888b84abe8
## What changes were proposed in this pull request? - [x] need to test by running R CMD check --as-cran - [x] sanity check vignettes ## How was this patch tested? Jenkins Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #17945 from felixcheung/rchangesforpackage.
477 lines
19 KiB
R
477 lines
19 KiB
R
#
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# Licensed to the Apache Software Foundation (ASF) under one or more
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# contributor license agreements. See the NOTICE file distributed with
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# this work for additional information regarding copyright ownership.
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# The ASF licenses this file to You under the Apache License, Version 2.0
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# (the "License"); you may not use this file except in compliance with
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# the License. You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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library(testthat)
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context("MLlib regression algorithms, except for tree-based algorithms")
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# Tests for MLlib regression algorithms in SparkR
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sparkSession <- sparkR.session(master = sparkRTestMaster, enableHiveSupport = FALSE)
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test_that("formula of spark.glm", {
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skip_on_cran()
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training <- suppressWarnings(createDataFrame(iris))
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# directly calling the spark API
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# dot minus and intercept vs native glm
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model <- spark.glm(training, Sepal_Width ~ . - Species + 0)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ . - Species + 0, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# feature interaction vs native glm
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model <- spark.glm(training, Sepal_Width ~ Species:Sepal_Length)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Species:Sepal.Length, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# glm should work with long formula
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training <- suppressWarnings(createDataFrame(iris))
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training$LongLongLongLongLongName <- training$Sepal_Width
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training$VeryLongLongLongLonLongName <- training$Sepal_Length
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training$AnotherLongLongLongLongName <- training$Species
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model <- spark.glm(training, LongLongLongLongLongName ~ VeryLongLongLongLonLongName +
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AnotherLongLongLongLongName)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Sepal.Length + Species, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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})
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test_that("spark.glm and predict", {
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training <- suppressWarnings(createDataFrame(iris))
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# gaussian family
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model <- spark.glm(training, Sepal_Width ~ Sepal_Length + Species)
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Sepal.Length + Species, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# poisson family
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model <- spark.glm(training, Sepal_Width ~ Sepal_Length + Species,
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family = poisson(link = identity))
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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rVals <- suppressWarnings(predict(glm(Sepal.Width ~ Sepal.Length + Species,
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data = iris, family = poisson(link = identity)), iris))
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# Gamma family
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x <- runif(100, -1, 1)
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y <- rgamma(100, rate = 10 / exp(0.5 + 1.2 * x), shape = 10)
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df <- as.DataFrame(as.data.frame(list(x = x, y = y)))
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model <- glm(y ~ x, family = Gamma, df)
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out <- capture.output(print(summary(model)))
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expect_true(any(grepl("Dispersion parameter for gamma family", out)))
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# tweedie family
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model <- spark.glm(training, Sepal_Width ~ Sepal_Length + Species,
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family = "tweedie", var.power = 1.2, link.power = 0.0)
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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# manual calculation of the R predicted values to avoid dependence on statmod
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#' library(statmod)
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#' rModel <- glm(Sepal.Width ~ Sepal.Length + Species, data = iris,
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#' family = tweedie(var.power = 1.2, link.power = 0.0))
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#' print(coef(rModel))
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rCoef <- c(0.6455409, 0.1169143, -0.3224752, -0.3282174)
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rVals <- exp(as.numeric(model.matrix(Sepal.Width ~ Sepal.Length + Species,
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data = iris) %*% rCoef))
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expect_true(all(abs(rVals - vals) < 1e-5), rVals - vals)
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# Test stats::predict is working
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x <- rnorm(15)
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y <- x + rnorm(15)
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expect_equal(length(predict(lm(y ~ x))), 15)
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})
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test_that("spark.glm summary", {
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# gaussian family
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training <- suppressWarnings(createDataFrame(iris))
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stats <- summary(spark.glm(training, Sepal_Width ~ Sepal_Length + Species))
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rStats <- summary(glm(Sepal.Width ~ Sepal.Length + Species, data = iris))
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# test summary coefficients return matrix type
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expect_true(class(stats$coefficients) == "matrix")
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expect_true(class(stats$coefficients[, 1]) == "numeric")
