66 lines
2.9 KiB
Markdown
66 lines
2.9 KiB
Markdown
# README
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This R package is used to train random competing risks forests, ideally for large data.
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It's based heavily off of [randomForestSRC](https://github.com/kogalur/randomForestSRC/), although there are some differences which are described in (TODO - link to paper here).
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This package is still in a pre-release state and so it not yet available on CRAN.
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To install it now, in R install the `devtools` package and run the following command:
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```
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R> devtools::install_git("https://git.joeltherrien.ca/joel/largeRCRF.git")
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```
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## System Requirements
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You need:
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* R version 3.4.2 or greater
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* The `rJava` package version 0.9-9 or greater
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* A Java runtime version 1.8 or greater
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## Troubleshooting
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### I get an `OutOfMemoryException` error but I have plenty of RAM
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`largeRCRF` makes use of the Java virtual machine, which unfortunately restricts itself by default to a quarter of your system memory.
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You can override the default by including **before** loading `largeRCRF` or any other `rJava` based package the following line:
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```
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R> options(java.parameters <- c("-Xmx13G", "-Xms13G"))
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```
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with `13G` replaced with a little less than your available system memory.
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### I get an `OutOfMemoryException` error and I'm short on RAM
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Obviously if you're short on RAM there is a limit on how large of a dataset you can train,
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but there are some techniques you can use to limit how much `largeRCRF` needs.
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* If your training dataset is large you might not want both R and `largeRCRF` to have their own separate copies
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(limitations due to Java require `largeRCRF` have its own copy). When specifying the `data` parameter into `train`,
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instead provide an environment containing one object called `data` which is the dataset. `largeRCRF` will delete that variable
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after importing it into the Java environment.
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Example:
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```
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R> data.env <- new.env()
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R> data.env$data <- trainingData
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R> rm(trainingData)
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R> model <- train(..., data=data.env, ...)
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```
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* Each core that is training trees requires its own memory; you can try limiting `largeRCRF` to train only one tree at a time by specifiying `cores=1`.
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* By default `largeRCRF` keeps the entire forest loaded in memory during training,
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when in practice only the trees being trained on need to be loaded.
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You can specify `savePath` to give a directory for `largeRCRF` to save trees in during training,
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which will allow to `largeRCRF` to conserve memory for only those trees being currently trained.
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### Training stalls immediately at 0 trees and the CPU is idle
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This issue has been observed before on one particular system (and only on that system) but it's not clear what causes it.
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It would be appreciated if you could report this bug to [joelt@sfu.ca](mailto:joelt@sfu.ca) and give your operating system
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and the version of Java installed (the entire output of `java --version`).
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As a workaround, this issue seems to occur randomly; so try restarting your code to see if it runs.
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