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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" />
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5 <title></title>
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6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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7 </head>
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8 <body>
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9 <div class="toolFormBody">
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10
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11 <div class="infomessage">Galaxy Tool "rglasso" run at 28/12/2014 13:07:57</div><br/>
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12 <div class="toolFormTitle">cox images and outputs</div>
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13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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14 <div><table class="simple" cellpadding="2" cellspacing="2">
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15 <tr>
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16 <td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf"><img src="cox_Coxglmnettest_glmnet_cvdeviance.png" title="Click to download a PDF of cox_Coxglmnettest_glmnet_cvdeviance.pdf" hspace="5" width="400"
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17 alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td>
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18
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19 <td><a href="cox_Coxglmnettest_glmnetdev.pdf"><img src="cox_Coxglmnettest_glmnetdev.png" title="Click to download a PDF of cox_Coxglmnettest_glmnetdev.pdf" hspace="5" width="400"
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20 alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td>
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21 </tr>
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22
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23 </table></div>
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24
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25 <div class="toolFormTitle">cox log output</div>
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26
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27 <pre>
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28
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29 [1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682
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30
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31 [1] Times each predictor was selected in CV models (excluding zero count predictors)
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32
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33 hits_lambda_1se hits_lambda_min
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34
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35 rhubarb 10 10
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36
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37 vegemite 3 10
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38
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39 apple 0 1
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40
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41 [1] @@@ Results preview:
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42
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43 regulator partial_likelihood forced_in glmnet_model best_lambda lambdaChoice alpha
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44
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45 rhubarb rhubarb 0.0012215 TRUE cox 0.04197 lambda.1se 0.95
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46
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47
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48 </pre>
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49
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50 <div class="toolFormTitle">rglasso log output</div>
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51
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52 <pre>
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53
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54 Loading required package: Matrix
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55
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56 Loading required package: methods
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57
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58 Loaded glmnet 1.9-8
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59
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60 Loaded lars 1.2
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61
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62 Loading required package: splines
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63
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64 Warning messages:
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65
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66 1: In if (is.na(predict_at)) { :
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67
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68 the condition has length > 1 and only the first element will be used
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69
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70 2: In if (class(p) == "try-error") { :
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71
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72 the condition has length > 1 and only the first element will be used
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73
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74 3: In plot.window(...) : "label" is not a graphical parameter
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75
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76 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
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77
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78 5: In axis(side = side, at = at, labels = labels, ...) :
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79
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80 "label" is not a graphical parameter
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81
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82 6: In axis(side = side, at = at, labels = labels, ...) :
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83
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84 "label" is not a graphical parameter
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85
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86 7: In box(...) : "label" is not a graphical parameter
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87
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88 8: In title(...) : "label" is not a graphical parameter
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89
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90
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91 </pre>
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92
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93 <div class="toolFormTitle">Other log output</div>
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94
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95 <pre>
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96
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97 ## Toolfactory running rglasso as Rscript script
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98
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99 [1] @@@ Using alpha = 0.95 for all models
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100
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101 [1] @@@@ Input has 500 samples and 3 predictors
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102
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103 [1] @@@ Cox model will predict yvar= status using cols= rhubarb,vegemite,apple n preds= 3 forced in= rhubarb
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104
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105 [1] @@@ SessionInfo for this R session:
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106
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107 R version 3.0.2 (2013-09-25)
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108
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109 Platform: x86_64-pc-linux-gnu (64-bit)
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110
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111 locale:
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112
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113 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
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114
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115 attached base packages:
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116
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117 [1] splines methods stats graphics grDevices utils datasets base
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118
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119 other attached packages:
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120
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121 [1] pec_2.4.4 survival_2.37-7 lars_1.2 glmnet_1.9-8 Matrix_1.1-4
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122
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123 loaded via a namespace (and not attached):
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124
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125 [1] codetools_0.2-9 foreach_1.4.2 grid_3.0.2 iterators_1.0.7 lattice_0.20-29 lava_1.3 prodlim_1.5.1
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126
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127 Warning messages:
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128
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129 1: In if (is.na(predict_at)) { ... :
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130
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131 the condition has length > 1 and only the first element will be used
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132
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133 2: In if (class(p) == "try-error") { ... :
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134
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135 the condition has length > 1 and only the first element will be used
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136
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137 3: In plot.window(...) : "label" is not a graphical parameter
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138
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139 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
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140
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141 5: In axis(side = side, at = at, labels = labels, ...) :
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142
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143 "label" is not a graphical parameter
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144
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145 6: In axis(side = side, at = at, labels = labels, ...) :
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146
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147 "label" is not a graphical parameter
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148
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149 7: In box(...) : "label" is not a graphical parameter
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150
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151 8: In title(...) : "label" is not a graphical parameter
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152
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153
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154 </pre>
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155
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156 <div class="toolFormTitle">All output files available for downloading</div>
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157
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158 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
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159
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160 <tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.3 KB</td></tr>
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161 <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.3 KB</td></tr>
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162 <tr><td><a href="cox_cross_validation_model_counts.xls">cox_cross_validation_model_counts.xls</a></td><td>47 B</td></tr>
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163 <tr class="odd_row"><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>563 B</td></tr>
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164 <tr><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>21.5 KB</td></tr>
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165 <tr class="odd_row"><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>803 B</td></tr>
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166 <tr><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.7 KB</td></tr>
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167 </table></div><br/>
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168 </div></body></html>
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