test
7 years agoUpdate fminer.rb master
davor [Tue, 4 Dec 2012 14:06:40 +0000 (15:06 +0100)]
Update fminer.rb

Rounded pValues.

8 years agoMerge branch 'development' v4.0.0
rautenberg [Mon, 16 Jul 2012 11:36:51 +0000 (13:36 +0200)]
Merge branch 'development'

8 years agoMerge branch 'release/v3.2.0'
rautenberg [Fri, 13 Jul 2012 07:52:35 +0000 (09:52 +0200)]
Merge branch 'release/v3.2.0'

8 years agoUpdated code. development
davor [Tue, 10 Jul 2012 14:28:12 +0000 (16:28 +0200)]
Updated code.

Note: Code moved to https://github.com/davor/bbrc-sample-client

8 years agoAdded random_seed param and statistics. release/v3.2.0
David Vorgrimmler [Sat, 23 Jun 2012 01:18:06 +0000 (03:18 +0200)]
Added random_seed param and statistics.

8 years agoUpdated scripts and added comments.
David Vorgrimmler [Wed, 20 Jun 2012 13:27:47 +0000 (15:27 +0200)]
Updated scripts and added comments.

8 years agoAdded subjectids.
David Vorgrimmler [Wed, 20 Jun 2012 12:34:53 +0000 (14:34 +0200)]
Added subjectids.

8 years agoRemoved fast_embedding in test_feature_value_plot
David Vorgrimmler [Tue, 19 Jun 2012 13:25:19 +0000 (15:25 +0200)]
Removed fast_embedding in test_feature_value_plot

8 years agoAdjusted r-urils test.
David Vorgrimmler [Tue, 19 Jun 2012 09:45:43 +0000 (11:45 +0200)]
Adjusted r-urils test.

8 years agoAdded min_frequency search.
David Vorgrimmler [Fri, 15 Jun 2012 16:47:49 +0000 (18:47 +0200)]
Added min_frequency search.

8 years agoAdded bbrc-sampling test scripts.
David Vorgrimmler [Wed, 13 Jun 2012 11:36:15 +0000 (13:36 +0200)]
Added bbrc-sampling test scripts.

8 years agoMinor modification.
David Vorgrimmler [Tue, 12 Jun 2012 21:06:28 +0000 (23:06 +0200)]
Minor modification.

8 years agoAdded test_match_pValue and fixed test_match
David Vorgrimmler [Mon, 11 Jun 2012 10:22:13 +0000 (12:22 +0200)]
Added test_match_pValue and fixed test_match

8 years agoModified lazar test.
David Vorgrimmler [Wed, 6 Jun 2012 16:21:43 +0000 (18:21 +0200)]
Modified lazar test.

8 years agoModified fminer tests.
David Vorgrimmler [Wed, 6 Jun 2012 16:05:00 +0000 (18:05 +0200)]
Modified fminer tests.

8 years agoMerge branch 'jl' into development
David Vorgrimmler [Fri, 20 Apr 2012 09:48:54 +0000 (11:48 +0200)]
Merge branch 'jl' into development

Conflicts:
cv/data/datasets.yaml
lazar.rb

8 years agofix RuntimeError: 'headers are no hash' in dataset test.
rautenberg [Tue, 10 Apr 2012 07:00:03 +0000 (09:00 +0200)]
fix RuntimeError: 'headers are no hash' in dataset test.

8 years agoadd metadata to calls, add test for k-fold-split method
mguetlein [Mon, 2 Apr 2012 14:14:27 +0000 (16:14 +0200)]
add metadata to calls, add test for k-fold-split method

8 years agoenable multithread test for dataset
mguetlein [Tue, 20 Mar 2012 15:10:45 +0000 (16:10 +0100)]
enable multithread test for dataset

8 years agodataset.rb merged
mguetlein [Tue, 20 Mar 2012 08:56:37 +0000 (09:56 +0100)]
dataset.rb merged

8 years agoadding dataset multithread test that fails - outcommented
mguetlein [Tue, 20 Mar 2012 08:53:36 +0000 (09:53 +0100)]
adding dataset multithread test that fails - outcommented

8 years agoMerge branch 'release/v3.1.0' into development
rautenberg [Tue, 13 Mar 2012 14:45:20 +0000 (15:45 +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 14:45:11 +0000 (15:45 +0100)]
Merge branch 'release/v3.1.0'

8 years agoadd missing subjectid release/v3.1.0
rautenberg [Tue, 13 Mar 2012 09:38:07 +0000 (10:38 +0100)]
add missing subjectid

8 years agoAdded script to create feature dataset. jl
davor [Mon, 27 Feb 2012 09:24:53 +0000 (10:24 +0100)]
Added script to create feature dataset.