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coefs <- stats$coefficients
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rCoefs <- rStats$coefficients
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expect_true(all(abs(rCoefs - coefs) < 1e-4))
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expect_true(all(
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rownames(stats$coefficients) ==
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c("(Intercept)", "Sepal_Length", "Species_versicolor", "Species_virginica")))
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expect_equal(stats$dispersion, rStats$dispersion)
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expect_equal(stats$null.deviance, rStats$null.deviance)
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expect_equal(stats$deviance, rStats$deviance)
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expect_equal(stats$df.null, rStats$df.null)
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expect_equal(stats$df.residual, rStats$df.residual)
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expect_equal(stats$aic, rStats$aic)
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out <- capture.output(print(stats))
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expect_match(out[2], "Deviance Residuals:")
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expect_true(any(grepl("AIC: 59.22", out)))
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# binomial family
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df <- suppressWarnings(createDataFrame(iris))
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training <- df[df$Species %in% c("versicolor", "virginica"), ]
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stats <- summary(spark.glm(training, Species ~ Sepal_Length + Sepal_Width,
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family = binomial(link = "logit")))
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rTraining <- iris[iris$Species %in% c("versicolor", "virginica"), ]
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rStats <- summary(glm(Species ~ Sepal.Length + Sepal.Width, data = rTraining,
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family = binomial(link = "logit")))
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coefs <- stats$coefficients
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rCoefs <- rStats$coefficients
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expect_true(all(abs(rCoefs - coefs) < 1e-4))
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expect_true(all(
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rownames(stats$coefficients) ==
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c("(Intercept)", "Sepal_Length", "Sepal_Width")))
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expect_equal(stats$dispersion, rStats$dispersion)
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expect_equal(stats$null.deviance, rStats$null.deviance)
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expect_equal(stats$deviance, rStats$deviance)
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expect_equal(stats$df.null, rStats$df.null)
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expect_equal(stats$df.residual, rStats$df.residual)
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expect_equal(stats$aic, rStats$aic)
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# Test spark.glm works with weighted dataset
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a1 <- c(0, 1, 2, 3)
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a2 <- c(5, 2, 1, 3)
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w <- c(1, 2, 3, 4)
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b <- c(1, 0, 1, 0)
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data <- as.data.frame(cbind(a1, a2, w, b))
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df <- createDataFrame(data)
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stats <- summary(spark.glm(df, b ~ a1 + a2, family = "binomial", weightCol = "w"))
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rStats <- summary(glm(b ~ a1 + a2, family = "binomial", data = data, weights = w))
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coefs <- stats$coefficients
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rCoefs <- rStats$coefficients
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expect_true(all(abs(rCoefs - coefs) < 1e-3))
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expect_true(all(rownames(stats$coefficients) == c("(Intercept)", "a1", "a2")))
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expect_equal(stats$dispersion, rStats$dispersion)
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expect_equal(stats$null.deviance, rStats$null.deviance)
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expect_equal(stats$deviance, rStats$deviance)
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expect_equal(stats$df.null, rStats$df.null)
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expect_equal(stats$df.residual, rStats$df.residual)
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expect_equal(stats$aic, rStats$aic)
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# Test summary works on base GLM models
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baseModel <- stats::glm(Sepal.Width ~ Sepal.Length + Species, data = iris)
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baseSummary <- summary(baseModel)
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expect_true(abs(baseSummary$deviance - 12.19313) < 1e-4)
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# Test spark.glm works with regularization parameter
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data <- as.data.frame(cbind(a1, a2, b))
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df <- suppressWarnings(createDataFrame(data))
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regStats <- summary(spark.glm(df, b ~ a1 + a2, regParam = 1.0))
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expect_equal(regStats$aic, 13.32836, tolerance = 1e-4) # 13.32836 is from summary() result
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# Test spark.glm works on collinear data
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A <- matrix(c(1, 2, 3, 4, 2, 4, 6, 8), 4, 2)
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b <- c(1, 2, 3, 4)
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data <- as.data.frame(cbind(A, b))
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df <- createDataFrame(data)
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stats <- summary(spark.glm(df, b ~ . - 1))
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coefs <- stats$coefficients
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expect_true(all(abs(c(0.5, 0.25) - coefs) < 1e-4))
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})
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test_that("spark.glm save/load", {
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skip_on_cran()
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training <- suppressWarnings(createDataFrame(iris))
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m <- spark.glm(training, Sepal_Width ~ Sepal_Length + Species)
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s <- summary(m)
