test-AcePreparationFixture.R
In NlsyLinks: Utilities and kinship information for research with the NLSY

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context("Clean Ace Sem Dataset")
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test_that("CleanSemAceDataset MathStandardized", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "MathStandardized_S1" 
  oName_S2 <- "MathStandardized_S2"
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2)
  
  dsClean <- CleanSemAceDataset( dsDirty=dsFull, dsGroupSummary, oName_S1, oName_S2, rName="R" )
  
  expectedRowCount <- 8338
  expectedColumnNames <- c('R', 'O1', 'O2', 'GroupID')
  expectedCompleteRows <- expectedRowCount
  expectedMeanR <- 0.41858059486687454465
  expectedMeanO1 <- 98.242084432717675213
  expectedMeanO2 <- 98.6032621731830119
  expectedMeanGroupID <- 2.3410889901655074219
  
  expect_equal(object=nrow(dsClean), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsClean), expected=expectedColumnNames, scale=1)
  expect_equal(object=mean(dsClean$R), expected=expectedMeanR, scale=1)
  expect_equal(object=mean(dsClean$O1), expected=expectedMeanO1, scale=1)
  expect_equal(object=mean(dsClean$O2), expected=expectedMeanO2, scale=1)
  expect_equal(object=mean(dsClean$GroupID), expected=expectedMeanGroupID, scale=1)  
  expect_equal(object=nrow(subset(dsClean, !is.na(R) & !is.na(O1) & !is.na(O2) & !is.na(GroupID))), expected=expectedCompleteRows, scale=1)
})
test_that("CleanSemAceDataset HeightZGenderAge", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "HeightZGenderAge_S1" 
  oName_S2 <- "HeightZGenderAge_S2" 
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2)
  
  dsClean <- CleanSemAceDataset( dsDirty=dsFull, dsGroupSummary, oName_S1, oName_S2, rName="R" )
  
  expectedRowCount <- 5884
  expectedColumnNames <- c('R', 'O1', 'O2', 'GroupID')
  expectedCompleteRows <- expectedRowCount
  expectedMeanR <- 0.421269544527532
  expectedMeanO1 <- -0.0241219488333721
  expectedMeanO2 <- -0.0516293302405181
  expectedMeanGroupID <- 2.36199864038069
  
  expect_equal(object=nrow(dsClean), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsClean), expected=expectedColumnNames, scale=1)
  expect_equal(object=mean(dsClean$R), expected=expectedMeanR, scale=1)
  expect_equal(object=mean(dsClean$O1), expected=expectedMeanO1, scale=1)
  expect_equal(object=mean(dsClean$O2), expected=expectedMeanO2, scale=1)
  expect_equal(object=mean(dsClean$GroupID), expected=expectedMeanGroupID, scale=1)
  expect_equal(object=nrow(subset(dsClean, !is.na(R) & !is.na(O1) & !is.na(O2) & !is.na(GroupID))), expected=expectedCompleteRows, scale=1)
})

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context("R Group Summary")
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test_that("Group Summary MathStandardized", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "MathStandardized_S1" #Stands for Manifest1
  oName_S2 <- "MathStandardized_S2" #Stands for Manifest2
   
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2)
  
  expectedRowCount <- 5
  expectedColumnNames <- c('R', 'Included', 'PairCount', 'O1Mean', 'O2Mean', 'O1Variance', 'O2Variance', 'O1O2Covariance', 'Correlation', 'Determinant', 'PosDefinite')
  expectedR <- c(.25, .375, .5, .75, 1)
  expectedIncluded <- c(T, T, T, F, T)
  expectedPairCount <- c(2691, 133, 5493, 2, 21)
  expectedO1Mean <- c(95.1142697881828, 93.5413533834586, 99.8883123975969, 108.5, 98.2142857142857)
  expectedO2Mean <- c(95.9810479375697, 93.4135338345865, 100.023393409794, 106, 96.0238095238095)
  expectedO1Variance <- c(126.890562096704, 163.07214057872, 168.734928924968, 220.5, 289.439285714286)
  expectedO2Variance <- c(150.10540276759, 131.55875484165, 172.916650390903, 18, 215.236904761905)
  expectedO1O2Covariance <- c(42.0434303937537, 46.5604209387104, 90.1246543803548, 63, 229.107142857143)
  expectedCorrelation <- c(0.304638873616383, 0.317882876874765, 0.527621772719931, 1, 0.917913001835716)
  expectedDeterminant <- c(17279.3088916572, 19285.6949659089, 21054.6253864743, 0, 9807.93306547619)
  expectedPosDefinite <- expectedIncluded
    
