# HG changeset patch # User iuc # Date 1424277431 18000 # Node ID 1948c6a82a9b8acddc69fdba0bcac7f1aec98a6e # Parent a061150f1d940e3a07108efb3b9749d9ce30a7e0 Uploaded diff -r a061150f1d94 -r 1948c6a82a9b rg_nri.xml --- a/rg_nri.xml Tue Jan 27 06:16:16 2015 -0500 +++ b/rg_nri.xml Wed Feb 18 11:37:11 2015 -0500 @@ -1,7 +1,7 @@ - + and other model improvement measures - R + R_3_1_1 graphicsmagick ghostscript glmnet_lars_2_14 diff -r a061150f1d94 -r 1948c6a82a9b rglasso_cox.xml --- a/rglasso_cox.xml Tue Jan 27 06:16:16 2015 -0500 +++ b/rglasso_cox.xml Wed Feb 18 11:37:11 2015 -0500 @@ -1,7 +1,7 @@ - + and cox regression using elastic net - R + R_3_1_1 graphicsmagick ghostscript glmnet_lars_2_14 @@ -132,7 +132,7 @@ - + @@ -150,7 +150,7 @@ - + diff -r a061150f1d94 -r 1948c6a82a9b test-data/coxlassotest.html --- a/test-data/coxlassotest.html Tue Jan 27 06:16:16 2015 -0500 +++ b/test-data/coxlassotest.html Wed Feb 18 11:37:11 2015 -0500 @@ -8,7 +8,7 @@
-
Galaxy Tool "rglasso" run at 28/12/2014 13:07:57

+
Galaxy Tool "rglasso" run at 18/02/2015 22:06:08

cox images and outputs
(Click on a thumbnail image to download the corresponding original PDF image)
@@ -34,9 +34,7 @@ rhubarb 10 10 -vegemite 3 10 - -apple 0 1 +vegemite 6 6 [1] @@@ Results preview: @@ -104,9 +102,9 @@ [1] @@@ SessionInfo for this R session: -R version 3.0.2 (2013-09-25) +R version 3.1.0 (2014-04-10) -Platform: x86_64-pc-linux-gnu (64-bit) +Platform: x86_64-unknown-linux-gnu (64-bit) locale: @@ -118,11 +116,11 @@ other attached packages: -[1] pec_2.4.4 survival_2.37-7 lars_1.2 glmnet_1.9-8 Matrix_1.1-4 +[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_0.2-9 foreach_1.4.2 grid_3.0.2 iterators_1.0.7 lattice_0.20-29 lava_1.3 prodlim_1.5.1 +[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: @@ -157,10 +155,10 @@
- + - - + + diff -r a061150f1d94 -r 1948c6a82a9b tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 27 06:16:16 2015 -0500 +++ b/tool_dependencies.xml Wed Feb 18 11:37:11 2015 -0500 @@ -1,7 +1,7 @@ - - + + @@ -13,8 +13,8 @@ - - + + https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/RColorBrewer_1.1-2.tar.gz?raw=true https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rglasso/MASS_7.3-35.tar.gz?raw=true @@ -79,8 +79,6 @@ Yee-Haw! Lasso for Galaxy! - Uses glmnet from the R CRAN. - See http://web.stanford.edu/~hastie/glmnet/glmnet_alpha.html
Output File Name (click to view)Size
cox_Coxglmnettest_glmnet_cvdeviance.pdf6.3 KB
cox_Coxglmnettest_glmnet_cvdeviance.pdf6.4 KB
cox_Coxglmnettest_glmnetdev.pdf5.3 KB
cox_cross_validation_model_counts.xls47 B
cox_rglasso.log563 B
cox_cross_validation_model_counts.xls42 B
cox_rglasso.log522 B
rglasso.Rscript21.5 KB
rglasso_error.log803 B
rglasso_runner.log1.7 KB