21ce7ce135
Removed some unnecessary dependencies in a test file.
2019-06-28 15:25:46 -07:00
22accdb263
Add support for providing an initial forest to add trees to
2019-06-07 19:55:44 -07:00
7da3bd14a5
Add test verifying that CIFs are averaged together in the same way as randomForestSRC
2019-06-05 15:13:08 -07:00
1e40b7ff9b
Add missing copyright notices
2019-05-10 16:02:59 -07:00
6f318db79e
Add support for seeds to control randomness when training forests
2019-05-10 16:02:33 -07:00
17ae3a9f5a
Refactor - rename GroupDifferentiators into SplitFinders
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SplitRule would have made more sense but it was already taken.
2019-05-08 16:09:09 -07:00
c5c74ad7e9
Fix bug where parallel forests never finish
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Add test to detect case
2019-04-29 11:02:14 -07:00
1e643385ee
Adjust MultipleLogRankDifferentiators to use actual implementation found in randomForestSRC
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Also merge SingleLogRankDifferentiators with the Group variants,
as they now reduce tot he simple case when given only one event of focus.
2019-04-23 17:34:39 -07:00
c8269ae285
Fix bug in test
2019-03-27 21:06:05 -07:00
585d6d3c5b
Make SplitRules their own class; independent of their Covariate parents.
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This was done so that when we serialize trees (and thus SplitRules) we don't awkwardly also serialize ntree versions of the Covariates,
which is really awkward when deserializing them.
2019-03-25 14:44:31 -07:00
76b2cdd3c4
WIP - Some changes to how trees are saved.
2019-03-25 10:59:55 -07:00
8014bd4629
Fix bug where NAs cause crash
2019-03-04 11:36:21 -08:00
a7f591c2d3
Add integration capabilities to RightContinuousStepFunction; use it for calculating mortality
2019-02-18 14:57:26 -08:00
e74ba23177
Small changes; more tests.
2019-02-18 14:57:13 -08:00
9f513ab75b
Add capabilities to get nodes of a certain type in a forest; used to produce summary statistics
2019-02-02 09:36:00 -08:00
d8e52ecd82
Add tests around NumericSplitRuleUpdater; fix minor bug.
2019-01-23 19:37:10 -08:00
ee137370a1
Add GPL-3 Copyright to code
2019-01-14 11:45:23 -08:00
e709c42da1
Update the competing risk GroupDifferentiators to make efficient use of the SplitRuleUpdater updates
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Results in a speed improvement of over 1/3 according to a timing of the TestCompetingRisk#testLogRankSingleGroupDifferentiatorAllCovariates() test
2019-01-11 22:58:56 -08:00
a5fe856857
Massive refactor; Use Iterators/Updaters when calculating difference scores for faster calculations.
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Changed the covariates to be more clever with how they produce the different splits. In the future (not yet implemented) a clever GroupDifferentiator
could update the current score calculation based just on how many rows moved from one hand to the other. There were a few other changes as well;
TreeTrainer#growTree now accepts a Random as a parameter which is used throughout the entire growing process. This means it's now theoretically
possible to grow trees using a seed, so that results can be fully reproducible.
2019-01-09 21:31:27 -08:00
e892076a05
Add a test for the composite log rank splitting rule.
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Add some debug toString capabilities on Nodes and Trees
2019-01-04 11:22:23 -08:00
ae40a2e664
Removed naive mortality error measurement
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Naive mortality error was an ad-hoc method I implemented earlier on. It
didn't provide any useful performance, nor was it theoretically
grounded. It's better to remove it before someone accidently uses it.
2018-10-27 19:15:59 -07:00
a887a3cc15
Fix bug in Utils.binarySearchLessThan
2018-10-25 11:21:45 -07:00
ae91dbe9e7
Explicitly store RightContinuousStepFunction in CompetingRiskFunctions
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Done so that RUtils is useful. Also optimized imports.
2018-10-25 10:49:43 -07:00
c68f67e47a
Massive optimizations;
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Refactored how MathFunctions are structured to use more primitives and
less objects.
Optimized competing risk group differentiators to run faster.
Removed alternative competing risk response combiners (may be added back
later)
2018-10-25 10:34:27 -07:00
7fba964af9
Optimize CompetingRiskResponseCombiner
2018-10-12 12:11:48 -07:00
aa733d5eba
Switch code to storing Covariate.Value using arrays instead of Maps
2018-09-18 11:17:15 -07:00
7008959999
Add functionality to analyze using validation sets
2018-09-13 12:09:20 -07:00
e0681763ef
Add convenience methods to improve R interface performance
2018-09-10 12:31:35 -07:00
b8024275a9
Fix a bug where CompetingRiskFunctions returns NaNs when using set times
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in response combiner
2018-09-01 09:43:42 -07:00
2fb80df5a5
Add test for CompetingRiskFunctions
2018-08-31 22:32:54 -07:00
8333579a1f
Code cleanup; fixed 3 minor bugs in the settings
2018-08-31 13:10:30 -07:00
75f34853ab
Migrate to Java 1.8
2018-08-31 12:48:39 -07:00
c85cebb59f
Broke two methods in CompetingRiskErrorRateCalculator into static
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methods in a new class.
2018-08-27 11:18:56 -07:00
6d65d48844
Increased test ntree; making test more stable.
2018-08-09 16:33:57 -07:00
55eab76610
Simplied code.
2018-08-08 15:57:28 -07:00
d85f4eb099
Refactored competing risk combiners and differentiators into their own
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packages.
2018-08-07 10:59:19 -07:00
bf56dfb59d
Add ability to compute different error rates.
2018-08-07 10:52:52 -07:00
d3994212b6
Fix a bug in naive mortality error measure; implement IPCW concordance
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measure if you can provide the censoring distribution.
2018-07-26 12:45:12 -07:00
e1caef6d56
Implement naive mortality error measure
2018-07-25 15:29:09 -07:00
650579a430
Implement naive version of concordance index.
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Note that results DO NOT MATCH with randomForestSRC; so take these
results with a grain of salt.
2018-07-25 14:18:50 -07:00
7a77851f94
WIP - Add a CompetingRiskErrorRateCalculator.
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Note that tests fail.
2018-07-24 14:35:27 -07:00
dc9d20aa1a
Add ability to load gziped CSV files
2018-07-18 10:05:49 -07:00
05f9122b58
Add capability to load trees back into memory.
2018-07-17 13:54:59 -07:00
fffdfe85bf
Finish competing risk implementation. Fix a bug in tree training
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algorithm.
2018-07-16 16:58:11 -07:00
462b0d9c35
Implement Response & GroupDifferentiators for CompetingRisk problems.
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Also adjusted how settings are done to allow for specifying
differentiators & responses that may require arguments.
Note that CompetingRisk code is untested at this point.
2018-07-10 14:43:51 -07:00
4bbb0e0948
Fix a bug whereby FactorCovariate fails when "NA" is provided.
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Also improved testing around this.
2018-07-06 13:33:58 -07:00
6b62ad95c3
Add support for loading datasets by CSV files.
2018-07-06 13:21:56 -07:00
fe9ff37dcf
Upgraded Settings class to allow for covariates to be built from
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provided values.
2018-07-05 19:04:26 -07:00
b010e79269
Add basic Settings class with persistence.
2018-07-05 13:59:52 -07:00
2cdcbe6cbf
Refactor different classes into subpackages.
2018-07-05 12:59:29 -07:00