8 years agoAdjusted parameter range.
davor [Mon, 27 Feb 2012 09:20:00 +0000 (10:20 +0100)]
Adjusted parameter range.

8 years agoCreated all datasets on ot0 (jl branch) and updated/added feature
davor [Mon, 27 Feb 2012 09:13:40 +0000 (10:13 +0100)]
Created all datasets on ot0 (jl branch) and updated/added feature
datasets (electronic,cpsa, constitutional, topological, hybrid and
joelib)

8 years agoFixed minor bug in csv file.
David Vorgrimmler [Thu, 23 Feb 2012 15:10:28 +0000 (16:10 +0100)]
Fixed minor bug in csv file.

8 years agoAdjusted tests to jl
Andreas Maunz [Thu, 23 Feb 2012 15:07:26 +0000 (16:07 +0100)]
Adjusted tests to jl

8 years agoCreated selected feature datasets (with rfe) for all pc descriptors and all
Andreas Maunz [Tue, 21 Feb 2012 09:12:37 +0000 (10:12 +0100)]
Created selected feature datasets (with rfe) for all pc descriptors and all
datasets (but MDD)

8 years agodelete subjectid after usage.
mr [Tue, 21 Feb 2012 09:05:54 +0000 (10:05 +0100)]
delete subjectid after usage.

8 years agoCreated merged dataset of all pc descriptors for all datasets, befor feature selectio...
Andreas Maunz [Mon, 20 Feb 2012 13:03:59 +0000 (14:03 +0100)]
Created merged dataset of all pc descriptors for all datasets, befor feature selection (see
https://github.com/opentox/test/blob/1a7d6eef755a67a92fbc9bca81a25e9258293e73/cv/data/datasets.yaml).

8 years agoMerged selected electronic,cpsa,constitutional,topological feature
Andreas Maunz [Mon, 20 Feb 2012 12:52:58 +0000 (13:52 +0100)]
Merged selected electronic,cpsa,constitutional,topological feature
datasets to *_all_pc for FHM and LOAEL

8 years agoMerge branch 'development' of github.com:opentox/test into development
davor [Wed, 15 Feb 2012 15:01:09 +0000 (16:01 +0100)]
Merge branch 'development' of github.com:opentox/test into development

8 years agoUpdated result interval
davor [Wed, 15 Feb 2012 14:59:12 +0000 (15:59 +0100)]
Updated result interval

8 years agouncomment code http://goo.gl/ybSy3 after positive test
mr [Wed, 15 Feb 2012 14:09:11 +0000 (15:09 +0100)]
uncomment code goo.gl/ybSy3 after positive test

8 years agoMerge branch 'pc_new_1' into development
Andreas Maunz [Wed, 15 Feb 2012 11:03:24 +0000 (12:03 +0100)]
Merge branch 'pc_new_1' into development

8 years agoAdded script to create selected feature dataset.
Andreas Maunz [Tue, 14 Feb 2012 15:59:42 +0000 (16:59 +0100)]
Added script to create selected feature dataset.

8 years agoAdded dependency for TestUtil and fixed test_csv.
davor [Tue, 14 Feb 2012 10:31:36 +0000 (11:31 +0100)]
Added dependency for TestUtil and fixed test_csv.

