validation
8 years agoMerge branch 'release/v3.2.0' master v4.0.0
rautenberg [Fri, 13 Jul 2012 07:58:10 +0000 (09:58 +0200)]
Merge branch 'release/v3.2.0'

8 years agoupdate README date release/v3.2.0
rautenberg [Fri, 13 Jul 2012 07:57:48 +0000 (09:57 +0200)]
update README date

8 years agoCreating R image commented out.
Andreas Maunz [Tue, 24 Apr 2012 14:02:26 +0000 (16:02 +0200)]
Creating R image commented out.

8 years agofix setting of alogrithm_params
mguetlein [Tue, 24 Apr 2012 07:51:55 +0000 (09:51 +0200)]
fix setting of alogrithm_params

8 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Tue, 24 Apr 2012 07:33:03 +0000 (09:33 +0200)]
Merge branch 'development' of github.com:opentox/validation into development

8 years agoadd redis index to algorihtm_uris, fix stratified cv r-util import, explictly add...
mguetlein [Tue, 24 Apr 2012 07:32:52 +0000 (09:32 +0200)]
add redis index to algorihtm_uris, fix stratified cv r-util import, explictly add self to access algorithm_params

8 years agoMerge branch 'jl' into development
David Vorgrimmler [Wed, 18 Apr 2012 14:08:48 +0000 (16:08 +0200)]
Merge branch 'jl' into development

8 years agoFixed forced conversion to string jl
Andreas Maunz [Wed, 11 Apr 2012 07:53:50 +0000 (09:53 +0200)]
Fixed forced conversion to string

8 years agonew stratified type super added to crossvalidation and traning-test-split validation...
mguetlein [Mon, 2 Apr 2012 14:11:28 +0000 (16:11 +0200)]
new stratified type super added to crossvalidation and traning-test-split validation, add some more metadata to crossvaldiation, add validation_uri to predictions in crossvaldiation-report

8 years agoadd concordance correlation coefficient, adjust feature value plotting
mguetlein [Mon, 26 Mar 2012 09:29:14 +0000 (11:29 +0200)]
add concordance correlation coefficient, adjust feature value plotting

8 years agofix loo-report-build: make sure values are int
mguetlein [Thu, 22 Mar 2012 14:35:19 +0000 (15:35 +0100)]
fix loo-report-build: make sure values are int

8 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Wed, 14 Mar 2012 08:43:30 +0000 (09:43 +0100)]
Merge branch 'development' of github.com:opentox/validation into development

8 years agofix 'skip results in loocv-reports'
mguetlein [Wed, 14 Mar 2012 08:43:14 +0000 (09:43 +0100)]
fix 'skip results in loocv-reports'

8 years agoMerge branch 'release/v3.1.0' into development
rautenberg [Tue, 13 Mar 2012 14:42:45 +0000 (15:42 +0100)]
Merge branch 'release/v3.1.0' into development

8 years agoMerge branch 'release/v3.1.0' v3.1.0
rautenberg [Tue, 13 Mar 2012 14:42:29 +0000 (15:42 +0100)]
Merge branch 'release/v3.1.0'

8 years agoskip results in loocv-reports
mguetlein [Tue, 13 Mar 2012 09:24:53 +0000 (10:24 +0100)]
skip results in loocv-reports

8 years agoset correct creator URI in cv dataset folds
mguetlein [Tue, 13 Mar 2012 09:16:55 +0000 (10:16 +0100)]
set correct creator URI in cv dataset folds

8 years agosubjectid from helper
rautenberg [Tue, 6 Mar 2012 15:10:20 +0000 (16:10 +0100)]
subjectid from helper

8 years agofix: do not always delete feature datasets in loo-cv
mguetlein [Fri, 2 Mar 2012 16:09:09 +0000 (17:09 +0100)]
fix: do not always delete feature datasets in loo-cv

