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4
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1 <tool id="cddssddspqapsssp2" name="Create script from the template file ">
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2 <description>
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3 used to create script file from user given input to build a model
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4 </description>
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5 <requirements>
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6 <requirement type="set_environment">CARET_TOOL2_PATH</requirement>
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7 <requirement type="set_environment">R_ROOT_DIR</requirement>
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8 <requirement type="package" version="3.2.0">R</requirement>
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9 <requirement type="package" version="1.0.0">caret-tools</requirement>
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10 </requirements>
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11 <command interpreter="python">
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12 #if $OPTION11.PARAMETERS == "Advance"
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13 modelBuilding.py --method $METHOD $RDATA --getdatainfoeval $OPTION11.GETDATAINFOEVAL --getdatainfoecho $OPTION11.GETDATAINFOECHO --getdatainforesult $OPTION11.GETDATAINFORESULT --missingfiltereval $OPTION11.CON1.MISSINGFILTEREVAL --missingfilterecho $OPTION11.CON1.MISSINGFILTERECHO --missingfilterresult $OPTION11.CON1.MISSINGFILTERRESULT --missingfilterthreshc $OPTION11.CON1.MISSINGFILTERTHRESHC --missingfilterthreshr $OPTION11.CON1.MISSINGFILTERTHRESHR --pcaeval $OPTION11.PCAEVAL --pcaecho $OPTION11.PCAECHO --pcaresult $OPTION11.PCARESULT --pcacomp $OPTION11.PCACOMP --pcaploteval $OPTION11.PCAPLOTEVAL --pcaplotecho $OPTION11.PCAPLOTECHO --pcaplotresult $OPTION11.PCAPLOTRESULT --pcaplotfig $OPTION11.PCAPLOTFIG --initialdataspliteval $OPTION11.CON2.INITIALDATASPLITEVAL --initialdatasplitecho $OPTION11.CON2.INITIALDATASPLITECHO --initialdatasplitresult $OPTION11.CON2.INITIALDATASPLITRESULT --saampling $OPTION11.CON2.SAAMPLING --percent $OPTION11.CON2.PERCENT --nzveval $OPTION11.CON3.NZVEVAL --nzvresult $OPTION11.CON3.NZVRESULT --nzvecho $OPTION11.CON3.NZVECHO --corrfiltereval $OPTION11.CON4.CORRFILTEREVAL --corrfilterresult $OPTION11.CON4.CORRFILTERRESULT --corrfilterecho $OPTION11.CON4.CORRFILTERECHO --threshholdcor $OPTION11.CON4.THRESHHOLDCOR --preproceval $OPTION11.CON5.PREPROCEVAL --preprocecho $OPTION11.CON5.PREPROCECHO --preprocresult $OPTION11.CON5.PREPROCRESULT --setupworkersecho $OPTION11.SETUPWORKERSECHO --setupworkersresult $OPTION11.SETUPWORKERSRESULT --numworkers $OPTION11.NUMWORKERS --setupresamplingecho $OPTION11.CON6.SETUPRESAMPLINGECHO --setupresamplingresult $OPTION11.CON6.SETUPRESAMPLINGRESULT --resampname $OPTION11.CON6.RESAMPNAME --resamplenumber $OPTION11.CON6.RESAMPLENUMBER --numrepeat $OPTION11.CON6.NUMREPEAT --resamplenumberpercent $OPTION11.CON6.RESAMPLENUMBERPERCENT --setupgridresult $OPTION11.SETUPGRIDRESULT --setupgridecho $OPTION11.SETUPGRIDECHO --setupgridsize $OPTION11.SETUPGRIDSIZE --fitmodelresult $OPTION11.FITMODELRESULT --fitmodelecho $OPTION11.FITMODELECHO --fitmodeleval $OPTION11.FITMODELEVAL --modeldescrecho $OPTION11.MODELDESCRECHO --modeldescrresult $OPTION11.MODELDESCRRESULT --resamptableecho $OPTION11.RESAMPTABLEECHO --resamptableresult $OPTION11.RESAMPTABLERESULT --profileplotecho $OPTION11.PROFILEPLOTECHO --profileplotfig $OPTION11.PROFILEPLOTFIG --stopworkersecho $OPTION11.STOPWORKERSECHO --stopworkersresult $OPTION11.STOPWORKERSRESULT --testpredresult $OPTION11.TESTPREDRESULT --testpredecho $OPTION11.TESTPREDECHO --classprobstexresult $OPTION11.CLASSPROBSTEXRESULT --classprobstexecho $OPTION11.CLASSPROBSTEXECHO --classprobstexresult1 $OPTION11.CLASSPROBSTEXRESULT1 --classprobstexecho1 $OPTION11.CLASSPROBSTEXECHO1 --savedataecho $OPTION11.SAVEDATAECHO --savedataresult $OPTION11.SAVEDATARESULT --datasets $datasets --outputmodel $model --outputresultpdf $document;
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14 #end if
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15 #if $OPTION11.PARAMETERS == "basic"
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16 modelBuilding.py --method $METHOD $RDATA --getdatainfoeval $OPTION11.GETDATAINFOEVAL --getdatainfoecho $OPTION11.GETDATAINFOECHO --getdatainforesult $OPTION11.GETDATAINFORESULT --missingfiltereval $OPTION11.MISSINGFILTEREVAL --missingfilterecho $OPTION11.MISSINGFILTERECHO --missingfilterresult $OPTION11.MISSINGFILTERRESULT --missingfilterthreshc $OPTION11.MISSINGFILTERTHRESHC --missingfilterthreshr $OPTION11.MISSINGFILTERTHRESHR --pcaeval $OPTION11.PCAEVAL --pcaecho $OPTION11.PCAECHO --pcaresult $OPTION11.PCARESULT --pcacomp $OPTION11.PCACOMP --pcaploteval $OPTION11.PCAPLOTEVAL --pcaplotecho $OPTION11.PCAPLOTECHO --pcaplotresult $OPTION11.PCAPLOTRESULT --pcaplotfig $OPTION11.PCAPLOTFIG --initialdataspliteval $OPTION11.INITIALDATASPLITEVAL --initialdatasplitecho $OPTION11.INITIALDATASPLITECHO --initialdatasplitresult $OPTION11.INITIALDATASPLITRESULT --saampling $OPTION11.SAAMPLING --percent $OPTION11.PERCENT --nzveval $OPTION11.NZVEVAL --nzvresult $OPTION11.NZVRESULT --nzvecho $OPTION11.NZVECHO --corrfiltereval $OPTION11.CORRFILTEREVAL --corrfilterresult $OPTION11.CORRFILTERRESULT --corrfilterecho $OPTION11.CORRFILTERECHO --threshholdcor $OPTION11.THRESHHOLDCOR --preproceval $OPTION11.PREPROCEVAL --preprocecho $OPTION11.PREPROCECHO --preprocresult $OPTION11.PREPROCRESULT --setupworkersecho $OPTION11.SETUPWORKERSECHO --setupworkersresult $OPTION11.SETUPWORKERSRESULT --numworkers $OPTION11.NUMWORKERS --setupresamplingecho $OPTION11.SETUPRESAMPLINGECHO --setupresamplingresult $OPTION11.SETUPRESAMPLINGRESULT --resampname $OPTION11.RESAMPNAME --resamplenumber $OPTION11.RESAMPLENUMBER --numrepeat $OPTION11.NUMREPEAT --resamplenumberpercent $OPTION11.RESAMPLENUMBERPERCENT --setupgridresult $OPTION11.SETUPGRIDRESULT --setupgridecho $OPTION11.SETUPGRIDECHO --setupgridsize $OPTION11.SETUPGRIDSIZE --fitmodelresult $OPTION11.FITMODELRESULT --fitmodelecho $OPTION11.FITMODELECHO --fitmodeleval $OPTION11.FITMODELEVAL --modeldescrecho $OPTION11.MODELDESCRECHO --modeldescrresult $OPTION11.MODELDESCRRESULT --resamptableecho $OPTION11.RESAMPTABLEECHO --resamptableresult $OPTION11.RESAMPTABLERESULT --profileplotecho $OPTION11.PROFILEPLOTECHO --profileplotfig $OPTION11.PROFILEPLOTFIG --stopworkersecho $OPTION11.STOPWORKERSECHO --stopworkersresult $OPTION11.STOPWORKERSRESULT --testpredresult $OPTION11.TESTPREDRESULT --testpredecho $OPTION11.TESTPREDECHO --classprobstexresult $OPTION11.CLASSPROBSTEXRESULT --classprobstexecho $OPTION11.CLASSPROBSTEXECHO --classprobstexresult1 $OPTION11.CLASSPROBSTEXRESULT1 --classprobstexecho1 $OPTION11.CLASSPROBSTEXECHO1 --savedataecho $OPTION11.SAVEDATAECHO --savedataresult $OPTION11.SAVEDATARESULT --datasets $datasets --outputmodel $model --outputresultpdf $document;
