Timeline



Dec 22, 2005:

9:48 PM Changeset [481] by Markus Ringnér
Initial versions that will not compile but are more documentation for …
9:35 PM Changeset [480] by Jari Häkkinen
Changed the statistics link once more. Added Markus to authors. Added …
9:32 PM Changeset [479] by Jari Häkkinen
Removed obsolete doxygen config entry.
9:17 PM Changeset [478] by Peter
removed KernelView? again - somehow the file was resurrected when the …
7:32 PM Changeset [477] by Jari Häkkinen
5:37 PM Changeset [476] by Markus Ringnér
Added interface class for supervised classifiers. Fixed NCC to comply …
5:15 PM Ticket #35 (modify interface to CrossSplitting) created by Peter
Interface modified and this object now owns data and target and hands …
4:03 PM Changeset [475] by Peter
I dont know what happened, but everything is changed…
3:57 PM Changeset [474] by Peter
adding Target and AveragerPairWeighted?
3:44 PM Changeset [473] by Peter
fixed the bugs!
11:59 AM Ticket #34 (implement << for std::vector) created by Peter

Dec 20, 2005:

9:28 PM Changeset [472] by Jari Häkkinen
Added mr Markus.
12:35 PM Ticket #21 (General view for vector and matrix) closed by Jari Häkkinen
fixed: Fixed by Peter. See classifier classes that implements general views, …
12:29 PM Ticket #33 (reimplement ROC::score_weighted) created by Peter
Speed up the implementation by first sorting the data and then use the …

Dec 19, 2005:

9:30 PM Changeset [471] by Peter
fixed ROC
8:46 PM Changeset [470] by Peter
compiling 3 tests fail
3:58 PM Changeset [469] by Peter
non compiling checking before revision after design meeting

Dec 18, 2005:

10:49 PM Ticket #16 (save and load SVM) closed by Peter
wontfix
10:47 PM Ticket #32 (add sensitivity to SVM) created by Peter
Given a training the SVM should be able to tell what inputs are …

Dec 17, 2005:

5:53 AM Ticket #31 (add Permutation test for weighted Score) created by Peter
Add this function in base class taking target, value, weight, and …
2:15 AM Changeset [468] by Peter
made gslapi::vector inherit from VectorAbstract?
1:59 AM Changeset [467] by Peter
added VectorView? and VectorAbstract?
1:07 AM Changeset [466] by Peter
Creating a private branch
12:19 AM Changeset [465] by Peter
implemented score for WilcoxonFoldChange?

Dec 16, 2005:

11:15 PM Changeset [464] by Peter
made median template
10:19 PM Ticket #30 (ConsensusInputRanker: move CrossSplitting ) created by Peter
CrossSplitting? should be created outside and sent in to the object. …
7:13 PM Ticket #29 (NaN in weighted statistics and Score) created by Peter
In all the weighted functionality a value x is accompanied by a weight …
6:59 PM Changeset [463] by Peter
fixed bug in KernelView? constructor and updated tests
6:02 PM Changeset [462] by Peter
changed link to svnstat plot to my place
4:34 PM Changeset [461] by Peter
?
1:40 PM Changeset [460] by Peter
changed name of class
1:38 PM Changeset [459] by Peter
only one class per line in Makefile.am
1:20 PM Changeset [458] by Markus Ringnér
namespace svm changed to classifier
1:20 PM Changeset [457] by Markus Ringnér
1:19 PM Changeset [456] by Markus Ringnér
Updated to use DataViews?
1:19 PM Changeset [455] by Markus Ringnér
Adding classes to support general views of matrices (and kernels). …
12:31 PM Ticket #28 (speed up CrossSplitting) created by Peter
Redesigned the whole thing
11:43 AM Changeset [454] by Markus Ringnér
Added class for Nearest Centroid Classifier

Dec 15, 2005:

