From ce112cec4f9bff222aa256893f94c316662a2a7e Mon Sep 17 00:00:00 2001 From: actuaryzhang Date: Tue, 31 Jan 2017 12:20:43 -0800 Subject: [SPARK-19395][SPARKR] Convert coefficients in summary to matrix ## What changes were proposed in this pull request? The `coefficients` component in model summary should be 'matrix' but the underlying structure is indeed list. This affects several models except for 'AFTSurvivalRegressionModel' which has the correct implementation. The fix is to first `unlist` the coefficients returned from the `callJMethod` before converting to matrix. An example illustrates the issues: ``` data(iris) df <- createDataFrame(iris) model <- spark.glm(df, Sepal_Length ~ Sepal_Width, family = "gaussian") s <- summary(model) > str(s$coefficients) List of 8 $ : num 6.53 $ : num -0.223 $ : num 0.479 $ : num 0.155 $ : num 13.6 $ : num -1.44 $ : num 0 $ : num 0.152 - attr(*, "dim")= int [1:2] 2 4 - attr(*, "dimnames")=List of 2 ..$ : chr [1:2] "(Intercept)" "Sepal_Width" ..$ : chr [1:4] "Estimate" "Std. Error" "t value" "Pr(>|t|)" > s$coefficients[, 2] $`(Intercept)` [1] 0.4788963 $Sepal_Width [1] 0.1550809 ``` This shows that the underlying structure of coefficients is still `list`. felixcheung wangmiao1981 Author: actuaryzhang Closes #16730 from actuaryzhang/sparkRCoef. --- .../tests/testthat/test_mllib_classification.R | 17 +++++++++----- R/pkg/inst/tests/testthat/test_mllib_clustering.R | 4 ++++ R/pkg/inst/tests/testthat/test_mllib_regression.R | 27 ++++++++++++---------- 3 files changed, 30 insertions(+), 18 deletions(-) (limited to 'R/pkg/inst/tests') diff --git a/R/pkg/inst/tests/testthat/test_mllib_classification.R b/R/pkg/inst/tests/testthat/test_mllib_classification.R index 2e0dea321e..5f84a620c1 100644 --- a/R/pkg/inst/tests/testthat/test_mllib_classification.R +++ b/R/pkg/inst/tests/testthat/test_mllib_classification.R @@ -68,12 +68,17 @@ test_that("spark.logit", { df <- suppressWarnings(createDataFrame(iris)) model <- spark.logit(df, Species ~ ., regParam = 0.5) summary <- summary(model) + + # test summary coefficients return matrix type + expect_true(class(summary$coefficients) == "matrix") + expect_true(class(summary$coefficients[, 1]) == "numeric") + versicolorCoefsR <- c(1.52, 0.03, -0.53, 0.04, 0.00) virginicaCoefsR <- c(-2.62, 0.27, -0.02, 0.16, 0.42) setosaCoefsR <- c(1.10, -0.29, 0.55, -0.19, -0.42) - versicolorCoefs <- unlist(summary$coefficients[, "versicolor"]) - virginicaCoefs <- unlist(summary$coefficients[, "virginica"]) - setosaCoefs <- unlist(summary$coefficients[, "setosa"]) + versicolorCoefs <- summary$coefficients[, "versicolor"] + virginicaCoefs <- summary$coefficients[, "virginica"] + setosaCoefs <- summary$coefficients[, "setosa"] expect_true(all(abs(versicolorCoefsR - versicolorCoefs) < 0.1)) expect_true(all(abs(virginicaCoefsR - virginicaCoefs) < 0.1)) expect_true(all(abs(setosaCoefs - setosaCoefs) < 0.1)) @@ -136,8 +141,8 @@ test_that("spark.logit", { summary <- summary(model) versicolorCoefsR <- c(3.94, -0.16, -0.02, -0.35, -0.78) virginicaCoefsR <- c(-3.94, 0.16, -0.02, 0.35, 0.78) - versicolorCoefs <- unlist(summary$coefficients[, "versicolor"]) - virginicaCoefs <- unlist(summary$coefficients[, "virginica"]) + versicolorCoefs <- summary$coefficients[, "versicolor"] + virginicaCoefs <- summary$coefficients[, "virginica"] expect_true(all(abs(versicolorCoefsR - versicolorCoefs) < 0.1)) expect_true(all(abs(virginicaCoefsR - virginicaCoefs) < 0.1)) @@ -145,7 +150,7 @@ test_that("spark.logit", { model <- spark.logit(training, Species ~ ., regParam = 0.5) summary <- summary(model) coefsR <- c(-6.08, 0.25, 0.16, 0.48, 1.04) - coefs <- unlist(summary$coefficients[, "Estimate"]) + coefs <- summary$coefficients[, "Estimate"] expect_true(all(abs(coefsR - coefs) < 0.1)) # Test prediction with string label diff --git a/R/pkg/inst/tests/testthat/test_mllib_clustering.R b/R/pkg/inst/tests/testthat/test_mllib_clustering.R index aad834bb64..28a6eeba2c 100644 --- a/R/pkg/inst/tests/testthat/test_mllib_clustering.R +++ b/R/pkg/inst/tests/testthat/test_mllib_clustering.R @@ -166,6 +166,10 @@ test_that("spark.kmeans", { expect_equal(k, 2) expect_equal(sort(collect(distinct(select(cluster, "prediction")))$prediction), c(0, 1)) + # test summary coefficients return matrix type + expect_true(class(summary.model$coefficients) == "matrix") + expect_true(class(summary.model$coefficients[1, ]) == "numeric") + # Test model save/load modelPath <- tempfile(pattern = "spark-kmeans", fileext = ".tmp") write.ml(model, modelPath) diff --git a/R/pkg/inst/tests/testthat/test_mllib_regression.R b/R/pkg/inst/tests/testthat/test_mllib_regression.R index c450a15171..81a5bdc414 100644 --- a/R/pkg/inst/tests/testthat/test_mllib_regression.R +++ b/R/pkg/inst/tests/testthat/test_mllib_regression.R @@ -87,11 +87,14 @@ test_that("spark.glm summary", { # gaussian family training <- suppressWarnings(createDataFrame(iris)) stats <- summary(spark.glm(training, Sepal_Width ~ Sepal_Length + Species)) - rStats <- summary(glm(Sepal.Width ~ Sepal.Length + Species, data = iris)) - coefs <- unlist(stats$coefficients) - rCoefs <- unlist(rStats$coefficients) + # test summary coefficients return matrix type + expect_true(class(stats$coefficients) == "matrix") + expect_true(class(stats$coefficients[, 1]) == "numeric") + + coefs <- stats$coefficients + rCoefs <- rStats$coefficients expect_true(all(abs(rCoefs - coefs) < 1e-4)) expect_true(all( rownames(stats$coefficients) == @@ -117,8 +120,8 @@ test_that("spark.glm summary", { rStats <- summary(glm(Species ~ Sepal.Length + Sepal.Width, data = rTraining, family = binomial(link = "logit"))) - coefs <- unlist(stats$coefficients) - rCoefs <- unlist(rStats$coefficients) + coefs <- stats$coefficients + rCoefs <- rStats$coefficients expect_true(all(abs(rCoefs - coefs) < 1e-4)) expect_true(all( rownames(stats$coefficients) == @@ -141,8 +144,8 @@ test_that("spark.glm summary", { stats <- summary(spark.glm(df, b ~ a1 + a2, family = "binomial", weightCol = "w")) rStats <- summary(glm(b ~ a1 + a2, family = "binomial", data = data, weights = w)) - coefs <- unlist(stats$coefficients) - rCoefs <- unlist(rStats$coefficients) + coefs <- stats$coefficients + rCoefs <- rStats$coefficients expect_true(all(abs(rCoefs - coefs) < 1e-3)) expect_true(all(rownames(stats$coefficients) == c("(Intercept)", "a1", "a2"))) expect_equal(stats$dispersion, rStats$dispersion) @@ -169,7 +172,7 @@ test_that("spark.glm summary", { data <- as.data.frame(cbind(A, b)) df <- createDataFrame(data) stats <- summary(spark.glm(df, b ~ . - 1)) - coefs <- unlist(stats$coefficients) + coefs <- stats$coefficients expect_true(all(abs(c(0.5, 0.25) - coefs) < 1e-4)) }) @@ -259,8 +262,8 @@ test_that("glm summary", { rStats <- summary(glm(Sepal.Width ~ Sepal.Length + Species, data = iris)) - coefs <- unlist(stats$coefficients) - rCoefs <- unlist(rStats$coefficients) + coefs <- stats$coefficients + rCoefs <- rStats$coefficients expect_true(all(abs(rCoefs - coefs) < 1e-4)) expect_true(all( rownames(stats$coefficients) == @@ -282,8 +285,8 @@ test_that("glm summary", { rStats <- summary(glm(Species ~ Sepal.Length + Sepal.Width, data = rTraining, family = binomial(link = "logit"))) - coefs <- unlist(stats$coefficients) - rCoefs <- unlist(rStats$coefficients) + coefs <- stats$coefficients + rCoefs <- rStats$coefficients expect_true(all(abs(rCoefs - coefs) < 1e-4)) expect_true(all( rownames(stats$coefficients) == -- cgit v1.2.3