forked from kscience/kmath
Minor refactoring
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d62bc66d4a
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@ -15,11 +15,24 @@ import space.kscience.kmath.complex.complex
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import space.kscience.kmath.operations.invoke
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import space.kscience.kmath.operations.invoke
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.DoubleBuffer
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import space.kscience.kmath.structures.DoubleBuffer
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import space.kscience.kmath.structures.getDouble
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import space.kscience.kmath.structures.permute
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@State(Scope.Benchmark)
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@State(Scope.Benchmark)
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internal class BufferBenchmark {
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internal class BufferBenchmark {
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@Benchmark
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@Benchmark
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fun genericDoubleBufferReadWrite(blackhole: Blackhole) {
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fun doubleArrayReadWrite(blackhole: Blackhole) {
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val buffer = DoubleArray(size) { it.toDouble() }
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var res = 0.0
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(0 until size).forEach {
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res += buffer[it]
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}
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blackhole.consume(res)
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}
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@Benchmark
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fun doubleBufferReadWrite(blackhole: Blackhole) {
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val buffer = DoubleBuffer(size) { it.toDouble() }
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val buffer = DoubleBuffer(size) { it.toDouble() }
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var res = 0.0
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var res = 0.0
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(0 until size).forEach {
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(0 until size).forEach {
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@ -28,6 +41,26 @@ internal class BufferBenchmark {
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blackhole.consume(res)
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blackhole.consume(res)
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}
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}
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@Benchmark
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fun bufferViewReadWrite(blackhole: Blackhole) {
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val buffer = DoubleBuffer(size) { it.toDouble() }.permute(reversedIndices)
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var res = 0.0
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(0 until size).forEach {
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res += buffer[it]
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}
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blackhole.consume(res)
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}
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@Benchmark
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fun bufferViewReadWriteSpecialized(blackhole: Blackhole) {
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val buffer = DoubleBuffer(size) { it.toDouble() }.permute(reversedIndices)
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var res = 0.0
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(0 until size).forEach {
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res += buffer.getDouble(it)
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}
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blackhole.consume(res)
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}
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@Benchmark
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@Benchmark
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fun complexBufferReadWrite(blackhole: Blackhole) = ComplexField {
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fun complexBufferReadWrite(blackhole: Blackhole) = ComplexField {
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val buffer = Buffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) }
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val buffer = Buffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) }
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@ -42,5 +75,6 @@ internal class BufferBenchmark {
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private companion object {
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private companion object {
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private const val size = 100
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private const val size = 100
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private val reversedIndices = IntArray(size){it}.apply { reverse() }
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}
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}
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}
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}
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@ -5,6 +5,7 @@ import kotlinx.html.FlowContent
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import kotlinx.html.h1
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import kotlinx.html.h1
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import space.kscience.kmath.operations.algebra
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import space.kscience.kmath.operations.algebra
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import space.kscience.kmath.operations.bufferAlgebra
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import space.kscience.kmath.operations.bufferAlgebra
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import space.kscience.kmath.stat.ksComparisonStatistic
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.slice
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import space.kscience.kmath.structures.slice
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import space.kscience.kmath.structures.toList
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import space.kscience.kmath.structures.toList
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@ -34,6 +35,8 @@ fun main() = with(Double.algebra.bufferAlgebra.seriesAlgebra()) {
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val s3: Buffer<Double> = s1.zip(s2) { l, r -> l + r } //s1 + s2
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val s3: Buffer<Double> = s1.zip(s2) { l, r -> l + r } //s1 + s2
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val s4 = ln(s3)
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val s4 = ln(s3)
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val kmTest = ksComparisonStatistic(s1, s2)
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Plotly.page {
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Plotly.page {
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h1 { +"This is my plot" }
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h1 { +"This is my plot" }
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plotSeries(s1)
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plotSeries(s1)
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@ -79,11 +79,19 @@ public class BufferExpanded<T>(
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/**
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/**
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* Zero-copy select a slice inside the original buffer
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* Zero-copy select a slice inside the original buffer
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*/
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*/
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public fun <T> Buffer<T>.slice(range: UIntRange): BufferView<T> = BufferSlice(
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public fun <T> Buffer<T>.slice(range: UIntRange): BufferView<T> = if (this is BufferSlice) {
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this,
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BufferSlice(
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range.first,
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origin,
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(range.last - range.first).toInt() + 1
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this.offset + range.first,
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)
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(range.last - range.first).toInt() + 1
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)
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} else {
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BufferSlice(
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this,
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range.first,
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(range.last - range.first).toInt() + 1
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)
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}
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/**
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/**
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* Resize original buffer to a given range using given [range], filling additional segments with [defaultValue].
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* Resize original buffer to a given range using given [range], filling additional segments with [defaultValue].