10:49 PM Changeset [453] by Peter
changed namespace svm to classifier in test
10:32 PM Changeset [452] by Peter
it should compile now
10:09 PM Changeset [451] by Peter
directory svm -> classifier
9:59 PM Changeset [450] by Peter
starting to move namespace svm, it wont work compiling for a while, …
9:11 PM Ticket #15 (Copy constructor for SVM) closed by Peter
fixed: Done. some member variables are copied shallow, so the constructor …
9:08 PM Ticket #25 (approximative calculation of p-value in Fisher's exact test) closed by Peter
fixed: Default is to use the approximation when all elements are at least 10.
9:06 PM Changeset [449] by Peter
added approximative p-value calculation using Chi2, fixed some bugs, …
9:03 PM Ticket #27 (Create Classifier::Ensemble) created by Peter
8:05 PM Changeset [448] by Peter
oops, at least compiling now
7:51 PM Changeset [447] by Peter
added copy constructor for KernelView? and added construction of …
7:20 PM Ticket #26 (throw exception in statistics::Fisher) created by Peter
6:16 PM Ticket #12 (Implement copy constructor for SVM::KernelView) closed by Peter
fixed: Not really coherent with vector, but a copy of a view is just a copy …
6:11 PM Changeset [446] by Peter
added copy constructor for KernelView? and added construction of …
5:52 PM Changeset [445] by Peter
added reset function and copy constructor to SVM
5:20 PM Changeset [444] by Markus Ringnér
cosmetic change of printout
4:28 PM Changeset [443] by Jari Häkkinen
Added missing virtual destructors.
3:17 PM Changeset [442] by Jari Häkkinen
Added include of needed header files.
3:14 PM Changeset [441] by Jari Häkkinen
Added include of cassert
3:11 PM Changeset [440] by Jari Häkkinen
Added include of cassert
2:43 PM Ticket #14 (add reset function to SVM) closed by Peter
fixed: Done! sets alpha_ to Zero and trained_=false
1:46 PM Changeset [439] by Markus Ringnér
Fixed istream parsing when separator is last on line: a trailing NaN …
10:10 AM Changeset [438] by Markus Ringnér
Fixed the test for checking for unexpected characters in vector …
9:32 AM Changeset [437] by Jari Häkkinen
Minor style fixes.
12:28 AM Changeset [436] by Markus Ringnér
Added support for NaN:s in read_to_int and read_to_double. Added …
12:25 AM Changeset [435] by Markus Ringnér
Changed to using stringstreams when checking types for strings
12:23 AM Changeset [434] by Markus Ringnér
Modified istream constructors to support both the old format and CSV …

Dec 14, 2005:

7:54 PM Ticket #24 (Averager classes should have constructors taking gslapi::vectors) closed by Peter
fixed: implemented (by MR) as a function (add).
5:13 PM Ticket #25 (approximative calculation of p-value in Fisher's exact test) created by Peter
use Chi2 approximation. interface in line with ROC class how to change …

Dec 13, 2005:

3:51 PM Changeset [433] by Markus Ringnér
Added member function to add all values in a gsl vector
3:49 PM Changeset [432] by Markus Ringnér
Added operator<< for pairs
3:48 PM Changeset [431] by Markus Ringnér
Added sort elements member function

Dec 12, 2005:

5:50 PM Ticket #24 (Averager classes should have constructors taking gslapi::vectors) created by Peter

Dec 9, 2005:

12:07 AM Ticket #23 (redesign OnedimensionalWeighted) created by Peter
redesign Regression::OnedimensionalWeighted? and its daughters. …

Dec 8, 2005:

11:53 PM Ticket #9 (theplu::statistics::regression::Local::fit (std::ostream &s, const ...) closed by Peter
fixed
11:53 PM Changeset [430] by Peter
changed interface of Regression::Local
8:51 PM Ticket #4 (Split weighted and non-weighted regressors) closed by Peter
fixed
8:50 PM Changeset [429] by Peter
separating weighted and non-weighted regression to different classes.
6:11 PM Ticket #22 (Implement class AveragerPairWeighted) created by Peter
Functions should fulfill the following: 1) all weights equal to unity …
5:20 PM Changeset [428] by Peter
improved doc in Score
4:47 PM Ticket #19 (Averager.n() return unsigned ) closed by Peter
fixed
4:46 PM Changeset [427] by Peter
modified Averagers so their size in unsigned
1:07 PM Ticket #21 (General view for vector and matrix) created by Peter
In GSL views are only supported for limited cases. A general view …

Dec 7, 2005:

7:59 PM Ticket #20 (implement WilcoxonFoldChange) created by Peter
At time being the non-weighted score is implemented in the naive way …
3:39 PM Changeset [426] by Jari Häkkinen
Removed obsolete branch (merged into trunk).
3:19 PM Ticket #11 (random class does not accept seed!!!) closed by Jari Häkkinen
fixed: The underlying rng had already support for setting seed. Added support …
3:14 PM Changeset [425] by Jari Häkkinen
Fixed bug in DiscreteUniform?. Added seeding support for classes …
3:09 PM WikiStart edited by Jari Häkkinen
(diff)
11:01 AM Changeset [424] by Jari Häkkinen
Fixed documentation and moved around code.