8 years agoremove unneeded dataset files when performing loo-cv
mguetlein [Tue, 28 Feb 2012 09:36:17 +0000 (10:36 +0100)]
remove unneeded dataset files when performing loo-cv

8 years agoadapt validation to r-util (split), add new r plots
mguetlein [Tue, 31 Jan 2012 11:37:36 +0000 (12:37 +0100)]
adapt validation to r-util (split), add new r plots

8 years agowrap plain split into taks
mguetlein [Wed, 18 Jan 2012 17:56:48 +0000 (18:56 +0100)]
wrap plain split into taks

8 years agoadd super-stratification split for training test splitting
mguetlein [Wed, 18 Jan 2012 16:54:11 +0000 (17:54 +0100)]
add super-stratification split for training test splitting

8 years agochange in validation: duplicates (with different values) in test-set are handled...
mguetlein [Tue, 10 Jan 2012 09:45:59 +0000 (10:45 +0100)]
change in validation: duplicates (with different values) in test-set are handled as one prediction each

8 years agofix: make sure subjectid is set in merged validation for comparison report
mguetlein [Thu, 5 Jan 2012 13:23:01 +0000 (14:23 +0100)]
fix: make sure subjectid is set in merged validation for comparison report

8 years agofix validation aa errors, add more verbose error msg for propbabilites feature
mguetlein [Wed, 4 Jan 2012 11:23:33 +0000 (12:23 +0100)]
fix validation aa errors, add more verbose error msg for propbabilites feature

8 years agoadd missing subjectid when loading validation for reports
mguetlein [Tue, 3 Jan 2012 12:38:58 +0000 (13:38 +0100)]
add missing subjectid when loading validation for reports

8 years agomake prediciton filtering robust to nil values
mguetlein [Wed, 14 Dec 2011 15:40:01 +0000 (16:40 +0100)]
make prediciton filtering robust to nil values

8 years agoadd filtering of validation reports
mguetlein [Tue, 13 Dec 2011 10:20:04 +0000 (11:20 +0100)]
add filtering of validation reports

8 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Wed, 7 Dec 2011 15:26:56 +0000 (16:26 +0100)]
Merge branch 'development' of github.com:opentox/validation into development

8 years agoadd computation of classification prediciton probabilities
mguetlein [Wed, 7 Dec 2011 15:26:41 +0000 (16:26 +0100)]
add computation of classification prediciton probabilities

8 years agoUpdated ruby-plot version to 0.6.0
davor [Wed, 30 Nov 2011 11:16:33 +0000 (12:16 +0100)]
Updated ruby-plot version to 0.6.0

8 years agoadd r-square plot, fix prediction updating, add weighted sample-correlation-coefficient
mguetlein [Fri, 25 Nov 2011 08:07:50 +0000 (09:07 +0100)]
add r-square plot, fix prediction updating, add weighted sample-correlation-coefficient

8 years agoenable reporting with external validations
mguetlein [Wed, 23 Nov 2011 16:12:14 +0000 (17:12 +0100)]
enable reporting with external validations

8 years agofix load validations for serialization
mguetlein [Wed, 23 Nov 2011 15:23:40 +0000 (16:23 +0100)]
fix load validations for serialization

8 years agoadjust yaml version for to-html
mguetlein [Wed, 23 Nov 2011 15:02:12 +0000 (16:02 +0100)]
adjust yaml version for to-html

8 years agoadd validation to pure-yaml code for serialization
mguetlein [Wed, 23 Nov 2011 14:57:10 +0000 (15:57 +0100)]
add validation to pure-yaml code for serialization

8 years agoMerge branch 'release/v3.0.0' v3.0.0
mr [Fri, 23 Sep 2011 10:22:40 +0000 (12:22 +0200)]
Merge branch 'release/v3.0.0'

9 years agoadd missing subjectid v3.0.1
mr [Fri, 19 Aug 2011 12:31:29 +0000 (14:31 +0200)]
add missing subjectid