8 years agoUpdated y-values of LOAEL to log(mol) pc_new_1
Andreas Maunz [Sun, 12 Feb 2012 13:10:35 +0000 (14:10 +0100)]
Updated y-values of LOAEL to log(mol)

8 years agoUpdated y-values of LOAEL to log(mg)
Andreas Maunz [Sat, 11 Feb 2012 23:55:00 +0000 (00:55 +0100)]
Updated y-values of LOAEL to log(mg)

8 years agoCreated new feature dataset with feature selection algo and updated
Andreas Maunz [Fri, 10 Feb 2012 16:32:42 +0000 (17:32 +0100)]
Created new feature dataset with feature selection algo and updated
dataset.yaml

8 years agoRemoved missing features from feature datasets and updated dataset.yaml
Andreas Maunz [Fri, 10 Feb 2012 09:03:15 +0000 (10:03 +0100)]
Removed missing features from feature datasets and updated dataset.yaml

8 years agoMerge branch 'pc_new_1' into development
Andreas Maunz [Thu, 9 Feb 2012 14:44:28 +0000 (15:44 +0100)]
Merge branch 'pc_new_1' into development

Conflicts:
algorithm.rb
dataset.rb
lazar.rb

8 years agoFixed tests
Andreas Maunz [Thu, 9 Feb 2012 14:42:36 +0000 (15:42 +0100)]
Fixed tests

8 years agoToggle comments
Andreas Maunz [Wed, 8 Feb 2012 09:59:36 +0000 (10:59 +0100)]
Toggle comments

8 years agoUpdated LOAEL feature datasets (removed "nominal" features)
Andreas Maunz [Wed, 8 Feb 2012 09:57:17 +0000 (10:57 +0100)]
Updated LOAEL feature datasets (removed "nominal" features)

8 years agoAdded LOAEL data and feature csv files (feature dataset with "nominal"
Andreas Maunz [Wed, 8 Feb 2012 09:31:22 +0000 (10:31 +0100)]
Added LOAEL data and feature csv files (feature dataset with "nominal"
features)

8 years agoAdded LOAEL feature datasets
Andreas Maunz [Wed, 8 Feb 2012 08:14:42 +0000 (09:14 +0100)]
Added LOAEL feature datasets

8 years agoadd dataframe modification test to r-util test
mguetlein [Tue, 7 Feb 2012 12:04:09 +0000 (13:04 +0100)]
add dataframe modification test to r-util test

8 years agoUpdated and moved scripts in new folder structure
davor [Wed, 1 Feb 2012 10:34:05 +0000 (11:34 +0100)]
Updated and moved scripts in new folder structure

8 years agoDeleted old files
davor [Tue, 31 Jan 2012 11:29:16 +0000 (12:29 +0100)]
Deleted old files

8 years agoMerge branch 'pc_new_1' of github.com:opentox/test into pc_new_1
davor [Tue, 31 Jan 2012 11:26:31 +0000 (12:26 +0100)]
Merge branch 'pc_new_1' of github.com:opentox/test into pc_new_1

Conflicts:
5x_cv/fs/MOU_ELECT2.R
5x_cv/fs/RAT_ELECT2.R

8 years agoDeleted old files
davor [Tue, 31 Jan 2012 11:23:58 +0000 (12:23 +0100)]
Deleted old files

8 years agoextend fminer test for nr_hits match
mguetlein [Tue, 31 Jan 2012 10:59:41 +0000 (11:59 +0100)]
extend fminer test for nr_hits match

8 years agoadd test for fminer matching
mguetlein [Tue, 31 Jan 2012 10:28:01 +0000 (11:28 +0100)]
add test for fminer matching

8 years agoremove a test if package is not installed
mguetlein [Tue, 31 Jan 2012 09:59:47 +0000 (10:59 +0100)]
remove a test if package is not installed

8 years agoMerge branch 'pc_new_1' of github.com:opentox/test into pc_new_1
Andreas Maunz [Tue, 31 Jan 2012 09:49:03 +0000 (10:49 +0100)]
Merge branch 'pc_new_1' of github.com:opentox/test into pc_new_1

8 years agoUpdated feature dataset URIs
Andreas Maunz [Tue, 31 Jan 2012 09:47:27 +0000 (10:47 +0100)]
Updated feature dataset URIs

8 years agoMerge branch 'pc_new_1' of github.com:opentox/test into pc_new_1
Andreas Maunz [Tue, 31 Jan 2012 09:27:37 +0000 (10:27 +0100)]
Merge branch 'pc_new_1' of github.com:opentox/test into pc_new_1