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modelPath <- tempfile(pattern = "spark-glm", fileext = ".tmp")
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write.ml(m, modelPath)
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expect_error(write.ml(m, modelPath))
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write.ml(m, modelPath, overwrite = TRUE)
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m2 <- read.ml(modelPath)
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s2 <- summary(m2)
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expect_equal(s$coefficients, s2$coefficients)
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expect_equal(rownames(s$coefficients), rownames(s2$coefficients))
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expect_equal(s$dispersion, s2$dispersion)
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expect_equal(s$null.deviance, s2$null.deviance)
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expect_equal(s$deviance, s2$deviance)
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expect_equal(s$df.null, s2$df.null)
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expect_equal(s$df.residual, s2$df.residual)
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expect_equal(s$aic, s2$aic)
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expect_equal(s$iter, s2$iter)
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expect_true(!s$is.loaded)
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expect_true(s2$is.loaded)
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unlink(modelPath)
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})
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test_that("formula of glm", {
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skip_on_cran()
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training <- suppressWarnings(createDataFrame(iris))
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# dot minus and intercept vs native glm
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model <- glm(Sepal_Width ~ . - Species + 0, data = training)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ . - Species + 0, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# feature interaction vs native glm
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model <- glm(Sepal_Width ~ Species:Sepal_Length, data = training)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Species:Sepal.Length, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# glm should work with long formula
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training <- suppressWarnings(createDataFrame(iris))
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training$LongLongLongLongLongName <- training$Sepal_Width
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training$VeryLongLongLongLonLongName <- training$Sepal_Length
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training$AnotherLongLongLongLongName <- training$Species
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model <- glm(LongLongLongLongLongName ~ VeryLongLongLongLonLongName + AnotherLongLongLongLongName,
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data = training)
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vals <- collect(select(predict(model, training), "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Sepal.Length + Species, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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})
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test_that("glm and predict", {
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skip_on_cran()
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training <- suppressWarnings(createDataFrame(iris))
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# gaussian family
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model <- glm(Sepal_Width ~ Sepal_Length + Species, data = training)
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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rVals <- predict(glm(Sepal.Width ~ Sepal.Length + Species, data = iris), iris)
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# poisson family
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model <- glm(Sepal_Width ~ Sepal_Length + Species, data = training,
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family = poisson(link = identity))
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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rVals <- suppressWarnings(predict(glm(Sepal.Width ~ Sepal.Length + Species,
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data = iris, family = poisson(link = identity)), iris))
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expect_true(all(abs(rVals - vals) < 1e-6), rVals - vals)
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# tweedie family
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model <- glm(Sepal_Width ~ Sepal_Length + Species, data = training,
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family = "tweedie", var.power = 1.2, link.power = 0.0)
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prediction <- predict(model, training)
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expect_equal(typeof(take(select(prediction, "prediction"), 1)$prediction), "double")
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vals <- collect(select(prediction, "prediction"))
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# manual calculation of the R predicted values to avoid dependence on statmod
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#' library(statmod)
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#' rModel <- glm(Sepal.Width ~ Sepal.Length + Species, data = iris,
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#' family = tweedie(var.power = 1.2, link.power = 0.0))
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#' print(coef(rModel))
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rCoef <- c(0.6455409, 0.1169143, -0.3224752, -0.3282174)
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rVals <- exp(as.numeric(model.matrix(Sepal.Width ~ Sepal.Length + Species,
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data = iris) %*% rCoef))
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expect_true(all(abs(rVals - vals) < 1e-5), rVals - vals)
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# Test stats::predict is working
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x <- rnorm(15)
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y <- x + rnorm(15)
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expect_equal(length(predict(lm(y ~ x))), 15)
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})
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test_that("glm summary", {
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skip_on_cran()
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# gaussian family
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training <- suppressWarnings(createDataFrame(iris))
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stats <- summary(glm(Sepal_Width ~ Sepal_Length + Species, data = training))
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rStats <- summary(glm(Sepal.Width ~ Sepal.Length + Species, data = iris))
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coefs <- stats$coefficients
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rCoefs <- rStats$coefficients
