18 15:29:55 -0700
dc9d20aa1a Add ability to load gziped CSV files Joel Therrien 2018-07-18 10:05:49 -0700
05f9122b58 Add capability to load trees back into memory. Joel Therrien 2018-07-17 13:54:59 -0700
fffdfe85bf Finish competing risk implementation. Fix a bug in tree training algorithm. Joel Therrien 2018-07-16 16:58:11 -0700
462b0d9c35 Implement Response & GroupDifferentiators for CompetingRisk problems. Joel Therrien 2018-07-10 14:43:51 -0700
4bbb0e0948 Fix a bug whereby FactorCovariate fails when "NA" is provided. Joel Therrien 2018-07-06 13:33:58 -0700