8 years agoMerge branch 'caret' into pc_new_1
Andreas Maunz [Tue, 31 Jan 2012 09:26:38 +0000 (10:26 +0100)]
Merge branch 'caret' into pc_new_1

8 years agoadd feature filtering and null-values check to dataset to r conversion
mguetlein [Tue, 31 Jan 2012 09:20:01 +0000 (10:20 +0100)]
add feature filtering and null-values check to dataset to r conversion

8 years agoAdjusted tests to new parameters (see http://goo.gl/lXJBS)
Andreas Maunz [Tue, 31 Jan 2012 07:46:55 +0000 (08:46 +0100)]
Adjusted tests to new parameters (see goo.gl/lXJBS)

8 years agoadjust to latest r-util changes
mguetlein [Mon, 30 Jan 2012 17:19:58 +0000 (18:19 +0100)]
adjust to latest r-util changes

8 years agoadd r-util tests
mguetlein [Mon, 30 Jan 2012 15:56:07 +0000 (16:56 +0100)]
add r-util tests

8 years agoAdded new structure for crossvalidations with backup of all regression
Andreas Maunz [Mon, 30 Jan 2012 13:49:19 +0000 (14:49 +0100)]
Added new structure for crossvalidations with backup of all regression
datasets

8 years agofix merge test with a&a enabled
mguetlein [Mon, 30 Jan 2012 11:33:17 +0000 (12:33 +0100)]
fix merge test with a&a enabled

8 years agoadd test for datset.merge method
mguetlein [Mon, 30 Jan 2012 11:20:41 +0000 (12:20 +0100)]
add test for datset.merge method

8 years agoUsing best selection (see Nestle report)
Andreas Maunz [Mon, 30 Jan 2012 09:24:44 +0000 (10:24 +0100)]
Using best selection (see Nestle report)

8 years agoFinished variable selection
Andreas Maunz [Thu, 26 Jan 2012 09:12:35 +0000 (10:12 +0100)]
Finished variable selection

8 years agoFeature Selection: data sets prepared
Andreas Maunz [Wed, 25 Jan 2012 16:00:05 +0000 (17:00 +0100)]
Feature Selection: data sets prepared

8 years agoAdded csv files of topological feature datasets
David Vorgrimmler [Sat, 21 Jan 2012 14:02:08 +0000 (15:02 +0100)]
Added csv files of topological feature datasets

8 years agoUpdated tests to current version
Andreas Maunz [Fri, 20 Jan 2012 16:59:56 +0000 (17:59 +0100)]
Updated tests to current version

8 years agoMerged MOU and MOU_pTD/ RAT and RAT_pTD
Andreas Maunz [Fri, 20 Jan 2012 16:22:31 +0000 (17:22 +0100)]
Merged MOU and MOU_pTD/ RAT and RAT_pTD

8 years agoAdded topological feature ds for MDD and FHM
Andreas Maunz [Fri, 20 Jan 2012 15:45:06 +0000 (16:45 +0100)]
Added topological feature ds for MDD and FHM

8 years agoAdded corrected topologoical feature ds and test/training ds for rat and
Andreas Maunz [Thu, 19 Jan 2012 15:39:01 +0000 (16:39 +0100)]
Added corrected topologoical feature ds and test/training ds for rat and
mouse

8 years agoAdded feature dataset
Andreas Maunz [Wed, 18 Jan 2012 16:02:10 +0000 (17:02 +0100)]
Added feature dataset

8 years agoUpdated datasets_nestle.yaml: Replaced all URIs with recent versions. MDD
Andreas Maunz [Wed, 18 Jan 2012 15:28:14 +0000 (16:28 +0100)]
Updated datasets_nestle.yaml: Replaced all URIs with recent versions. MDD
bases on FDA_v3b_Maximum_Recommended_Daily_Dose_LOGINV_mmol_outl.csv. FHM bases on
EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_LOGINV_mmol_oul.csv. RAT and
MOU base now on the data from Bercu paper
(Bercu_CPDB_9March2010_rat_pTD50.csv and
Bercu_CPDB_9March2010_mouse_pTD50.csv). All csv file are available at
Dropbox/Lazar-Modellvergleich/Daten/Nestle_regression.

