Mercurial > repos > fubar > rglasso
diff test-data/coxlassotest.html @ 4:fb4959ed5b2b draft
Fixes to paths in git for deps
| author | fubar |
|---|---|
| date | Sat, 31 Oct 2015 02:26:24 -0400 |
| parents | cf295f36d606 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coxlassotest.html Sat Oct 31 02:26:24 2015 -0400 @@ -0,0 +1,167 @@ +<!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> +