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17 #end if
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18
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19 </command>
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20 <inputs>
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21 <param name="METHOD" type="select" label="SELECT METHOD FOR MODEL BUILDING" >
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22 <option value="pls">Partial Least Square</option>
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23 <option value="nnet">Neural Network</option>
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24 <option value="bagFDA">bag-Fourier Discriminant Analysis</option>
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25 <option value="blackboost">black-boost- Boosting Method</option>
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26 <option value="earth">Earth-MARS based method</option>
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27 <option value="rf">Random Forest</option>
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28 <option value="RRF">RRFglobal -Variant of Random Forest</option>
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29 <option value="svmRadial">SVM-Radial</option>
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30 <option value="svmPoly">SVM-Polynomial</option>
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31 <option value="ada">ada-boost</option>
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32 <option value="glm">Generalised linear model </option>
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33 <option value="treebag">tree based bagging method</option>
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34 <option value="nb">Naive Bayes</option>
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35 <option value="knn">K-nearest neighbour</option>
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36 <option value="C5.0">C5.0 </option>
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37 </param>
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38 <param name="RDATA" type="data" label="SELECT FILE CONATINING INPUT DATA" help="RData format" />
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39
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40
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41 <conditional name="OPTION11">
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42 <param name="PARAMETERS" type="select">
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43 <option value="basic" selected="TRUE" >Use optimized parameters </option>
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44 <option value="Advance"> Customized parameters </option>
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45 </param>
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46
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47 <when value="basic">
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48
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49 <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" />
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50
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51 <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
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52 <param name="GETDATAINFORESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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53
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54 <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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55
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56 <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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57
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58 <param name="MISSINGFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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59
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60 <param name="MISSINGFILTERTHRESHC" type="hidden" value="0.2" help="For column wise default is 0.2"/>
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61
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62 <param name="MISSINGFILTERTHRESHR" type="hidden" value="0.2" help="For row wise default is 0.2"/>
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63
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64 <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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65
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66 <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
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67
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68 <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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69
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70 <param name="PCACOMP" type="hidden" value="3" help="set according to need. Default is 3"/>
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71
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72 <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/>
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73
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74 <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/>
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75
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76 <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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77