8 years agoRemoved old datasets_nestle backup and added an new backup
Andreas Maunz [Wed, 18 Jan 2012 15:26:45 +0000 (16:26 +0100)]
Removed old datasets_nestle backup and added an new backup

8 years agoMoved csv files
Andreas Maunz [Wed, 18 Jan 2012 14:22:34 +0000 (15:22 +0100)]
Moved csv files

8 years agoAdded folder structure
Andreas Maunz [Wed, 18 Jan 2012 14:15:42 +0000 (15:15 +0100)]
Added folder structure

8 years agoAdded MOU_pTD and RAT_pTD
davor [Tue, 17 Jan 2012 13:21:28 +0000 (14:21 +0100)]
Added MOU_pTD and RAT_pTD

8 years agoMerge branch 'pc_new_1' of github.com:opentox/test into pc_new_1
Andreas Maunz [Tue, 17 Jan 2012 09:10:33 +0000 (10:10 +0100)]
Merge branch 'pc_new_1' of github.com:opentox/test into pc_new_1

8 years agoAdjusted tests for commit 4aafc9b30
Andreas Maunz [Tue, 17 Jan 2012 09:09:29 +0000 (10:09 +0100)]
Adjusted tests for commit 4aafc9b30

8 years agoUpdated files
davor [Mon, 16 Jan 2012 17:03:01 +0000 (18:03 +0100)]
Updated files

8 years agoAdded some validation tool for pc ds
davor [Mon, 16 Jan 2012 16:59:59 +0000 (17:59 +0100)]
Added some validation tool for pc ds

8 years agoAdded feature ds for outl and improved inchi check
davor [Mon, 16 Jan 2012 16:57:49 +0000 (17:57 +0100)]
Added feature ds for outl and improved inchi check

8 years agoAdjusted tests to commit 1aeb705
davor [Mon, 16 Jan 2012 12:38:50 +0000 (13:38 +0100)]
Adjusted tests to commit 1aeb705

https://github.com/opentox/opentox-ruby/commit/1aeb705695a0f908760088a4666554393121160d

8 years agoRe-adjusted neighbors to 132
davor [Fri, 13 Jan 2012 13:37:35 +0000 (14:37 +0100)]
Re-adjusted neighbors to 132

8 years agoFixed SVD test
davor [Fri, 13 Jan 2012 13:17:12 +0000 (14:17 +0100)]
Fixed SVD test

8 years agoUpdated and checked datasets
davor [Fri, 13 Jan 2012 12:14:07 +0000 (13:14 +0100)]
Updated and checked datasets

8 years agoAdjusted tests to fingerprint fix
davor [Fri, 13 Jan 2012 11:31:37 +0000 (12:31 +0100)]
Adjusted tests to fingerprint fix

see https://github.com/opentox/algorithm/commit/eff86c3f6c7e99a19edf1e38dee577a9e9080bf7

8 years agoAdjusted tests
davor [Tue, 10 Jan 2012 07:30:49 +0000 (08:30 +0100)]
Adjusted tests

8 years agoUpdated tests
davor [Mon, 9 Jan 2012 14:45:42 +0000 (15:45 +0100)]
Updated tests

8 years agofix validation-comparison-test with aa
mguetlein [Thu, 5 Jan 2012 13:21:54 +0000 (14:21 +0100)]
fix validation-comparison-test with aa

8 years agoEnabled pcr test
davor [Wed, 4 Jan 2012 14:57:02 +0000 (15:57 +0100)]
Enabled pcr test

8 years agoUpdated csv files and feature datasets
davor [Wed, 4 Jan 2012 10:46:47 +0000 (11:46 +0100)]
Updated csv files and feature datasets

8 years agoreplaced @@subjectid with AA_SERVER when checking for aa-enabled
mguetlein [Tue, 3 Jan 2012 13:37:22 +0000 (14:37 +0100)]
replaced @@subjectid with AA_SERVER when checking for aa-enabled

8 years agofix assert-rest-call-error method
mguetlein [Tue, 3 Jan 2012 12:37:23 +0000 (13:37 +0100)]
fix assert-rest-call-error method

8 years agoUpdated tests for PC
davor [Mon, 2 Jan 2012 15:58:36 +0000 (16:58 +0100)]
Updated tests for PC