9 years agoadding tttestable attributes list
mguetlein [Thu, 18 Aug 2011 15:16:21 +0000 (17:16 +0200)]
adding tttestable attributes list

9 years agoadd ppv and npv to bar plot, remove debug output
mguetlein [Thu, 18 Aug 2011 14:34:50 +0000 (16:34 +0200)]
add ppv and npv to bar plot, remove debug output

9 years agoadd npv calculation, add ppv (renamed from precision) and npv to important classifica...
mguetlein [Thu, 18 Aug 2011 11:46:10 +0000 (13:46 +0200)]
add npv calculation, add ppv (renamed from precision) and npv to important classificaiton stats

9 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Thu, 18 Aug 2011 10:58:22 +0000 (12:58 +0200)]
Merge branch 'development' of github.com:opentox/validation into development

9 years agoadd confidence plots for various classification stats
mguetlein [Thu, 18 Aug 2011 10:57:33 +0000 (12:57 +0200)]
add confidence plots for various classification stats

9 years agoMerge branch 'development' of github.com:opentox/validation into development
mr [Thu, 18 Aug 2011 10:28:53 +0000 (12:28 +0200)]
Merge branch 'development' of github.com:opentox/validation into development

9 years agoadd missing subjectids
mr [Thu, 18 Aug 2011 10:28:47 +0000 (12:28 +0200)]
add missing subjectids

9 years agofix ROC stuff [2]
mguetlein [Thu, 18 Aug 2011 09:25:39 +0000 (11:25 +0200)]
fix ROC stuff [2]

9 years agofix ROC stuff, rename weighted_auc to average_auc
mguetlein [Thu, 18 Aug 2011 08:38:51 +0000 (10:38 +0200)]
fix ROC stuff, rename weighted_auc to average_auc

9 years agoadding qmrf jars
mguetlein [Mon, 15 Aug 2011 07:53:59 +0000 (09:53 +0200)]
adding qmrf jars

9 years agoadd search with model in crossvalidation and qmrf report as discussed with nina in...
mguetlein [Mon, 15 Aug 2011 07:15:56 +0000 (09:15 +0200)]
add search with model in crossvalidation and qmrf report as discussed with nina in munich

9 years agoadd bootstrapping description
mguetlein [Sat, 13 Aug 2011 12:20:18 +0000 (14:20 +0200)]
add bootstrapping description

9 years agoMerge remote branch 'origin/development' v2.1.0
mr [Fri, 5 Aug 2011 11:12:12 +0000 (13:12 +0200)]
Merge remote branch 'origin/development'

9 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Fri, 5 Aug 2011 10:59:21 +0000 (12:59 +0200)]
Merge branch 'development' of github.com:opentox/validation into development

9 years agofix cv when no predictions on a fold
mguetlein [Thu, 4 Aug 2011 17:30:16 +0000 (19:30 +0200)]
fix cv when no predictions on a fold

9 years agoMerge branch 'release/v2.1.0'
mr [Thu, 4 Aug 2011 16:40:44 +0000 (18:40 +0200)]
Merge branch 'release/v2.1.0'

9 years agoadd subjectid to crossvalidation call
mr [Mon, 1 Aug 2011 20:31:54 +0000 (22:31 +0200)]
add subjectid to crossvalidation call

9 years agoresuce correlation coeffiction computation errors
mguetlein [Mon, 18 Jul 2011 07:34:52 +0000 (09:34 +0200)]
resuce correlation coeffiction computation errors

9 years agoadded correlation coefficient to regression reports
mguetlein [Wed, 13 Jul 2011 08:58:19 +0000 (10:58 +0200)]
added correlation coefficient to regression reports

9 years agofix valid prediction values check for regression validation
mguetlein [Wed, 13 Jul 2011 08:15:47 +0000 (10:15 +0200)]
fix valid prediction values check for regression validation

9 years agominor fix for new regression plotting: dont count nil values as omitted value
mguetlein [Tue, 12 Jul 2011 11:58:27 +0000 (13:58 +0200)]
minor fix for new regression plotting: dont count nil values as omitted value