  expect_equal(object=nrow(dsGroupSummary), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsGroupSummary), expected=expectedColumnNames, scale=1)
  expect_equal(object=dsGroupSummary$R, expected=expectedR, scale=1)
  expect_equal(object=dsGroupSummary$Included, expected=expectedIncluded, scale=1)
  expect_equal(object=dsGroupSummary$PairCount, expected=expectedPairCount, scale=1)
  expect_equal(object=dsGroupSummary$O1Mean, expected=expectedO1Mean, scale=1)
  expect_equal(object=dsGroupSummary$O2Mean, expected=expectedO2Mean, scale=1)
  expect_equal(object=dsGroupSummary$O1Variance, expected=expectedO1Variance, scale=1)
  expect_equal(object=dsGroupSummary$O2Variance, expected=expectedO2Variance, scale=1)
  expect_equal(object=dsGroupSummary$O1O2Covariance, expected=expectedO1O2Covariance, scale=1)
  expect_equal(object=dsGroupSummary$Correlation, expected=expectedCorrelation, scale=1)
  expect_equal(object=dsGroupSummary$Determinant, expected=expectedDeterminant, scale=1)
  expect_equal(object=dsGroupSummary$PosDefinite, expected=expectedPosDefinite, scale=1)
})
test_that("Group Summary HeightZGenderAge", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "HeightZGenderAge_S1"
  oName_S2 <- "HeightZGenderAge_S2"
  
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2)
  
  expectedRowCount <- 5
  expectedColumnNames <- c('R', 'Included', 'PairCount', 'O1Mean', 'O2Mean', 'O1Variance', 'O2Variance', 'O1O2Covariance', 'Correlation', 'Determinant', 'PosDefinite')
  expectedR <- c(.25, .375, .5, .75, 1)
  expectedIncluded <- c(T, T, T, F, T)
  expectedPairCount <- c(1862, 46, 3960, 0, 16)
  expectedO1Mean <- c(-0.0656364910243787, 0.220021938792836, -0.00701925328898143, NA, -0.127696863629105)
  expectedO2Mean <- c(-0.0810552323175826, -0.10598269817887, -0.036536371675191, NA, -0.206430523000536)
  expectedO1Variance <- c(1.03961713881969, 1.06618757651653, 0.973121078779517, NA, 0.989812601868269)
  expectedO2Variance <- c(1.04022348588538, 0.96155858700553, 0.957650757558288, NA, 1.062981918949)
  expectedO1O2Covariance <- c(0.268806438004843, 0.429343906702951, 0.391073094984259, NA, 0.947322488484283)
  expectedCorrelation <- c(0.258487545858257, 0.424033940313456, 0.405108093793955, NA, 0.923545760601445)
  expectedDeterminant <- c(1.00917726301635, 0.84086562933513, 0.778971972668575, NA, 0.154733001745783)
  expectedPosDefinite <- expectedIncluded
  
  expect_equal(object=nrow(dsGroupSummary), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsGroupSummary), expected=expectedColumnNames, scale=1)
  expect_equal(object=dsGroupSummary$R, expected=expectedR, scale=1)
  expect_equal(object=dsGroupSummary$Included, expected=expectedIncluded, scale=1)
  expect_equal(object=dsGroupSummary$PairCount, expected=expectedPairCount, scale=1)
  expect_equal(object=dsGroupSummary$O1Mean, expected=expectedO1Mean, scale=1)
  expect_equal(object=dsGroupSummary$O2Mean, expected=expectedO2Mean, scale=1)
  expect_equal(object=dsGroupSummary$O1Variance, expected=expectedO1Variance, scale=1)
  expect_equal(object=dsGroupSummary$O2Variance, expected=expectedO2Variance, scale=1)
  expect_equal(object=dsGroupSummary$O1O2Covariance, expected=expectedO1O2Covariance, scale=1)
  expect_equal(object=dsGroupSummary$Correlation, expected=expectedCorrelation, scale=1)
  expect_equal(object=dsGroupSummary$Determinant, expected=expectedDeterminant, scale=1)
  expect_equal(object=dsGroupSummary$PosDefinite, expected=expectedPosDefinite, scale=1)
})

test_that("Group Summary Changed Variable Name for 'R'", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "HeightZGenderAge_S1"
  oName_S2 <- "HeightZGenderAge_S2"
  rName <- "RRR"
  dsFull <- RenameNlsyColumn(dsFull, "R", rName)
                         
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2, rName)
  
  expectedRowCount <- 5
  expectedColumnNames <- c('RRR', 'Included', 'PairCount', 'O1Mean', 'O2Mean', 'O1Variance', 'O2Variance', 'O1O2Covariance', 'Correlation', 'Determinant', 'PosDefinite')
  expectedR <- c(.25, .375, .5, .75, 1)
  expectedIncluded <- c(T, T, T, F, T)
  expectedPairCount <- c(1862, 46, 3960, 0, 16)
  expectedO1Mean <- c(-0.0656364910243787, 0.220021938792836, -0.00701925328898143, NA, -0.127696863629105)
  expectedO2Mean <- c(-0.0810552323175826, -0.10598269817887, -0.036536371675191, NA, -0.206430523000536)
  expectedO1Variance <- c(1.03961713881969, 1.06618757651653, 0.973121078779517, NA, 0.989812601868269)
  expectedO2Variance <- c(1.04022348588538, 0.96155858700553, 0.957650757558288, NA, 1.062981918949)
  expectedO1O2Covariance <- c(0.268806438004843, 0.429343906702951, 0.391073094984259, NA, 0.947322488484283)
  expectedCorrelation <- c(0.258487545858257, 0.424033940313456, 0.405108093793955, NA, 0.923545760601445)
  expectedDeterminant <- c(1.00917726301635, 0.84086562933513, 0.778971972668575, NA, 0.154733001745783)
  expectedPosDefinite <- expectedIncluded
  
