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comparison test-data/coxlassotest.html @ 0:cf295f36d606 draft

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Initial commit for iuc/test rglasso
author fubar
date Sat, 31 Oct 2015 01:07:28 -0400
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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">
2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" />
5 <title></title>
6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
7 </head>
8 <body>
9 <div class="toolFormBody">
10
11 <div class="infomessage">Galaxy Tool "rglasso" run at 18/02/2015 22:06:08</div><br/>
12 <div class="toolFormTitle">cox images and outputs</div>
13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
14 <div><table class="simple" cellpadding="2" cellspacing="2">
15 <tr>
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"
17 alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td>
18
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"
20 alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td>
21 </tr>
22
23 </table></div>
24
25 <div class="toolFormTitle">cox log output</div>
26
27 <pre>
28
29 [1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682
30
31 [1] Times each predictor was selected in CV models (excluding zero count predictors)
32
33 hits_lambda_1se hits_lambda_min
34
35 rhubarb 10 10
36
37 vegemite 6 6
38
39 [1] @@@ Results preview:
40
41 regulator partial_likelihood forced_in glmnet_model best_lambda lambdaChoice alpha
42
43 rhubarb rhubarb 0.0012215 TRUE cox 0.04197 lambda.1se 0.95
44
45
46 </pre>
47
48 <div class="toolFormTitle">rglasso log output</div>
49
50 <pre>
51
52 Loading required package: Matrix
53
54 Loading required package: methods
55
56 Loaded glmnet 1.9-8
57
58 Loaded lars 1.2
59
60 Loading required package: splines
61
62 Warning messages:
63
64 1: In if (is.na(predict_at)) { :
65
66 the condition has length > 1 and only the first element will be used
67
68 2: In if (class(p) == "try-error") { :
69
70 the condition has length > 1 and only the first element will be used
71
72 3: In plot.window(...) : "label" is not a graphical parameter
73
74 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
75
76 5: In axis(side = side, at = at, labels = labels, ...) :
77
78 "label" is not a graphical parameter
79
80 6: In axis(side = side, at = at, labels = labels, ...) :
81
82 "label" is not a graphical parameter
83
84 7: In box(...) : "label" is not a graphical parameter
85
86 8: In title(...) : "label" is not a graphical parameter
87
88
89 </pre>
90
91 <div class="toolFormTitle">Other log output</div>
92
93 <pre>
94
95 ## Toolfactory running rglasso as Rscript script
96
97 [1] @@@ Using alpha = 0.95 for all models
98
99 [1] @@@@ Input has 500 samples and 3 predictors
100
101 [1] @@@ Cox model will predict yvar= status using cols= rhubarb,vegemite,apple n preds= 3 forced in= rhubarb
102
103 [1] @@@ SessionInfo for this R session:
104
105 R version 3.1.0 (2014-04-10)
106
107 Platform: x86_64-unknown-linux-gnu (64-bit)
108
109 locale:
110
111 [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
112
113 attached base packages:
114
115 [1] splines methods stats graphics grDevices utils datasets base
116
117 other attached packages:
118
119 [1] pec_2.4.4 survival_2.37-7 lars_1.2 glmnet_1.9-8 Matrix_1.1-5
120
121 loaded via a namespace (and not attached):
122
123 [1] codetools_0.2-10 foreach_1.4.2 grid_3.1.0 iterators_1.0.7 lattice_0.20-29 lava_1.3 prodlim_1.5.1
124
125 Warning messages:
126
127 1: In if (is.na(predict_at)) { ... :
128
129 the condition has length > 1 and only the first element will be used
130
131 2: In if (class(p) == "try-error") { ... :
132
133 the condition has length > 1 and only the first element will be used
134
135 3: In plot.window(...) : "label" is not a graphical parameter
136
137 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
138
139 5: In axis(side = side, at = at, labels = labels, ...) :
140
141 "label" is not a graphical parameter
142
143 6: In axis(side = side, at = at, labels = labels, ...) :
144
145 "label" is not a graphical parameter
146
147 7: In box(...) : "label" is not a graphical parameter
148
149 8: In title(...) : "label" is not a graphical parameter
150
151
152 </pre>
153
154 <div class="toolFormTitle">All output files available for downloading</div>
155
156 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
157
158 <tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr>
159 <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.3 KB</td></tr>
160 <tr><td><a href="cox_cross_validation_model_counts.xls">cox_cross_validation_model_counts.xls</a></td><td>42 B</td></tr>
161 <tr class="odd_row"><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>522 B</td></tr>
162 <tr><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>21.5 KB</td></tr>
163 <tr class="odd_row"><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>803 B</td></tr>
164 <tr><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.7 KB</td></tr>
165 </table></div><br/>
166 </div></body></html>
167