Skip to content

Latest commit

 

History

History
145 lines (96 loc) · 4.04 KB

NOTES.md

File metadata and controls

145 lines (96 loc) · 4.04 KB
Raw

Code base notes

This document is meant to guide developers through the code base. It will:

  • Explain the purposes of the different classes, giving some explanation on relevant implementation details
  • Go over the unit tests in a logical order

Configuring JNI for MoSSE C libraries

Building requires fftw3 and Java 8 on your OS (Ubuntu is recommended).

Install fftw3 on ubuntu

sudo apt-get install -y libfftw3-dev

Install Java 8

sudo apt-get install openjdk-8-jdk

To build the JNI methods

cd SSE/jni
make

To configure your IDE to access the C libraries.

For IntelliJ, go to Run -> Edit configurations

Then, add the JNI path to your Java VM option

-Djava.library.path=/your_path/SSE/jni

Running mosse unit tests also require the java library path to be added in the JUnit configuration (following same steps as above).

Note: Instructions for Mac and Windows OS coming soon.

QuaSSE classes

QuaSSEProcess

TODO

QuaSSEDistribution

TODO

MoSSEDistribution

TODO

QuaSSE unit tests

QuaSSEFunctionsTest

See validation/r_scripts/QuaSSEFunctionsTest_JUnitTest.R for where expectations come from.

  • testLogistic: tests the LogisticFunction class, which converts an x (continuous trait) value into a y (macroevolutionary parameter, e.g., the birth rate) value

  • testConstant: tests the ConstantLinkFn class, which converts an x (continuous trait) value and maps to a constant scalar value for y (a macroevolutionary parameter, e.g., the death rate)

  • testQu2MacroevolFailLogistic: tests LogisticFunction throws an exception if the number of bins for x and y differ

  • testQu2MacroevolFailConstant: tests ConstantLinkFn throws an exception if the number of bins for x and y differ

PropagatesQuaSSETest

See validation/r_script/PropagatesQuaSSETest_JUnitTest.R for where expectations come from

None of the tests here depend on, nor test, the initialization of likelihood classes (i.e., we do not test if arrays are declared with the right dimensions and correctly populated with initial values).

  • testPropagateTimeOneChQuaSSETest: tests SSEUtils.propagateEandDinTQuaSSEinPlace.

    It uses a manually creates array of random values as input, with a total of 32 bins. It checks that both E's and D's are propagated in time correctly.

  • testPropagateTimeOneChQuaSSETestSSTJavaFftService: tests SSEUtils.propagateEandDinTQuasseInPlaceSSTJavaFftService.

    It uses a manually created array of random values, spread over an array while skipping even indices, as required by SST's JavaFftService (which is tested elsewhere!).

    (Note that we do not use SST in this test, this is just to make sure this method skips indices correctly.)

  • testMakeNormalKernInPlaceAndFftAndIfft: tests both SSEUtils.makeNormalKernelInPlace and FFTing with JTransforms.

    The Normal kernel assigns a different probability to each of 'nXbins' bins. Note that x here is not a value a continuous trait can have, but instead, a certain delta-trait-value. So most of the probability mass of this kernel is centered around zero (we are assuming the continuous trait evolves according to a Brownian motion model).

    Now for some technical reason, we put the bins that would have the highest probabilities in the first 'nRightFlankBins' to the left, and the last 'nLeftFlankBins' to the right. The middle x bins are assigned probabilities of zero.

    This test assumes 32 bins and 2 flanking bins to the left, and to the right.

  • testMakeNormalKernInPlaceAndFftAndIfftSSTModalFftService: tests both SSEUtils.makeNormalKernelInPlace and FFTing with the SST library, using RealArray methods (which invoke ModalFfftService).

    (See test above for more details.)

  • testConvolve:

  • testConvolveSSTModalFftService:

  • testConvolveSSTJavaFftService:

  • testPropagateChOneCh32QuaSSE:

  • testPropagateChOneCh1024QuaSSE:

  • testPropagateChOneCh4096QuaSSE:

  • testPropagateChOneCh4096QuaSSEModalFftService:

  • testPropagateChOneCh4096QuaSSEJavaFftService:

QuaSSEDistributionTest

TODO