  expect_equal(object=nrow(dsGroupSummary), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsGroupSummary), expected=expectedColumnNames, scale=1)
  expect_equal(object=dsGroupSummary$R, expected=expectedR, scale=1)
  expect_equal(object=dsGroupSummary$Included, expected=expectedIncluded, scale=1)
  expect_equal(object=dsGroupSummary$PairCount, expected=expectedPairCount, scale=1)
  expect_equal(object=dsGroupSummary$O1Mean, expected=expectedO1Mean, scale=1)
  expect_equal(object=dsGroupSummary$O2Mean, expected=expectedO2Mean, scale=1)
  expect_equal(object=dsGroupSummary$O1Variance, expected=expectedO1Variance, scale=1)
  expect_equal(object=dsGroupSummary$O2Variance, expected=expectedO2Variance, scale=1)
  expect_equal(object=dsGroupSummary$O1O2Covariance, expected=expectedO1O2Covariance, scale=1)
  expect_equal(object=dsGroupSummary$Correlation, expected=expectedCorrelation, scale=1)
  expect_equal(object=dsGroupSummary$Determinant, expected=expectedDeterminant, scale=1)
  expect_equal(object=dsGroupSummary$PosDefinite, expected=expectedPosDefinite, scale=1)
})

test_that("Single Group Summary MathStandardized", {
  dsFull <- Links79PairExpanded #Start with the built-in data.frame in NlsyLinks
  oName_S1 <- "MathStandardized_S1" #Stands for Manifest1
  oName_S2 <- "MathStandardized_S2" #Stands for Manifest2
  dsFull$DummyGroup <- 1
  rName <- "DummyGroup"
  
  dsFull <- dsFull[dsFull$RelationshipPath=='Gen2Siblings', ]
  dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2, rName)
  
  expectedRowCount <- 1
  expectedColumnNames <- c('DummyGroup', 'Included', 'PairCount', 'O1Mean', 'O2Mean', 'O1Variance', 'O2Variance', 'O1O2Covariance', 'Correlation', 'Determinant', 'PosDefinite')
  expectedR <- 1
  expectedIncluded <- T
  expectedPairCount <- 8340
  expectedO1Mean <- 98.2445443645084
  expectedO2Mean <- 98.605035971223
  expectedO1Variance <- 160.681736631321
  expectedO2Variance <- 168.910299614967
  expectedO1O2Covariance <- 78.8060054127222
  expectedCorrelation <- 0.478352435603954
  expectedDeterminant <- 20930.4137879396
  expectedPosDefinite <- expectedIncluded
  
  expect_equal(object=nrow(dsGroupSummary), expected=expectedRowCount, scale=1)
  expect_equal(object=colnames(dsGroupSummary), expected=expectedColumnNames, scale=1)
  expect_equal(object=dsGroupSummary[, rName], expected=expectedR, scale=1)
  
  expect_equal(object=dsGroupSummary$Included, expected=expectedIncluded, scale=1)
  expect_equal(object=dsGroupSummary$PairCount, expected=expectedPairCount, scale=1)
  expect_equal(object=dsGroupSummary$O1Mean, expected=expectedO1Mean, scale=1)
  expect_equal(object=dsGroupSummary$O2Mean, expected=expectedO2Mean, scale=1)
  expect_equal(object=dsGroupSummary$O1Variance, expected=expectedO1Variance, scale=1)
  expect_equal(object=dsGroupSummary$O2Variance, expected=expectedO2Variance, scale=1)
  expect_equal(object=dsGroupSummary$O1O2Covariance, expected=expectedO1O2Covariance, scale=1)
  expect_equal(object=dsGroupSummary$Correlation, expected=expectedCorrelation, scale=1)
  expect_equal(object=dsGroupSummary$Determinant, expected=expectedDeterminant, scale=1)
  expect_equal(object=dsGroupSummary$PosDefinite, expected=expectedPosDefinite, scale=1)
})
# # 
# # dsGroupSummary <- RGroupSummary(dsFull, oName_S1, oName_S2)
# # rName <- "R"
# paste0(colnames(dsGroupSummary), collapse="', '")
# # paste0(dsGroupSummary[, rName], collapse=", ")
# paste0(dsGroupSummary$Included, collapse=", ")
# paste0(dsGroupSummary$PairCount, collapse=", ")
# paste0(dsGroupSummary$O1Mean, collapse=", ")
# paste0(dsGroupSummary$O2Mean, collapse=", ")
# paste0(dsGroupSummary$O1Variance, collapse=", ")
# paste0(dsGroupSummary$O2Variance, collapse=", ")
# paste0(dsGroupSummary$O1O2Covariance, collapse=", ")
# paste0(dsGroupSummary$Correlation, collapse=", ")
# paste0(dsGroupSummary$Determinant, collapse=", ")
# paste0(dsGroupSummary$PosDefinite, collapse=", ")