Mercurial > repos > fubar > rglasso_1_9_8
view test-data/coxlassotest.html @ 17:0e87f636bdd8 draft
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| author | iuc |
|---|---|
| date | Tue, 28 Apr 2015 22:56:48 -0400 (2015-04-29) |
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> <title></title> <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> </head> <body> <div class="toolFormBody"> <div class="infomessage">Galaxy Tool "rglasso" run at 18/02/2015 22:06:08</div><br/> <div class="toolFormTitle">cox images and outputs</div> (Click on a thumbnail image to download the corresponding original PDF image)<br/> <div><table class="simple" cellpadding="2" cellspacing="2"> <tr> <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" alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td> <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" alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td> </tr> </table></div> <div class="toolFormTitle">cox log output</div> <pre> [1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682 [1] Times each predictor was selected in CV models (excluding zero count predictors) hits_lambda_1se hits_lambda_min rhubarb 10 10 vegemite 6 6 [1] @@@ Results preview: regulator partial_likelihood forced_in glmnet_model best_lambda lambdaChoice alpha rhubarb rhubarb 0.0012215 TRUE cox 0.04197 lambda.1se 0.95 </pre> <div class="toolFormTitle">rglasso log output</div> <pre> Loading required package: Matrix Loading required package: methods Loaded glmnet 1.9-8 Loaded lars 1.2 Loading required package: splines Warning messages: 1: In if (is.na(predict_at)) { : the condition has length > 1 and only the first element will be used 2: In if (class(p) == "try-error") { : the condition has length > 1 and only the first element will be used 3: In plot.window(...) : "label" is not a graphical parameter 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter 5: In axis(side = side, at = at, labels = labels, ...) : "label" is not a graphical parameter 6: In axis(side = side, at = at, labels = labels, ...) : "label" is not a graphical parameter 7: In box(...) : "label" is not a graphical parameter 8: In title(...) : "label" is not a graphical parameter </pre> <div class="toolFormTitle">Other log output</div> <pre> ## Toolfactory running rglasso as Rscript script [1] @@@ Using alpha = 0.95 for all models [1] @@@@ Input has 500 samples and 3 predictors [1] @@@ Cox model will predict yvar= status using cols= rhubarb,vegemite,apple n preds= 3 forced in= rhubarb [1] @@@ SessionInfo for this R session: R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [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 attached base packages: [1] splines methods stats graphics grDevices utils datasets base other attached packages: [1] pec_2.4.4 survival_2.37-7 lars_1.2 glmnet_1.9-8 Matrix_1.1-5 loaded via a namespace (and not attached): [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 Warning messages: 1: In if (is.na(predict_at)) { ... : the condition has length > 1 and only the first element will be used 2: In if (class(p) == "try-error") { ... : the condition has length > 1 and only the first element will be used 3: In plot.window(...) : "label" is not a graphical parameter 4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter 5: In axis(side = side, at = at, labels = labels, ...) : "label" is not a graphical parameter 6: In axis(side = side, at = at, labels = labels, ...) : "label" is not a graphical parameter 7: In box(...) : "label" is not a graphical parameter 8: In title(...) : "label" is not a graphical parameter </pre> <div class="toolFormTitle">All output files available for downloading</div> <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> <tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr> <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.3 KB</td></tr> <tr><td><a href="cox_cross_validation_model_counts.xls">cox_cross_validation_model_counts.xls</a></td><td>42 B</td></tr> <tr class="odd_row"><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>522 B</td></tr> <tr><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>21.5 KB</td></tr> <tr class="odd_row"><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>803 B</td></tr> <tr><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.7 KB</td></tr> </table></div><br/> </div></body></html>