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78 <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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79
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80 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
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81
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82 <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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83
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84 <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/>
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85
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86 <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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87
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88 <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/>
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89
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90 <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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91
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92 <param name="NZVRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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93
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94 <param name="NZVECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/>
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95
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96 <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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97
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98 <param name="CORRFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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99
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100 <param name="CORRFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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101
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102 <param name="THRESHHOLDCOR" type="hidden" value="0.75" help="set according to need .default is 0.75"/>
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103
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104 <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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105
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106 <param name="PREPROCECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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107
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108 <param name="PREPROCRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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109
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110 <param name="SETUPWORKERSEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. default is False"/>
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111
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112 <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/>
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113
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114 <param name="SETUPWORKERSRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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115
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116 <param name="NUMWORKERS" type="hidden" value="1" help ="default is 1"/>
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117
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118 <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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119
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120 <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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121
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122 <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/>
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123
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124 <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/>
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125
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126 <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/>
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127
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128 <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/>
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129
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130 <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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131
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132 <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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133
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134 <param name="SETUPGRIDSIZE" type="hidden" value="3" help="default is 3 "/>
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135
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136 <param name="FITMODELEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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137
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138 <param name="FITMODELRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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139
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140 <param name="FITMODELECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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141
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142 <param name="MODELDESCRECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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143
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144 <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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145
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146 <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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147
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148 <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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149