Dec 6, 2005:

6:44 PM Ticket #19 (Averager.n() return unsigned ) created by Peter
number of data points is never negative, so the function should return …

Dec 2, 2005:

3:42 PM Changeset [423] by Jari Häkkinen
Fixed gnuplot to generate png.
12:39 PM Changeset [422] by Peter
Fixed statistics script. png generation must be fixed.
1:30 AM Ticket #18 (const vector matrix::operator*(const vector&) const) created by Jari Häkkinen
Non-sense implementation is currently implemented. Remove it or fix it.
1:28 AM Changeset [421] by Jari Häkkinen
Created non-sense matrix*vector operator.
1:15 AM Changeset [420] by Jari Häkkinen
Merged better_matrix_class changes r402:419 into the trunk.
12:52 AM Changeset [419] by Jari Häkkinen
Added more matrix tests.
12:52 AM Changeset [418] by Jari Häkkinen
Made output from matrix and vector coherrent.
12:05 AM Ticket #5 (Does this view work properly) closed by Jari Häkkinen
fixed
12:00 AM Ticket #17 (constness of views do not work ... or do they?) created by Jari Häkkinen
In test/matrix_test.cc there is a test that examines what happens when …

Dec 1, 2005:

11:20 PM Changeset [417] by Jari Häkkinen
Fixed delete bug in matrix dextructor, added more matrix tests.
9:54 PM Changeset [416] by Jari Häkkinen
Made knni_matrix.data file somewhat irregular.
4:52 PM Changeset [415] by Jari Häkkinen
Removed some gslapi copy intensive operators. Made gslapi assignment …
4:42 PM Ticket #3 (Restrict access to vector and matrix internal GSL stuff) closed by Jari Häkkinen
wontfix: Access to the internal GSL structures must be allowed since other …
4:38 PM Ticket #16 (save and load SVM) created by Peter
Define format how to save an trained SVM with corresponding kernel and data
4:35 PM Ticket #15 (Copy constructor for SVM) created by Peter
4:33 PM Ticket #14 (add reset function to SVM) created by Peter
sets all alpha to zero and makes SVM untrained
4:31 PM Ticket #13 (Go through SMO code in SVM.train) created by Peter
Look for and remove unwanted copying, a general speed up
4:25 PM Ticket #12 (Implement copy constructor for SVM::KernelView) created by Peter
Should it be a view or a reel copy? Be coherent with vector view
4:17 PM Changeset [414] by Peter
adding FoldChange? class and fixing bugs in Score classes

Nov 30, 2005:

10:35 PM Changeset [413] by Jari Häkkinen
All check passes, but more matrix checks needed.
6:58 PM Changeset [412] by Peter
fixing bug with window in both ends
5:20 PM Changeset [411] by Jari Häkkinen
Move todo items to trac.
5:06 PM Ticket #11 (random class does not accept seed!!!) created by Jari Häkkinen
The same seed is always used!
5:02 PM Ticket #10 (theplu::utility::read_to_double (std::istream &is, std::vector< double ...) created by Jari Häkkinen
Change the implementation of this function to follow C/C++ style …
3:11 PM Changeset [410] by Peter
removed p-value from Score baseclass interface
12:08 PM Ticket #9 (theplu::statistics::regression::Local::fit (std::ostream &s, const ...) created by Jari Häkkinen
Change interface. Make class contain pointers to the regressors.
12:01 PM Ticket #8 (Member theplu::random::DiscreteUniform::DiscreteUniform (const u_long n)) created by Jari Häkkinen
Exception should be thrown, when n is out of range. This applies for …
11:54 AM Ticket #7 (Document theplu::utility::IO_error) created by Jari Häkkinen
11:49 AM Ticket #6 (Rework theplu::statistics::AveragerWeighted) created by Jari Häkkinen
Check the implementation. Add link to peters stats_weighted.tex …
11:40 AM Ticket #5 (Does this view work properly) created by Jari Häkkinen
Check what happens with const gslapi::vector get_eigenvector( …
11:38 AM Ticket #4 (Split weighted and non-weighted regressors) created by Peter
Vi var ju inte nöjda med regression interfacet. Till den diskussionen …

Nov 28, 2005:

1:15 AM Changeset [409] by Jari Häkkinen
More view fixing.
12:40 AM Changeset [408] by Jari Häkkinen
Continued fixing with views related to matrix.

Nov 27, 2005:

11:40 PM Changeset [407] by Jari Häkkinen
Added documentation. Started with view implementation.
11:39 PM Changeset [406] by Jari Häkkinen
Polished code and documentation, removed inclusion of nonused header files.
11:35 PM Changeset [405] by Jari Häkkinen
Minor change to IO_error exception.
1:31 AM Changeset [404] by Jari Häkkinen
gslapi compiles, but matrix.cc not complete.
1:26 AM Changeset [403] by Jari Häkkinen
Updated matrix class, but matrix view not considered yet.

Nov 26, 2005:

10:16 PM Ticket #3 (Restrict access to vector and matrix internal GSL stuff) created by Jari Häkkinen
Maybe the gslapi interface should be changed so that internal GSL …
9:54 PM Ticket #2 (Add exceptions to gsl usage) created by Jari Häkkinen
The error conditions of underlying GSL calls should be reported back …
4:04 PM Changeset [402] by Jari Häkkinen
Created branch for fixing of the matrix class.

Nov 25, 2005:

7:37 PM Ticket #1 (Checking of write permissions to files in FileIO does not work) created by Jari Häkkinen
A call like FileIO().access_rights("filename","w") will complain about …
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