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expect_true(all(abs(rCoefs - coefs) < 1e-4))
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expect_true(all(
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rownames(stats$coefficients) ==
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c("(Intercept)", "Sepal_Length", "Species_versicolor", "Species_virginica")))
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expect_equal(stats$dispersion, rStats$dispersion)
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expect_equal(stats$null.deviance, rStats$null.deviance)
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expect_equal(stats$deviance, rStats$deviance)
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expect_equal(stats$df.null, rStats$df.null)
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expect_equal(stats$df.residual, rStats$df.residual)
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expect_equal(stats$aic, rStats$aic)
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# binomial family
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df <- suppressWarnings(createDataFrame(iris))
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training <- df[df$Species %in% c("versicolor", "virginica"), ]
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stats <- summary(glm(Species ~ Sepal_Length + Sepal_Width, data = training,
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family = binomial(link = "logit")))
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rTraining <- iris[iris$Species %in% c("versicolor", "virginica"), ]
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rStats <- summary(glm(Species ~ Sepal.Length + Sepal.Width, data = rTraining,
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family = binomial(link = "logit")))
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coefs <- stats$coefficients
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rCoefs <- rStats$coefficients
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expect_true(all(abs(rCoefs - coefs) < 1e-4))
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expect_true(all(
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rownames(stats$coefficients) ==
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c("(Intercept)", "Sepal_Length", "Sepal_Width")))
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expect_equal(stats$dispersion, rStats$dispersion)
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expect_equal(stats$null.deviance, rStats$null.deviance)
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expect_equal(stats$deviance, rStats$deviance)
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expect_equal(stats$df.null, rStats$df.null)
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expect_equal(stats$df.residual, rStats$df.residual)
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expect_equal(stats$aic, rStats$aic)
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# Test summary works on base GLM models
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baseModel <- stats::glm(Sepal.Width ~ Sepal.Length + Species, data = iris)
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baseSummary <- summary(baseModel)
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expect_true(abs(baseSummary$deviance - 12.19313) < 1e-4)
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})
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test_that("glm save/load", {
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skip_on_cran()
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training <- suppressWarnings(createDataFrame(iris))
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m <- glm(Sepal_Width ~ Sepal_Length + Species, data = training)
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s <- summary(m)
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modelPath <- tempfile(pattern = "glm", fileext = ".tmp")
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write.ml(m, modelPath)
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expect_error(write.ml(m, modelPath))
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write.ml(m, modelPath, overwrite = TRUE)
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m2 <- read.ml(modelPath)
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s2 <- summary(m2)
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expect_equal(s$coefficients, s2$coefficients)
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expect_equal(rownames(s$coefficients), rownames(s2$coefficients))
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expect_equal(s$dispersion, s2$dispersion)
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expect_equal(s$null.deviance, s2$null.deviance)
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expect_equal(s$deviance, s2$deviance)
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expect_equal(s$df.null, s2$df.null)
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expect_equal(s$df.residual, s2$df.residual)
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expect_equal(s$aic, s2$aic)
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expect_equal(s$iter, s2$iter)
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expect_true(!s$is.loaded)
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expect_true(s2$is.loaded)
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unlink(modelPath)
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})
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test_that("spark.isoreg", {
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label <- c(7.0, 5.0, 3.0, 5.0, 1.0)
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feature <- c(0.0, 1.0, 2.0, 3.0, 4.0)
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weight <- c(1.0, 1.0, 1.0, 1.0, 1.0)
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data <- as.data.frame(cbind(label, feature, weight))
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df <- createDataFrame(data)
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model <- spark.isoreg(df, label ~ feature, isotonic = FALSE,
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weightCol = "weight")
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# only allow one variable on the right hand side of the formula
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expect_error(model2 <- spark.isoreg(df, ~., isotonic = FALSE))
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result <- summary(model)
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expect_equal(result$predictions, list(7, 5, 4, 4, 1))
|
|
|
|
# Test model prediction
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|
predict_data <- list(list(-2.0), list(-1.0), list(0.5),
|
|
list(0.75), list(1.0), list(2.0), list(9.0))
|
|
predict_df <- createDataFrame(predict_data, c("feature"))
|
|
predict_result <- collect(select(predict(model, predict_df), "prediction"))
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|
expect_equal(predict_result$prediction, c(7.0, 7.0, 6.0, 5.5, 5.0, 4.0, 1.0))
|
|
|
|
# Test model save/load
|
|
modelPath <- tempfile(pattern = "spark-isoreg", fileext = ".tmp")
|
|
write.ml(model, modelPath)
|
|
expect_error(write.ml(model, modelPath))
|
|
write.ml(model, modelPath, overwrite = TRUE)
|
|
model2 <- read.ml(modelPath)
|
|
expect_equal(result, summary(model2))
|
|
|
|
unlink(modelPath)
|
|
})