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150 <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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151
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152 <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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153
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154 <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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155
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156 <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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157
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158 <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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159
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160 <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
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161
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162 <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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163
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164 <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
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165
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166 <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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167
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168 <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
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169
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170 <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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171
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172 <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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173
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174 </when>
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175
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176
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177 <when value="Advance">
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178 <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" />
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179 <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
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180 <param name="GETDATAINFORESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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181
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182 <conditional name="CON1">
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183 <param name="PARAMAETERS1" type="select" label="1. REMOVE MISSING VALUES FROM THE INPUT DATA">
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184 <option value="YES">YES </option>
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185 <option value="NO" selected="true">NO </option>
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186 </param>
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187
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188 <when value="YES">
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189 <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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190 <param name="MISSINGFILTERECHO" type="select" label="1(i). Write Code in Document" help="set True if wish to print .default is False" >
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191 <option value="FALSE" selected="true">false</option>
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192 <option value="TRUE">true</option>
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193 </param>
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194 <param name="MISSINGFILTERRESULT" type="select" label="1(ii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
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195 <option value="hide">hide-result will not written in file</option>
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196 <option value="tex" selected="true">tex-result will written in file</option>
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197 </param>
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198 <param name="MISSINGFILTERTHRESHC" type="select" label="1(iii). Set Cutoff Value for Missing Data value Columwise" help="For column wise default is 0.1 means column which has missing value more than 10% will be removed ">
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199 <option value="0.1">0.1</option>
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200 <option value="0.2">0.2</option>
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201 <option value="0.25">0.25</option>
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202 <option value="0.3">0.3</option>
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203 <option value="0.35">0.35</option>
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204 <option value="0.4">0.4</option>
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205 <option value="0.45">0.45</option>
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206 <option value="0.5">0.5</option>
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207 <option value="0.55">0.55</option>
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208 <option value="0.6">0.6</option>
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209 <option value="0.65">0.65</option>
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210 <option value="0.7">0.7</option>
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211 <option value="0.75">0.75</option>
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212 <option value="0.8">0.8</option>
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213 </param>
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214 <param name="MISSINGFILTERTHRESHR" type="select" label="1(iv). Set Cutoff Value for Missing Data Value Rowwise " help="For row wise default is 0.1 means row having more than 10% missing values will be removed">
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215 <option value="0.1">0.1</option>
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216 <option value="0.2">0.2</option>
