diff --git a/tests/testthat/test-challenge.R b/tests/testthat/test-challenge.R index 819d1c5..16ff24d 100644 --- a/tests/testthat/test-challenge.R +++ b/tests/testthat/test-challenge.R @@ -1,633 +1,633 @@ # Copyright (c) German Cancer Research Center (DKFZ) # All rights reserved. # # This file is part of challengeR. # # challengeR is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 2 of the License, or # (at your option) any later version. # # challengeR is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with challengeR. If not, see . test_that("empty attribute 'taskName' raises error for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1")) expect_error(as.challenge(data, taskName="", algorithm="algo", case="case", value="value", smallBetter=FALSE), "Argument 'taskName' is empty.", fixed=TRUE) }) test_that("only whitespaces in attribute 'taskName' raises error for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1")) expect_error(as.challenge(data, taskName=" ", algorithm="algo", case="case", value="value", smallBetter=FALSE), "Argument 'taskName' is empty.", fixed=TRUE) }) test_that("attributes are set for single-task challenge with specified task name", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1")) actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE) expect_equal(attr(actualChallenge, "annotator"), NULL) expect_equal(attr(actualChallenge, "by"), "task") expect_equal(attr(actualChallenge, "smallBetter"), FALSE) expect_equal(attr(actualChallenge, "check"), TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C1")) expect_equal(as.vector(actualChallenge$T1$task), c("T1", "T1")) # expect that there's no attribute "task" expect_equal(attr(actualChallenge, "task"), NULL) expect_equal(attr(actualChallenge$T1, "task"), NULL) expect_equal(attr(actualChallenge$T2, "task"), NULL) }) test_that("attributes are set for single-task challenge with dummy task name", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1")) actualChallenge <- as.challenge(data, algorithm="algo", case="case", value="value", smallBetter=FALSE) expect_equal(attr(actualChallenge, "annotator"), NULL) expect_equal(attr(actualChallenge, "by"), "task") expect_equal(attr(actualChallenge, "smallBetter"), FALSE) expect_equal(attr(actualChallenge, "check"), TRUE) expect_equal(as.vector(actualChallenge$dummyTask$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$dummyTask$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$dummyTask$case), c("C1", "C1")) expect_equal(as.vector(actualChallenge$dummyTask$task), c("dummyTask", "dummyTask")) # expect that there's no attribute "task" expect_equal(attr(actualChallenge, "task"), NULL) expect_equal(attr(actualChallenge$dummyTask, "task"), NULL) expect_equal(attr(actualChallenge$dummyTask, "task"), NULL) }) test_that("leading and trailing whitespaces are trimmed for attribute 'taskName'", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1")) actualChallenge <- as.challenge(data, taskName=" T1 ", algorithm="algo", case="case", value="value", smallBetter=FALSE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) }) test_that("attributes are set for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A2", value=0.3, case="C1") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=TRUE) expect_equal(attr(actualChallenge, "annotator"), NULL) expect_equal(attr(actualChallenge, "by"), "task") expect_equal(attr(actualChallenge, "smallBetter"), TRUE) expect_equal(attr(actualChallenge, "check"), TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C1")) expect_equal(as.vector(actualChallenge$T1$task), c("T1", "T1")) expect_equal(as.vector(actualChallenge$T2$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.2, 0.3)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C1")) expect_equal(as.vector(actualChallenge$T2$task), c("T2", "T2")) # expect that there's no attribute "task" expect_equal(attr(actualChallenge, "task"), NULL) expect_equal(attr(actualChallenge$T1, "task"), NULL) expect_equal(attr(actualChallenge$T2, "task"), NULL) }) test_that("attributes are set for multi-task challenge with sanity check disabled", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A2", value=0.3, case="C1") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=TRUE, check=FALSE) expect_equal(attr(actualChallenge, "annotator"), NULL) expect_equal(attr(actualChallenge, "by"), "task") expect_equal(attr(actualChallenge, "smallBetter"), TRUE) expect_equal(attr(actualChallenge, "check"), FALSE) expect_equal(as.vector(actualChallenge$algo), c("A1", "A2", "A1", "A2")) expect_equal(as.vector(actualChallenge$value), c(0.8, 0.6, 0.2, 0.3)) expect_equal(as.vector(actualChallenge$case), c("C1", "C1", "C1", "C1")) expect_equal(as.vector(actualChallenge$task), c("T1", "T1", "T2", "T2")) }) test_that("attribute 'taskName' is ignored for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C1") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A2", value=0.3, case="C1") )) data <- rbind(dataTask1, dataTask2) expect_warning(as.challenge(data, taskName="T1", by="task", algorithm="algo", case="case", value="value", smallBetter=TRUE), "Argument 'taskName' is ignored for multi-task data set.", fixed=TRUE) }) test_that("missing algorithm performances are added as NAs for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2")) expect_message(actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), - "Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, NA, NA, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) expect_equal(as.vector(actualChallenge$T1$task), c("T1", "T1", "T1", "T1")) }) test_that("multi-task data set containing one task is interpreted as single-task data set, missing algorithm performances are added", { data <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2") )) # do not specify parameter "by" to interpret multi-task data set as single-task data set expect_message(actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), - "Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, NA, NA, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) }) test_that("missing algorithm performances are added as NAs for multi-task challenge (2 tasks in data set)", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A1", value=0.3, case="C2"), data.frame(algo="A2", value=0.4, case="C1") )) data <- rbind(dataTask1, dataTask2) expect_message(actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE), - "Performance of not all algorithms has been observed for all cases in task 'T1'. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases in task 'T1'.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, NA, NA, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) expect_equal(as.vector(actualChallenge$T1$task), c("T1", "T1", "T1", "T1")) expect_equal(as.vector(actualChallenge$T2$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.2, 0.3, 0.4, NA)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C2", "C1", "C2")) expect_equal(as.vector(actualChallenge$T2$task), c("T2", "T2", "T2", "T2")) }) test_that("missing algorithm performances are not added as NA with sanity check disabled for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2")) actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, check=FALSE) expect_equal(as.vector(actualChallenge$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$case), c("C1", "C2")) }) test_that("missing algorithm performances are not added as NA with sanity check disabled for multi-task challenge (2 tasks in data set)", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A1", value=0.3, case="C2"), data.frame(algo="A2", value=0.4, case="C1") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, check=FALSE) expect_equal(as.vector(actualChallenge$algo), c("A1", "A2", "A1", "A1", "A2")) expect_equal(as.vector(actualChallenge$value), c(0.8, 0.6, 0.2, 0.3, 0.4)) expect_equal(as.vector(actualChallenge$case), c("C1", "C2", "C1", "C2", "C1")) }) test_that("case cannot appear more than once per algorithm for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1")) expect_error(as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1", fixed=TRUE) }) test_that("multi-task data set containing one task is interpreted as single-task data set, case cannot appear more than once per algorithm", { data <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1") )) # do not specify parameter "by" to interpret multi-task data set as single-task data set expect_error(as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1", fixed=TRUE) }) test_that("case cannot appear more than once per algorithm for multi-task challenge (1 task in data set)", { data <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1") )) expect_error(as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1", fixed=TRUE) }) test_that("cases cannot appear more than once per algorithm for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.7, case="C1"), data.frame(algo="A1", value=0.5, case="C2"), data.frame(algo="A2", value=0.6, case="C2"), data.frame(algo="A2", value=0.6, case="C2")) expect_error(as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1, C2", fixed=TRUE) }) test_that("cases cannot appear more than once per algorithm for multi-task challenge (1 task in data set)", { data <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.7, case="C1"), data.frame(algo="A1", value=0.5, case="C2"), data.frame(algo="A2", value=0.6, case="C2"), data.frame(algo="A2", value=0.6, case="C2") )) expect_error(as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1, C2", fixed=TRUE) }) test_that("cases cannot appear more than once per algorithm for multi-task challenge (2 tasks in data set)", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1") # let T1 pass )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.7, case="C1"), data.frame(algo="A1", value=0.5, case="C2"), data.frame(algo="A2", value=0.6, case="C2"), data.frame(algo="A2", value=0.6, case="C2") )) data <- rbind(dataTask1, dataTask2) expect_error(as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm in task 'T2'. Please revise.\nCase(s): C1, C2", fixed=TRUE) }) test_that("cases cannot appear more than once per algorithm when missing data was added for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2"), data.frame(algo="A2", value=0.6, case="C2")) expect_error(as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1, C2", fixed=TRUE) }) test_that("user is notified of duplicate cases when multi-task data set is interpreted as single-task data set (2 tasks in data set)", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.8, case="C1") )) data <- rbind(dataTask1, dataTask2) # do not specify parameter "by" to interpret multi-task data set as single-task data set expect_error(as.challenge(data, taskName="New task", algorithm="algo", case="case", value="value", smallBetter=FALSE), "The following case(s) appear(s) more than once for the same algorithm. Please revise. Or are you considering a multi-task challenge and forgot to specify argument 'by'?\nCase(s): C1", fixed=TRUE) }) test_that("user is notified of missing algorithm performance when multi-task data set is interpreted as single-task data set (2 tasks in data set)", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A2", value=0.6, case="C2") )) data <- rbind(dataTask1, dataTask2) # do not specify parameter "by" to interpret multi-task data set as single-task data set expect_message(as.challenge(data, taskName="New task", algorithm="algo", case="case", value="value", smallBetter=FALSE), - "Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) }) test_that("NAs are replaced by numeric value for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2"), data.frame(algo="A2", value=0.6, case="C1"), data.frame(algo="A2", value=NA, case="C2")) actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=0) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.0, 0.6, 0.0)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) }) test_that("NAs are replaced by numeric value