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1 c_strDir <- file.path(getwd( ),"..")
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2
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3 source(file.path(c_strDir,"lib","Constants.R"))
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4 source(file.path(c_strDir,"lib","Utility.R"))
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5
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6 context("Test funcRename")
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7 test_that("Test that unclassified and none otus are represented as 2 terminal clades and others are 1",{
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8 expect_equal(funcRename(paste("A","B","C","D",c_strUnclassified, sep=c_cFeatureDelim)),paste("D",c_strUnclassified, sep=c_cFeatureDelim))
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9 expect_equal(funcRename(paste("A","B","C","D","101", sep=c_cFeatureDelim)),paste("D","101", sep=c_cFeatureDelim))
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10 expect_equal(funcRename(paste("A","B","C","D", sep=c_cFeatureDelim)),paste("D", sep=c_cFeatureDelim))
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11 expect_equal(funcRename(paste("A", sep=c_cFeatureDelim)),paste("A", sep=c_cFeatureDelim))
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12 expect_equal(funcRename(paste(c_strUnclassified, sep=c_cFeatureDelim)),paste(c_strUnclassified, sep=c_cFeatureDelim))
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13 expect_equal(funcRename(paste("101", sep=c_cFeatureDelim)),paste("101", sep=c_cFeatureDelim))
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14 })
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15
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16 context("Test funcColorHelper")
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17 test_that("Test that min is min and max is max and average is average even if given as NA",{
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18 expect_equal(funcColorHelper( dMax = 1, dMin = 1, dMed = NA ), list( dMin = 1, dMax = 1, dMed = 1))
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19 expect_equal(funcColorHelper( dMax = -3, dMin = 10, dMed = NA ), list( dMin = -3, dMax = 10, dMed = 3.5))
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20 expect_equal(funcColorHelper( dMax = 1, dMin = 11, dMed = NA ), list( dMin = 1, dMax = 11, dMed = 6))
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21 expect_equal(funcColorHelper( dMax = 4, dMin = 10, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
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22 expect_equal(funcColorHelper( dMax = 10, dMin = 4, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
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23 })
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24
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25 context("Test funcTrim")
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26 test_that("Test that white spaces at the beginning and end of s string are removed",{
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27 expect_equal(funcTrim("TRIM"),"TRIM")
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28 expect_equal(funcTrim(" TRIM"),"TRIM")
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29 expect_equal(funcTrim(" TRIM"),"TRIM")
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30 expect_equal(funcTrim(" TRIM "),"TRIM")
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31 expect_equal(funcTrim("TRIM "),"TRIM")
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32 expect_equal(funcTrim(" TRIM "),"TRIM")
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33 expect_equal(funcTrim("TR IM"),"TR IM")
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34 expect_equal(funcTrim(" TR IM"),"TR IM")
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35 expect_equal(funcTrim(" TR I M"),"TR I M")
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36 expect_equal(funcTrim(" TR IM "),"TR IM")
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37 expect_equal(funcTrim("T R IM "),"T R IM")
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38 expect_equal(funcTrim(" T RIM "),"T RIM")
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39 })
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40
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41 #TODO currently the capture versio of this does not produce a tabbed table (or default table delim) which is not consistent with the rest of the code base.
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42 context("Test funcWrite")
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43 #Answer files
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44 c_sAnswerWriteFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTemp1.txt")
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45 c_sAnswerWriteFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTemp2.txt")
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46 print("c_sAnswerWriteFile2")
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47 print(c_sAnswerWriteFile2)
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48 c_sAnswerWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTempDF1.txt")
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49 c_sAnswerWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTempDF2.txt")
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50
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51 #Working files
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52 c_sTempWriteFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTemp1.txt")
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53 c_sTempWriteFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTemp2.txt")
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54 c_sTempWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTempDF1.txt")
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55 c_sTempWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTempDF2.txt")
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56 dfTest = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
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57 sWriteString = "Testing, 1,2,3 anything but that."