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217 <option value="0.25">0.25</option>
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218 <option value="0.3">0.3</option>
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219 <option value="0.35">0.35</option>
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220 <option value="0.4">0.4</option>
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221 <option value="0.45">0.45</option>
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222 <option value="0.5">0.5</option>
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223 <option value="0.55">0.55</option>
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224 <option value="0.6">0.6</option>
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225 <option value="0.65">0.65</option>
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226 <option value="0.7">0.7</option>
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227 <option value="0.75">0.75</option>
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228 <option value="0.8">0.8</option>
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229 </param>
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230 </when>
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231 <when value="NO">
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232 <param name="MISSINGFILTEREVAL" type="hidden" value= "FALSE" help="set TRUE if wish to evaluate. default is FALSE"/>
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233
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234 <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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235
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236 <param name="MISSINGFILTERRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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237
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238 <param name="MISSINGFILTERTHRESHC" type="hidden" value="0" />
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239
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240 <param name="MISSINGFILTERTHRESHR" type="hidden" value="0" />
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241
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242 </when>
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243 </conditional>
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244
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245 <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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246
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247 <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
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248
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249 <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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250
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251 <param name="PCACOMP" type="select" label="2. FIND NUMBER OF PRINCIPLE COMPONENT" help="performs PCA and gives number of PC. Default is 3 ">
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252 <option value="3">3</option>
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253 <option value="4">4</option>
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254 <option value="5">5</option>
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255 <option value="6">6</option>
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256 <option value="7">7</option>
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257 <option value="8">8</option>
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258 <option value="9">9</option>
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259 <option value="10">10</option>
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260 </param>
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261
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262 <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/>
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263
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264 <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/>
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265
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266 <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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267
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268 <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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269
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270
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271 <conditional name="CON2">
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272 <param name="PARAMAETERS2" type="select" label="3. CUSTOMIZE PARAMETERS FOR DATA SPLITTING " help="splits data in test and train set.">
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273 <option value="YES2">YES </option>
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274 <option value="NO2" selected="true">NO </option>
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275 </param>
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276 <when value="YES2">
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277 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
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278 <param name="SAAMPLING" type="select" label="3(i). Select Sampling Method" help="Defualt is with No sampling. you may choose downsample or upsample" >
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279 <option value="garBage" selected="true">No Sampling</option>
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280 <option value="downsampling">downsample</option>
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281 <option value="upsampling">upsample</option>
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282 </param>
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283 <param name="INITIALDATASPLITECHO" type="select" label="3(ii). Write Code in Document" help="set True if wish to print .default is False" >
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284 <option value="FALSE">false</option>
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285 <option value="TRUE">true</option>
