Joel Therrien
f1c5b292ed
Add serialVersionUID to Serializable classes
...
This makes forests between versions more compatible if only method definitions changed.
2019-08-02 15:10:48 -07:00
Joel Therrien
a56ad4433d
Add variable importance methods to library
2019-07-29 12:21:35 -07:00
Joel Therrien
f23ee21ef3
Add utility function for R package
2019-07-24 14:26:08 -07:00
Joel Therrien
186de413ed
Merge branch 'master' into ibs
2019-07-22 11:38:15 -07:00
Joel Therrien
aa1f544ea2
Upgrade Jackson in executable project
...
Jackson has some security vulnerability that can only be exploited in a server environment;
not relevant here whatsoever, but might as well update.
2019-07-22 11:36:29 -07:00
Joel Therrien
86f6c195d7
Fix unused imports
2019-07-22 11:29:37 -07:00
Joel Therrien
9258f75e4e
Add integrated Brier score error measure
2019-07-22 11:23:34 -07:00
Joel Therrien
7371dab4f1
Fix two bugs on how RightContinuousStepFunction is integrated.
...
Specifically, the integration returned an NaN if the integration was
*up to* an NaN (real inegrals are robust); and the results were negative
if integrating from a to b where a > b.
2019-07-19 14:14:36 -07:00
Joel Therrien
ae9a6b9a3f
Add binary and unary operations to RightContinuousStepFunctions
2019-07-18 15:14:01 -07:00
d7cdc9f6e7
Split into two Maven modules
...
One for the library (same as before),
the other for the executable part.
2019-07-03 09:37:19 -07:00
ee4b513298
Remove dependencies from project
...
This project is now purely a library only; the code for running directly from the command line will be
put into a new project. This was important because we were including large dependencies into the R code
that weren't needed and created some minor licensing inconveniences.
2019-07-02 16:54:58 -07:00
bc2c240823
Update Jackson to 2.9.9
...
Apparently older versions of Jackson contain a security vulnerability
(not really important for this project, given that users are only ever
using Jackson on their own settings files)
2019-07-02 15:39:33 -07:00
21ce7ce135
Removed some unnecessary dependencies in a test file.
2019-06-28 15:25:46 -07:00
88dc1c2316
Add README file
2019-06-28 10:54:42 -07:00
78ca8bad73
Update pom to build package with minimal dependencies
2019-06-27 15:34:09 -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
4aac73b868
Improve progress tracking to terminate when all trees are trained
...
Instead of only checking every second
2019-05-29 15:05:48 -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
...
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
...
Add test to detect case
2019-04-29 11:02:14 -07:00
de3de300cf
Change how parallel trees are trained to be more robust to Threads getting terminated.
...
This will hopefully make the package more stable on cluster systems, where sometimes the forests
immediately stall.
2019-04-26 11:04:03 -07:00
1e643385ee
Adjust MultipleLogRankDifferentiators to use actual implementation found in randomForestSRC
...
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
c6a5787975
Use UUIDs to save trees instead of tree number.
...
Benefits are for when we restart a previously parallel task
in which, say, trees 1, 2, and 4 were completed but tree 3
never did complete. Under the previous implementation we'd start
at tree 4 (we'd just count how many trees were done). To fix this
would require some additional effort. Since the order of trees
is irrelevant, it made sense to just stop ordering them.
2019-04-16 12:58:23 -07:00
fb20b08a23
Add debugging information to RUtils
2019-04-16 12:55:57 -07:00
f1f507d2df
Add out-of-bag predict methods for R to use
2019-04-07 15:11:06 -07:00
50b4a3cd89
Fix and optimize how progress is displayed while training trees
2019-04-05 11:22:59 -07:00
ea176cff9a
An an evaluateSerial function to Forest
...
parallelStream doesn't seem to work very well on the ComputeCanada.ca cluster
2019-04-05 11:13:23 -07:00
bf168bc2a5
Improve performance of CompetingRiskFunctionCombiner
...
Estimate of time improvement is at least 10x faster
2019-03-27 21:06:15 -07:00
c8269ae285
Fix bug in test
2019-03-27 21:06:05 -07:00
526a127b9d
Change Forest to keep trees in a List instead of a Collection
2019-03-27 10:57:01 -07:00
585d6d3c5b
Make SplitRules their own class; independent of their Covariate parents.
...
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
76614ee68b
Better memory management to help prevent OutOfMemoryExceptions
2019-03-25 10:59:26 -07:00
d65e010c48
Very minor improvement to how tree filenames are saved.
2019-03-13 11:21:51 -07:00
02b7a5cb9a
Rebrand project as largeRCRF
2019-03-13 10:47:37 -07:00
cfa3a6f432
Attempting memory optimizations
2019-03-13 10:39:18 -07:00
8014bd4629
Fix bug where NAs cause crash
2019-03-04 11:36:21 -08:00
91cf299362
Add some R utility functions to help data get quickly loaded
2019-03-04 11:23:31 -08:00
29b154110a
Fix bug where template.yaml gets replaced whenever user wants to look at help dialog
2019-02-28 11:12:21 -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
77ec780304
Fix theoretical bug
2019-01-29 13:38:45 -08:00
d8e52ecd82
Add tests around NumericSplitRuleUpdater; fix minor bug.
2019-01-23 19:37:10 -08:00
115c57f829
Improve documentation and add a final to MeanResponseCombiner.
2019-01-22 11:01:21 -08:00
d935fe0bc0
Improve WeightedVarianceGroupDifferentiator to be faster
2019-01-22 10:56:31 -08:00
ee137370a1
Add GPL-3 Copyright to code
2019-01-14 11:45:23 -08:00
Joel Therrien
7a5a8ab0fc
Merge branch 'optimizations' of joel/RandomSurvivalForests into master
2019-01-14 19:08:14 +00:00