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@ -5,7 +5,8 @@ import space.kscience.kmath.misc.UnstableKMathAPI
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/**
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/**
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* Non-boxing access to primitive [Double]
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* Non-boxing access to primitive [Double]
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*/
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*/
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@OptIn(UnstableKMathAPI::class)
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@UnstableKMathAPI
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public fun Buffer<Double>.getDouble(index: Int): Double = if (this is BufferView) {
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public fun Buffer<Double>.getDouble(index: Int): Double = if (this is BufferView) {
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val originIndex = originIndex(index)
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val originIndex = originIndex(index)
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if( originIndex>=0) {
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if( originIndex>=0) {
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@ -22,7 +23,7 @@ public fun Buffer<Double>.getDouble(index: Int): Double = if (this is BufferView
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/**
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/**
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* Non-boxing access to primitive [Int]
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* Non-boxing access to primitive [Int]
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*/
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*/
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@OptIn(UnstableKMathAPI::class)
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@UnstableKMathAPI
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public fun Buffer<Int>.getInt(index: Int): Int = if (this is BufferView) {
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public fun Buffer<Int>.getInt(index: Int): Int = if (this is BufferView) {
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val originIndex = originIndex(index)
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val originIndex = originIndex(index)
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if( originIndex>=0) {
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if( originIndex>=0) {
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@ -1,5 +1,6 @@
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package space.kscience.kmath.stat
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package space.kscience.kmath.stat
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import space.kscience.kmath.misc.UnstableKMathAPI
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import space.kscience.kmath.operations.*
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import space.kscience.kmath.operations.*
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.Buffer
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import space.kscience.kmath.structures.BufferFactory
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import space.kscience.kmath.structures.BufferFactory
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@ -20,12 +21,20 @@ public fun <T : Comparable<T>> StatisticalAlgebra<T, *, *>.ecdf(buffer: Buffer<T
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}
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}
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/**
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/**
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* Resulting value of kolmogorov-smirnov two-sample statistic
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*/
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@UnstableKMathAPI
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public data class KMComparisonResult<T : Comparable<T>>(val n: Int, val m: Int, val value: T)
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/**
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* Kolmogorov-Smirnov sample comparison test
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* Implementation copied from https://commons.apache.org/proper/commons-math/javadocs/api-3.6.1/index.html?org/apache/commons/math3/stat/inference/KolmogorovSmirnovTest.html
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* Implementation copied from https://commons.apache.org/proper/commons-math/javadocs/api-3.6.1/index.html?org/apache/commons/math3/stat/inference/KolmogorovSmirnovTest.html
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*/
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*/
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public fun <T : Comparable<T>, A, BA : BufferAlgebra<T, A>> StatisticalAlgebra<T, A, BA>.kolmogorovSmirnovTest(
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@UnstableKMathAPI
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public fun <T : Comparable<T>, A, BA : BufferAlgebra<T, A>> StatisticalAlgebra<T, A, BA>.ksComparisonStatistic(
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x: Buffer<T>,
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x: Buffer<T>,
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y: Buffer<T>,
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y: Buffer<T>,
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): T where A : Group<T>, A : NumericAlgebra<T> = elementAlgebra.invoke {
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): KMComparisonResult<T> where A : Group<T>, A : NumericAlgebra<T> = elementAlgebra.invoke {
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// Copy and sort the sample arrays
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// Copy and sort the sample arrays
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val sx = x.sorted()
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val sx = x.sorted()
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val sy = y.sorted()
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val sy = y.sorted()
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@ -41,19 +50,19 @@ public fun <T : Comparable<T>, A, BA : BufferAlgebra<T, A>> StatisticalAlgebra<T
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do {
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do {
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val z = if (sx[rankX] <= sy[rankY]) sx[rankX] else sy[rankY]
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val z = if (sx[rankX] <= sy[rankY]) sx[rankX] else sy[rankY]
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while (rankX < n && sx[rankX].compareTo(z) == 0) {
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while (rankX < n && sx[rankX].compareTo(z) == 0) {
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rankX += 1;
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rankX += 1
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curD += number(m);
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curD += number(m)
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}
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}
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while (rankY < m && sy[rankY].compareTo(z) == 0) {
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while (rankY < m && sy[rankY].compareTo(z) == 0) {
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rankY += 1;
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rankY += 1
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curD -= number(n);
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curD -= number(n)
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}
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}
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when {
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when {
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curD > supD -> supD = curD
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curD > supD -> supD = curD
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-curD > supD -> supD = -curD
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-curD > supD -> supD = -curD
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}
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}
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} while (rankX < n && rankY < m);
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} while (rankX < n && rankY < m)
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return supD;
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return KMComparisonResult(n, m, supD)
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}
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}
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