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286 </param>
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287 <param name="INITIALDATASPLITRESULT" type="select" value="tex" label="3(iii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
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288 <option value="tex" selected="true">tex-result will written in file</option>
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289 <option value="hide">hide-result will not written in file</option>
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290 </param>
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291 <param name="PERCENT" type="select" label="3(iv) .Set Value at Which Data Will be Splitted in Train and Test Set" help="default is 0.8">
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292 <option value="0.8">0.8</option>
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293 <option value="0.75">0.75</option>
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294 <option value="0.6">0.6</option>
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295 <option value="0.5">0.5</option>
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296 <option value="2">use entire data set</option>
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297 </param>
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298 </when>
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299 <when value="NO2">
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300 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
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301
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302 <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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303
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304 <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/>
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305
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306 <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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307
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308 <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/>
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309
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310 </when>
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311 </conditional>
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312
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313 <conditional name="CON3">
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314 <param name="PARAMAETERS3" type="select" label="4. REMOVE NEAR ZERO VARIANCE " help="removes NZV from train and test set.">
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315 <option value="YES3">YES </option>
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316 <option value="NO3" selected="true">NO </option>
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317 </param>
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318 <when value="YES3">
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319
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320 <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
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321
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322
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323 <param name="NZVECHO" type="select" label="4(i). Write Code in Document" help="set True if wish to print .default is False">
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324 <option value="FALSE">false</option>
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325 <option value="TRUE">true</option>
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|
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326 </param>
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327
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328 <param name="NZVRESULT" type="select" label="4(ii). Write Result in document" help="Set tex if wish to write result in output pdf file. default is tex">
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329 <option value="hide">hide-result will not written in file</option>
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330 <option value="tex" selected="true">tex-result will written in file</option>
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331 </param>
|
|
|
332 </when>
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333 <when value="NO3">
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334 <param name="NZVEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/>
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|
|
335 <param name="NZVECHO" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/>
|
|
|
336 <param name="NZVRESULT" type="hidden" value="hide" help="set TRUE if wish to evaluate."/>
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|
|
337 </when>
|
|
|
338 </conditional>
|
|
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339
|
|
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340 <!--param name="NZVECHO" type="select" label="Write Code in Document" help="set True if wish to print .default is False">
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|
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341 <option value="FALSE">false</option>
|
|
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342 <option value="TRUE">true</option>
|
|
|
343 </param-->
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344
|
|
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345 <conditional name="CON4">
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|
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346 <param name="PARAMAETERS4" type="select" label="5. REMOVE CORRELATED VALUES" help="removes correlated attributes from train and test set.">
|
|
|
347 <option value="YES4">YES </option>
|
|
|
348 <option value="NO4" selected="true">NO </option>
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|
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349 </param>
|
|
|
350 <when value="YES4">
|
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351 <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
|
|