|
|
|
|
test_that("spark.survreg", {
|
|
# R code to reproduce the result.
|
|
#
|
|
#' rData <- list(time = c(4, 3, 1, 1, 2, 2, 3), status = c(1, 1, 1, 0, 1, 1, 0),
|
|
#' x = c(0, 2, 1, 1, 1, 0, 0), sex = c(0, 0, 0, 0, 1, 1, 1))
|
|
#' library(survival)
|
|
#' model <- survreg(Surv(time, status) ~ x + sex, rData)
|
|
#' summary(model)
|
|
#' predict(model, data)
|
|
#
|
|
# -- output of 'summary(model)'
|
|
#
|
|
# Value Std. Error z p
|
|
# (Intercept) 1.315 0.270 4.88 1.07e-06
|
|
# x -0.190 0.173 -1.10 2.72e-01
|
|
# sex -0.253 0.329 -0.77 4.42e-01
|
|
# Log(scale) -1.160 0.396 -2.93 3.41e-03
|
|
#
|
|
# -- output of 'predict(model, data)'
|
|
#
|
|
# 1 2 3 4 5 6 7
|
|
# 3.724591 2.545368 3.079035 3.079035 2.390146 2.891269 2.891269
|
|
#
|
|
data <- list(list(4, 1, 0, 0), list(3, 1, 2, 0), list(1, 1, 1, 0),
|
|
list(1, 0, 1, 0), list(2, 1, 1, 1), list(2, 1, 0, 1), list(3, 0, 0, 1))
|
|
df <- createDataFrame(data, c("time", "status", "x", "sex"))
|
|
model <- spark.survreg(df, Surv(time, status) ~ x + sex)
|
|
stats <- summary(model)
|
|
coefs <- as.vector(stats$coefficients[, 1])
|
|
rCoefs <- c(1.3149571, -0.1903409, -0.2532618, -1.1599800)
|
|
expect_equal(coefs, rCoefs, tolerance = 1e-4)
|
|
expect_true(all(
|
|
rownames(stats$coefficients) ==
|
|
c("(Intercept)", "x", "sex", "Log(scale)")))
|
|
p <- collect(select(predict(model, df), "prediction"))
|
|
expect_equal(p$prediction, c(3.724591, 2.545368, 3.079035, 3.079035,
|
|
2.390146, 2.891269, 2.891269), tolerance = 1e-4)
|
|
|
|
# Test model save/load
|
|
modelPath <- tempfile(pattern = "spark-survreg", fileext = ".tmp")
|
|
write.ml(model, modelPath)
|
|
expect_error(write.ml(model, modelPath))
|
|
write.ml(model, modelPath, overwrite = TRUE)
|
|
model2 <- read.ml(modelPath)
|
|
stats2 <- summary(model2)
|
|
coefs2 <- as.vector(stats2$coefficients[, 1])
|
|
expect_equal(coefs, coefs2)
|
|
expect_equal(rownames(stats$coefficients), rownames(stats2$coefficients))
|
|
|
|
unlink(modelPath)
|
|
|
|
# Test survival::survreg
|
|
if (requireNamespace("survival", quietly = TRUE)) {
|
|
rData <- list(time = c(4, 3, 1, 1, 2, 2, 3), status = c(1, 1, 1, 0, 1, 1, 0),
|
|
x = c(0, 2, 1, 1, 1, 0, 0), sex = c(0, 0, 0, 0, 1, 1, 1))
|
|
expect_error(
|
|
model <- survival::survreg(formula = survival::Surv(time, status) ~ x + sex, data = rData),
|
|
NA)
|
|
expect_equal(predict(model, rData)[[1]], 3.724591, tolerance = 1e-4)
|
|
}
|
|
})
|
|
|
|
sparkR.session.stop()
|