9 years agoregression plot in 2 different scales
mguetlein [Tue, 12 Jul 2011 11:21:27 +0000 (13:21 +0200)]
regression plot in 2 different scales

9 years agofixed sqrt domain error in regression validation, added check for NaN and Infinity
mguetlein [Tue, 12 Jul 2011 09:41:32 +0000 (11:41 +0200)]
fixed sqrt domain error in regression validation, added check for NaN and Infinity

9 years agofix error when making regression validations w/o confidence
mguetlein [Wed, 6 Jul 2011 12:57:53 +0000 (14:57 +0200)]
fix error when making regression validations w/o confidence

9 years agosmall bugifx in building error msg
mguetlein [Fri, 1 Jul 2011 09:35:59 +0000 (11:35 +0200)]
small bugifx in building error msg

9 years agoadd control of t-tests to algorihtm-comparison reports
mguetlein [Fri, 1 Jul 2011 09:18:41 +0000 (11:18 +0200)]
add control of t-tests to algorihtm-comparison reports

9 years agoadding confidence-weighted regression stats
mguetlein [Thu, 30 Jun 2011 21:49:22 +0000 (23:49 +0200)]
adding confidence-weighted regression stats

9 years agoadd dataset cleanup method
mguetlein [Wed, 29 Jun 2011 09:56:31 +0000 (11:56 +0200)]
add dataset cleanup method

9 years agodo delete policies in background with sleeps, fix cleanup method
mguetlein [Wed, 29 Jun 2011 09:19:02 +0000 (11:19 +0200)]
do delete policies in background with sleeps, fix cleanup method

9 years agofix chart keys (removing 'default', adding crossvalidation fold)
mguetlein [Fri, 17 Jun 2011 14:19:11 +0000 (16:19 +0200)]
fix chart keys (removing 'default', adding crossvalidation fold)

9 years agodo not empty subjectid to jnlp when a&A is disabled
mguetlein [Fri, 17 Jun 2011 13:54:20 +0000 (15:54 +0200)]
do not empty subjectid to jnlp when a&A is disabled

9 years agoprefer prediction_feature, use Model.dependentVariables if no prediction feature...
mguetlein [Fri, 17 Jun 2011 10:11:02 +0000 (12:11 +0200)]
prefer prediction_feature, use Model.dependentVariables if no prediction feature is specified

9 years agoreport stylesheet moved from ortona to validation service
mguetlein [Thu, 16 Jun 2011 22:27:44 +0000 (00:27 +0200)]
report stylesheet moved from ortona to validation service

9 years agoMerge branch 'development' of github.com:opentox/validation into development
mguetlein [Thu, 16 Jun 2011 22:12:50 +0000 (00:12 +0200)]
Merge branch 'development' of github.com:opentox/validation into development

9 years agoadd post forms
mguetlein [Thu, 16 Jun 2011 21:52:31 +0000 (23:52 +0200)]
add post forms

9 years agoclean merge with hotfix
mr [Wed, 15 Jun 2011 11:19:12 +0000 (13:19 +0200)]
clean merge with hotfix

9 years agoMerge branch 'hotfix/qmrf_mysqlite'
mr [Wed, 15 Jun 2011 11:12:34 +0000 (13:12 +0200)]
Merge branch 'hotfix/qmrf_mysqlite'

9 years agohotfix close R
mr [Wed, 15 Jun 2011 11:12:31 +0000 (13:12 +0200)]
hotfix close R

9 years agohotfix qmrf sqlite
mr [Wed, 15 Jun 2011 11:06:20 +0000 (13:06 +0200)]
hotfix qmrf sqlite

9 years agohalts (partially) substituted by OpenTox errors
Christoph Helma [Mon, 6 Jun 2011 16:54:56 +0000 (16:54 +0000)]
halts (partially) substituted by OpenTox errors