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352 <param name="THRESHHOLDCOR" type="select" label="5(i). cutoff for correlated Value " help="set according to need .default is 0.75 means attributes have 75% or more correlation are ommited from the data">
|
|
|
353 <option value="0.75">0.75</option>
|
|
|
354 <option value="0.4">0.4</option>
|
|
|
355 <option value="0.45">0.45</option>
|
|
|
356 <option value="0.5">0.5</option>
|
|
|
357 <option value="0.55">0.55</option>
|
|
|
358 <option value="0.6">0.6</option>
|
|
|
359 <option value="0.65">0.65</option>
|
|
|
360 <option value="0.7">0.7</option>
|
|
|
361 <option value="0.8">0.8</option>
|
|
|
362 <option value="0.85">0.85</option>
|
|
|
363 <option value="0.9">0.9</option>
|
|
|
364 <option value="0.95">0.95</option>
|
|
|
365 </param>
|
|
|
366 <param name="CORRFILTERECHO" type="select" label="5(ii). Write Code in Document" help="set True if wish to print .default is False" >
|
|
|
367 <option value="FALSE">false</option>
|
|
|
368 <option value="TRUE">true</option>
|
|
|
369 </param>
|
|
|
370 <param name="CORRFILTERRESULT" type="select" label="5(iii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
|
|
|
371 <option value="hide">hide-result will not written in file</option>
|
|
|
372 <option value="tex" selected="true">tex-result will written in file</option>
|
|
|
373 </param>
|
|
|
374 </when>
|
|
|
375 <when value="NO4">
|
|
|
376 <param name="CORRFILTEREVAL" type="hidden" value="FALSE"/>
|
|
|
377
|
|
|
378 <param name="CORRFILTERRESULT" type="hidden" value="hide" />
|
|
|
379
|
|
|
380 <param name="CORRFILTERECHO" type="hidden" value="FALSE" />
|
|
|
381
|
|
|
382 <param name="THRESHHOLDCOR" type="hidden" value="0" />
|
|
|
383 </when>
|
|
|
384 </conditional>
|
|
|
385
|
|
|
386 <conditional name="CON5">
|
|
|
387 <param name="PARAMAETERS5" type="select" label="6. PERFORM CENTERING AND SCALING OF DATA " help="centering and scaling of train and test set.">
|
|
|
388 <option value="YES5">YES </option>
|
|
|
389 <option value="NO5" selected="true">NO </option>
|
|
|
390 </param>
|
|
|
391
|
|
|
392 <when value="YES5">
|
|
|
393 <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
|
|
|
394 <param name="PREPROCECHO" type="select" label="6(i). Write Code in Document" help="set True if wish to write code in document .default is False" >
|
|
|
395 <option value="FALSE">false</option>
|
|
|
396 <option value="TRUE">true</option>
|
|
|
397 </param>
|
|
|
398 <param name="PREPROCRESULT" type="select" label="6(ii). Write Result in document " help="Set tex if wish to write result in output pdf file. default is tex">
|
|
|
399 <option value="hide">hide-result will not written in file</option>
|
|
|
400 <option value="tex" selected="true">tex-result will written in file</option>
|
|
|
401 </param>
|
|
|
402 </when>
|
|
|
403 <when value="NO5">
|
|
|
404 <param name="PREPROCEVAL" type="hidden" value="FALSE"/>
|
|
|
405
|
|
|
406 <param name="PREPROCECHO" type="hidden" value="FALSE" />
|
|
|
407
|
|
|
408 <param name="PREPROCRESULT" type="hidden" value="hide" />
|
|
|
409
|
|
|
410 </when>
|
|
|
411 </conditional>
|
|
|
412
|
|
|
413 <param name="SETUPWORKERSEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is False"/>
|
|
|
414 <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
|
|
|
415 <param name="NUMWORKERS" type="select" label="7. SET NUMBER OF PROCESSORS " help ="default is 1">
|
|
|
416 <option value="1">1</option>
|
|
|
417 <option value="2">2</option>
|
|
|
418 <option value="4">4</option>
|
|
|
419 <option value="6">6</option>
|
|
|
420 <option value="8">8</option>
|
|
|
421 <option value="16">16</option>
|
|
|
422 </param>
|
|
|
423 <param name="SETUPWORKERSRESULT" type="hidden" value="hide" />
|
|
|
424
|
|
|
425 <conditional name="CON6">
|
|
|
426
|
|
|
427 <param name="PARAMAETERS6" type="select" label="8. CUSTOMIZE RESAMPLING PARAMETERS" help="resampling for cross validation">
|
|
|
428 <option value="YES6">YES </option>
|
|
|
429 <option value="NO6" selected="true">NO </option>
|
|
|
430 </param>
|
|
|
431 <when value="YES6">
|
|
|
432 <param name="SETUPRESAMPLINGECHO" type="select" label="8(i). write code for resampling" help="set True if wish to print .default is False">
|
|
|
433 <option value="FALSE">false</option>
|
|
|
434 <option value="TRUE">true</option>
|
|
|
435 </param>
|
|
|
436 <param name="SETUPRESAMPLINGRESULT" type="select" label="8(ii). Write Result in document " help="Set tex if wish to write in output pdf file. default is hide">
|
|
|
437 <option value="hide">hide-result will not written in file</option>
|
|
|
438 <option value="tex">tex-result will written in file</option>
|
|
|
439 </param>
|
|
|
440
|
|
|
441
|
|
|
442 <param name="RESAMPNAME" type="select" label="8(iii). select Resample method for cross validation" help="default is boot632 ">
|
|
|
443 <option value="boot632" selected="true">boot632</option>
|
|
|
444 <option value="boot">boot</option>
|
|
|
445 <option value="cv">cv</option>
|
|
|
446 <option value="repeatedcv">repeatedcv</option>
|
|
|
447 <option value="LOOCV">LOOCV - leave one out</option>
|
|
|
448 </param>
|
|
|
449
|
|
|
450 <param name="RESAMPLENUMBER" type="select" label="8(iv). Set Number of times Resample" help="default is 10 ">
|
|
|
451 <option value="10" selected="true">10</option>
|
|
|
452 <option value="5">5</option>
|
|
|
453 <option value="15">15</option>
|
|
|
454 <option value="20">20</option>
|
|
|
455 <option value="25">25</option>
|
|
|
456 </param>
|
|
|
457
|
|
|
458 <param name="NUMREPEAT" type="select" label="8(v). Set Number of times to repeat" help="default is 3 ">
|
|
|
459 <option value="3" selected="true">3</option>
|
|
|
460 <option value="1">1</option>
|
|
|
461 <option value="5">5</option>
|
|
|
462 <option value="10">10</option>
|
|
|
463 </param>
|
|
|
464 <param name="RESAMPLENUMBERPERCENT" type="select" label="8(vi). Set Percent splitting of data for resampling" help="default is 0.75">
|
|
|
465 <option value="0.75" selected="true">0.75</option>
|
|
|
466 <option value="0.4">0.4</option>
|
|
|
467 <option value="0.45">0.45</option>
|
|
|
468 <option value="0.5">0.5</option>
|
|
|
469 <option value="0.55">0.55</option>
|
|
|
470 <option value="0.6">0.6</option>
|
|
|
471 <option value="0.65">0.65</option>
|
|
|
472 <option value="0.7">0.7</option>
|
|
|
473 <option value="0.8">0.8</option>
|
|
|
474 </param>
|
|
|
475 </when>
|
|
|
476 <when value="NO6">
|
|
|
477
|
|
|
478 <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
|
|