for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A2", value=NA, case="C1"), data.frame(algo="A2", value=0.5, case="C2") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=0) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.0)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2")) expect_equal(as.vector(actualChallenge$T2$algo), c("A2", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.0, 0.5)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C2")) }) test_that("NAs are replaced by function value for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2"), data.frame(algo="A2", value=0.6, case="C1"), data.frame(algo="A2", value=NA, case="C2")) replacementFunction <- function(x) { 2 } actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=replacementFunction) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 2.0, 0.6, 2.0)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) }) test_that("NAs are replaced by function value for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A2", value=NA, case="C1"), data.frame(algo="A2", value=0.5, case="C2") )) data <- rbind(dataTask1, dataTask2) replacementFunction <- function(x) { 2 } actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=replacementFunction) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 2.0)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2")) expect_equal(as.vector(actualChallenge$T2$algo), c("A2", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(2.0, 0.5)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C2")) }) test_that("NAs are removed for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2"), data.frame(algo="A2", value=0.6, case="C1"), data.frame(algo="A2", value=NA, case="C2")) actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat="na.rm") expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C1")) }) test_that("NAs are removed for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=NA, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A2", value=NA, case="C1"), data.frame(algo="A2", value=0.5, case="C2") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat="na.rm") expect_equal(as.vector(actualChallenge$T1$algo), c("A1")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8)) expect_equal(as.vector(actualChallenge$T1$case), c("C1")) expect_equal(as.vector(actualChallenge$T2$algo), c("A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.5)) expect_equal(as.vector(actualChallenge$T2$case), c("C2")) }) test_that("automatically added NAs are replaced by numeric value for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2")) expect_message(actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=0), - "Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.0, 0.0, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) }) test_that("automatically added NAs are replaced by numeric value for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A1", value=0.3, case="C2"), data.frame(algo="A2", value=0.4, case="C1") )) data <- rbind(dataTask1, dataTask2) expect_message(actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=0), - "Performance of not all algorithms has been observed for all cases in task 'T1'. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases in task 'T1'.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.0, 0.0, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2", "C1", "C2")) expect_equal(as.vector(actualChallenge$T2$algo), c("A1", "A1", "A2", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.2, 0.3, 0.4, 0.0)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C2", "C1", "C2")) }) test_that("automatically added NAs are removed for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2")) expect_message(actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat="na.rm"), - "Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2")) }) test_that("automatically added NAs are removed for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A2", value=0.6, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.2, case="C1"), data.frame(algo="A1", value=0.3, case="C2"), data.frame(algo="A2", value=0.4, case="C1") )) data <- rbind(dataTask1, dataTask2) expect_message(actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat="na.rm"), - "Performance of not all algorithms has been observed for all cases in task 'T1'. Therefore, missings have been inserted in the following cases:", fixed=TRUE) + "Performance of not all algorithms has been observed for all cases in task 'T1'.\nTherefore, missings have been inserted in the following cases:", fixed=TRUE) expect_equal(as.vector(actualChallenge$T1$algo), c("A1", "A2")) expect_equal(as.vector(actualChallenge$T1$value), c(0.8, 0.6)) expect_equal(as.vector(actualChallenge$T1$case), c("C1", "C2")) expect_equal(as.vector(actualChallenge$T2$algo), c("A1", "A1", "A2")) expect_equal(as.vector(actualChallenge$T2$value), c(0.2, 0.3, 0.4)) expect_equal(as.vector(actualChallenge$T2$case), c("C1", "C2", "C1")) }) test_that("class of 'algorithm' column must be 'factor' for single-task challenge", { data <- rbind( data.frame(algo="A1", value=0.8, case="C1"), data.frame(algo="A1", value=0.7, case="C2"), data.frame(algo="A2", value=0.6, case="C1"), data.frame(algo="A2", value=0.5, case="C2")) actualChallenge <- as.challenge(data, taskName="T1", algorithm="algo", case="case", value="value", smallBetter=FALSE, na.treat=0) expect_equal(class(actualChallenge$T1$algo), "factor") }) test_that("class of 'algorithm' column must be 'factor' for multi-task challenge", { dataTask1 <- cbind(task="T1", rbind( data.frame(algo="A1", value=0.81, case="C1"), data.frame(algo="A2", value=0.72, case="C1"), data.frame(algo="A1", value=0.65, case="C2"), data.frame(algo="A2", value=0.95, case="C2") )) dataTask2 <- cbind(task="T2", rbind( data.frame(algo="A1", value=0.75, case="C1"), data.frame(algo="A2", value=0.82, case="C1"), data.frame(algo="A1", value=0.66, case="C2"), data.frame(algo="A2", value=0.84, case="C2") )) data <- rbind(dataTask1, dataTask2) actualChallenge <- as.challenge(data, by="task", algorithm="algo", case="case", value="value", smallBetter=TRUE) expect_equal(class(actualChallenge$T1$algo), "factor") expect_equal(class(actualChallenge$T2$algo), "factor") })