9 years agoquit r instance after statistical test, will hopefully solve timeout problem
mguetlein [Tue, 31 May 2011 20:26:34 +0000 (22:26 +0200)]
quit r instance after statistical test, will hopefully solve timeout problem

9 years agoretry hack for mysql lite
mguetlein [Tue, 31 May 2011 18:17:01 +0000 (20:17 +0200)]
retry hack for mysql lite

9 years agofix algparams with multiple '='
mguetlein [Mon, 30 May 2011 13:02:38 +0000 (15:02 +0200)]
fix algparams with multiple '='

9 years agochange qmrfreport address from qmrfreport2 to qmrfreport
mguetlein [Mon, 30 May 2011 12:29:21 +0000 (14:29 +0200)]
change qmrfreport address from qmrfreport2 to qmrfreport

9 years agofix percentage completed for cv
mguetlein [Fri, 27 May 2011 15:36:11 +0000 (17:36 +0200)]
fix percentage completed for cv

9 years agofix error msg
mguetlein [Fri, 27 May 2011 09:41:54 +0000 (11:41 +0200)]
fix error msg

9 years agoadding more verbose error message when feature_type is unknown
mguetlein [Fri, 27 May 2011 08:38:53 +0000 (10:38 +0200)]
adding more verbose error message when feature_type is unknown

9 years agoremove hack to determine prediction feature
mguetlein [Fri, 27 May 2011 08:09:35 +0000 (10:09 +0200)]
remove hack to determine prediction feature

9 years agoimplemented loo crossvalidation
mguetlein [Thu, 26 May 2011 16:06:50 +0000 (18:06 +0200)]
implemented loo crossvalidation

9 years agoA&A reporting fix
mguetlein [Thu, 26 May 2011 13:18:02 +0000 (15:18 +0200)]
A&A reporting fix

9 years agofix for last commit: fixes in reports for crossvaldiation with few predictions
mguetlein [Thu, 26 May 2011 13:16:26 +0000 (15:16 +0200)]
fix for last commit: fixes in reports for crossvaldiation with few predictions

9 years agofixes in reports for crossvaldiation with few predictions
mguetlein [Thu, 26 May 2011 12:15:54 +0000 (14:15 +0200)]
fixes in reports for crossvaldiation with few predictions

9 years agofix error for stratified regression cv
mguetlein [Thu, 26 May 2011 10:07:33 +0000 (12:07 +0200)]
fix error for stratified regression cv

9 years agouse accept_values method instead of accessing metadata directly
mguetlein [Thu, 26 May 2011 08:57:32 +0000 (10:57 +0200)]
use accept_values method instead of accessing metadata directly

9 years agofix: bar-plot format changed from svg to png
mguetlein [Wed, 25 May 2011 12:08:58 +0000 (14:08 +0200)]
fix: bar-plot format changed from svg to png

9 years agosort validation and crossvalidation lists
mguetlein [Wed, 25 May 2011 12:07:57 +0000 (14:07 +0200)]
sort validation and crossvalidation lists

9 years agoreplace +- in reports with corresponding html-char
mguetlein [Wed, 25 May 2011 08:35:37 +0000 (10:35 +0200)]
replace +- in reports with corresponding html-char

9 years agoadd cv debug msg to see number of folds
mguetlein [Wed, 25 May 2011 08:07:33 +0000 (10:07 +0200)]
add cv debug msg to see number of folds

9 years agoadjust to ruby-plot version 0.5, simplification + support for various max youden...
mguetlein [Tue, 24 May 2011 17:44:06 +0000 (19:44 +0200)]
adjust to ruby-plot version 0.5, simplification + support for various max youden-index points

9 years agoadd rdf version for crossvalidation statistics
mguetlein [Tue, 24 May 2011 15:29:07 +0000 (17:29 +0200)]
add rdf version for crossvalidation statistics

9 years agoremove debug output
mguetlein [Tue, 24 May 2011 14:21:49 +0000 (16:21 +0200)]
remove debug output