|
479
|
|
|
480 <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
|
|
|
481
|
|
|
482 <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/>
|
|
|
483
|
|
|
484 <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/>
|
|
|
485
|
|
|
486 <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/>
|
|
|
487
|
|
|
488 <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/>
|
|
|
489
|
|
|
490
|
|
|
491 </when>
|
|
|
492 </conditional>
|
|
|
493 <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
|
|
|
494
|
|
|
495 <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
|
|
|
496
|
|
|
497 <param name="SETUPGRIDSIZE" type="select" label="9. SET SIZE OF GRID" help="default is 3 ">
|
|
|
498 <option value="3">3</option>
|
|
|
499 <option value="4">4</option>
|
|
|
500 <option value="5">5</option>
|
|
|
501 <option value="6">6</option>
|
|
|
502 <option value="7">7</option>
|
|
|
503 <option value="8">8</option>
|
|
|
504 <option value="9">9</option>
|
|
|
505 <option value="10">10</option>
|
|
|
506 <option value="11">11</option>
|
|
|
507 <option value="12">12</option>
|
|
|
508 <option value="13">13</option>
|
|
|
509 <option value="14">14</option>
|
|
|
510 <option value="15">15</option>
|
|
|
511 <option value="16">16</option>
|
|
|
512 <option value="17">17</option>
|
|
|
513 <option value="18">18</option>
|
|
|
514 <option value="19">19</option>
|
|
|
515 <option value="20">20</option>
|
|
|
516 </param>
|
|
|
517
|
|
|
518 <param name="FITMODELEVAL" type="boolean" checked="true" value="true" label="10. BUILD A MODEL AND WRITE RESULT IN DOCUMENT" help="default is TRUE"/>
|
|
|
519 <param name="FITMODELRESULT" type="hidden" value="tex" />
|
|
|
520 <param name="FITMODELECHO" type="select" label="10(i). Write Code for model building in Document" help="set True if wish to write code in document .default is False" >
|
|
|
521 <option value="FALSE">false</option>
|
|
|
522 <option value="TRUE">true</option>
|
|
|
523 </param>
|
|
|
524 <param name="MODELDESCRECHO" type="select" label="10(ii). Write code for Model Description " help="set True if wish to print .default is False" >
|
|
|
525 <option value="FALSE">false</option>
|
|
|
526 <option value="TRUE">true</option>
|
|
|
527 </param>
|
|
|
528 <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
|
|
|
529
|
|
|
530 <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
|
|
|
531
|
|
|
532 <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
|
|
|
533
|
|
|
534 <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
|
|
|
535
|
|
|
536 <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
|
|
|
537
|
|
|
538 <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
|
|
|
539
|
|
|
540 <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/>
|
|
|
541
|
|
|
542 <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/>
|
|
|
543
|
|
|
544 <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
|
|
|
545
|
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|
546 <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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547
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548 <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
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549
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550 <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
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551
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552 <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
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553
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554 <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
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555
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556 <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
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557
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558 </when>
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559 </conditional>
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560 </inputs>
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561
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562 <outputs>
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563 <data format="RData" label="$METHOD Model" name="model" />
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564 <data format="pdf" label="Document for $METHOD" name="document" />
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565 <data format="RData" label="Datasets used for model building " name="datasets" />
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566 </outputs>
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567 <help>
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568
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569 .. class:: infomark
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570
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571
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572
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573 **Instruction**
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574
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575 ----------
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576
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577 Users may change any parameter as their requirement. For normal practice
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578
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579 user required to provide only input csv file and method for model building.
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580
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581 More details are given in user manual.Please click here
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582
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583
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584
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585
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586 </help>
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587
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588
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589
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590 </tool>
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