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58 unlink(c_sTempWriteFile1)
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59 unlink(c_sTempWriteFile2)
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60 unlink(c_sTempWriteDFFile1)
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61 unlink(c_sTempWriteDFFile2)
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62 funcWrite(sWriteString,c_sTempWriteFile1)
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63 funcWrite(sWriteString,c_sTempWriteFile2)
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64 funcWrite(sWriteString,c_sTempWriteFile2)
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65 funcWrite(dfTest,c_sTempWriteDFFile1)
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66 funcWrite(dfTest,c_sTempWriteDFFile2)
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67 funcWrite(dfTest,c_sTempWriteDFFile2)
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68
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69 test_that("Test that a test file is written and appended to for strings and dataframes.",{
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70 expect_equal(readLines(c_sTempWriteFile1),readLines(c_sAnswerWriteFile1))
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71 expect_equal(readLines(c_sTempWriteFile2),readLines(c_sAnswerWriteFile2))
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72 expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
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73 expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
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74 })
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75
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76 context("Test funcWriteTable")
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77 #Answer files
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78 c_sAnswerWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTableTempDF1.txt")
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79 c_sAnswerWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTableTempDF2.txt")
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80
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81 #Working files
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82 c_sTempWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTableTempDF1.txt")
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83 c_sTempWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTableTempDF2.txt")
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84 unlink(c_sTempWriteDFFile1)
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85 unlink(c_sTempWriteDFFile2)
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86 funcWriteTable(dfTest,c_sTempWriteDFFile1)
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87 funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)
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88 funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)
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89
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90 test_that("Test that a test file is written and appended to for dataframes.",{
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91 expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
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92 expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
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93 })
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94
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95 context("Test funcCoef2Col")
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96 dfTestWithFactors = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
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97 colnames(dfTestWithFactors)=c("A","B","C")
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98 dfTestWithFactors["B"]=as.factor(as.character(dfTestWithFactors[["B"]]))
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99 test_that("Test that a coefficients are found or not given if they exist",{
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100 expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c()),"C")
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101 expect_equal(funcCoef2Col(strCoef="A",frmeData=dfTestWithFactors,astrCols=c()),"A")
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102 expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
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103 expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
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104 expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
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105 expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c("A","B","C")),"C")
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106 expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("A","B")),"B")
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107 expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B","C")),"B")
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108 expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B")),"B")
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109 })
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110
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111 context("Test funcMFAValue2Col")
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112 dfTestWithFactors = data.frame(A=c(1,3,3,4,5,6,7,8),B=c(1.0,2.0, 5.8,4.6,4.7,8.9,9.0,2.0),C=c("one","two","one","two","one","two","one","two"),D=c("1","2","1","2","1","2","1","2"))
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113 dfTestWithFactors["three"]=as.factor(dfTestWithFactors[["three"]])
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114 test_that("Test that a column names is found or not given if they exist",{
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115 expect_equal(funcMFAValue2Col(xValue=5.8,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"B")
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116 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"A")
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117 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
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118 expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
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119 expect_equal(funcMFAValue2Col(xValue=paste("D","1",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
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120 expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
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121 expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,3)),NULL)
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122 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2,3)),NULL)
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123 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
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124 expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
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125 expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2)),"B")
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126 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1)),"A")
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127 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(3)),"C")
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128 expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(4)),"D")
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129 })
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130
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131 context("Test funcFormulaStrToList")
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132 test_that("List of covariates are given, from lm or mixed model formulas",{
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133 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate`"),c("1Covariate"))
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134 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate`"),c("1Covariate","2Covariate"))
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135 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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136 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate`"),c("1Covariate"))
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137 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate`"),c("1Covariate","2Covariate"))
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138 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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139 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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140 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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141 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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142 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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143 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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144 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
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145 })
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146
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147 context("Test funcFormulaListToString")
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148 test_that("The correct string formula for a lm or mixed model is created from a list of covariates",{
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149 expect_equal(funcFormulaListToString(NULL),c(NA,NA))
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150 expect_equal(funcFormulaListToString(c("1Covariate")),c("adCur ~ `1Covariate`",NA))
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151 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate")),c("adCur ~ `1Covariate` + `2Covariate`",NA))
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152 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate","3Covariate")),c("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`",NA))
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153 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate"),c("3Covariate")),c(NA,"adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"))
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154 expect_equal(funcFormulaListToString(c("1Covariate","3Covariate"),c("2Covariate")),c(NA,"adCur ~ `1Covariate` + `3Covariate` + 1|`2Covariate`"))
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155 expect_equal(funcFormulaListToString(c("2Covariate","3Covariate"),c("1Covariate")),c(NA,"adCur ~ `2Covariate` + `3Covariate` + 1|`1Covariate`"))
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156 expect_equal(funcFormulaListToString(c("2Covariate"),c("1Covariate","3Covariate")),c(NA,"adCur ~ `2Covariate` + 1|`1Covariate` + 1|`3Covariate`"))
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157 expect_equal(funcFormulaListToString(c("1Covariate"),c("2Covariate","3Covariate")),c(NA,"adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"))
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158 expect_equal(funcFormulaListToString(c("3Covariate"),c("1Covariate","2Covariate")),c(NA,"adCur ~ `3Covariate` + 1|`1Covariate` + 1|`2Covariate`"))
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159 }) |
