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Remove dev pav bug #93

Merged
merged 3 commits into from
Oct 15, 2023
Merged

Remove dev pav bug #93

merged 3 commits into from
Oct 15, 2023

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vergep
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@vergep vergep commented Oct 15, 2023

pull 'remove_devPAV_bug' into 'TLM'

akaIDIOT and others added 3 commits September 15, 2023 17:49
@akaIDIOT
Set release stage to use auth token specific to the lir package (#76)
1c43984 
Org-wide password was updated, projects will get their own tokens.
Bump version to 0.1.24
0391655
@vergep
fixed bug in detection of pathological cases in devPAV
fcafeb7 
- made new detection of pathological cases
- created output for pathological cases
- adjusted tests
@vergep vergep merged commit 4423990 into TLM Oct 15, 2023
wowtor added a commit that referenced this pull request Oct 25, 2023
@wowtor
Squashed commit of the following:
9c6b276 
commit 1b659b6
Author: wb <20113294+wowtor@users.noreply.github.com>
Date:   Wed Oct 25 15:36:06 2023 +0200

    static methods

commit 4ae11b2
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Oct 19 15:40:36 2023 +0200

    corrected path definitions

commit 210b879
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Oct 19 15:18:56 2023 +0200

    changed datadirectory from data to recources

commit a14ad9a
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Oct 19 14:57:40 2023 +0200

    removed redundant 'dummmy' file and added pandas to setup.py

commit 203317f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Oct 19 14:52:21 2023 +0200

    bugfix: in predict_proba changed return array.reshape to np.transpose (array)

commit 0c71c5f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Oct 17 12:17:47 2023 +0200

    some cosmetics

commit 71926bf
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Oct 17 09:13:00 2023 +0200

    fixed bug in predict_proba

commit dca5bd7
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Oct 16 16:55:48 2023 +0200

    added some more comments

commit 80bff2e
Merge: e42990e 4423990
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Oct 16 16:16:46 2023 +0200

    Merge branch 'TLM' of https://github.com/NetherlandsForensicInstitute/lir into TLM

commit 4423990
Merge: 65bd6e4 fcafeb7
Author: vergep <65766436+vergep@users.noreply.github.com>
Date:   Sun Oct 15 15:45:39 2023 +0200

    Merge pull request #93 from NetherlandsForensicInstitute/remove_devPAV_bug

    Remove dev pav bug

commit e42990e
Merge: e617afb fcafeb7
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Sun Oct 15 15:28:23 2023 +0200

    Merge branch 'remove_devPAV_bug' into TLM

commit fcafeb7
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Sun Oct 15 15:26:19 2023 +0200

    fixed bug in detection of pathological cases in devPAV
    - made new detection of pathological cases
    - created output for pathological cases
    - adjusted tests

commit 65bd6e4
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Mon Oct 9 15:04:31 2023 +0200

    Removed ValueError for difference in shapes of references and traces.

commit 8cd06bc
Merge: e617afb c423bfe
Author: vergep <65766436+vergep@users.noreply.github.com>
Date:   Mon Oct 9 13:17:28 2023 +0200

    Merge pull request #91 from NetherlandsForensicInstitute/predict_log10_LR

    TwoLevelModelNormalKDE class and functions ready for review

commit c423bfe
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Oct 5 13:47:14 2023 +0200

    predict-lr takes multiple samples

commit f2df21d
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Oct 5 10:42:26 2023 +0200

    clean tests

commit 8fd4837
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Fri Sep 29 15:44:26 2023 +0200

    changed TwoLevelModel to TwoLevelModelNormalKDE and fixed minor bug in fit function

commit f64d508
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Fri Sep 29 15:28:14 2023 +0200

    added check that n_features is the same in train, trace and ref

commit 7169922
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Fri Sep 29 14:58:17 2023 +0200

    added tests for fit&_predict_LLR, fit&transform and fit&predict_proba

commit 7bc2f50
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Fri Sep 29 11:43:08 2023 +0200

    Added script for ln_den_terms to class and test
    Added script for calculation of log10 LRs according to formula in Bolck et al and test

commit 7b1aacc
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 28 17:36:36 2023 +0200

    Made old code working again for debugging new code.
    Added script for ln_num1 to class and test

commit 464a98e
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 28 16:58:39 2023 +0200

    added code and tests for updated_ref_mean (mu_h)

commit 57ee3bd
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Thu Sep 28 14:24:20 2023 +0200

    Renamed the U variables and added some clearer explanation in the docstring. And fixed some minor issues.

commit 8daed0b
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 17:29:38 2023 +0200

    added class Test_TwoLevelModel_predict_functions and performed first test

commit 2b37823
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 16:53:56 2023 +0200

    changed names of TLM folder to 'two_level_model'

commit 329cb96
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 16:53:09 2023 +0200

    changed names of TLM folder to 'two_level_model'

commit 6a3240e
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 16:50:13 2023 +0200

    changed names of data folder to 'resources' and changed names of input data

commit aac38d6
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 16:47:38 2023 +0200

    added between_cov to two_level_model and test

commit 7335ff3
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 16:18:44 2023 +0200

    Added the H0 (between covariance) calculations to the tlm class and test. Not yet functional.

commit 191230f
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 15:51:13 2023 +0200

    Included calculations for kernel bandwidth in the tlm class and test.

commit 9bbae92
Merge: dd04940 1aca264
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 15:32:07 2023 +0200

    merged main TLM branch into this predict_log10_LR branch.

commit 1aca264
Merge: 14dbc2c 6f6517d
Author: camillevandijk <144999965+camillevandijk@users.noreply.github.com>
Date:   Tue Sep 26 15:23:35 2023 +0200

    Merge pull request #80 from NetherlandsForensicInstitute/means_z

    added code for calculation and test of means_z and implemented the comments.

commit 6f6517d
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 15:21:09 2023 +0200

    Removed redundant files

commit c3f1c27
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 15:19:45 2023 +0200

    Added the means function to the tlm class and updated the test accordingly.

commit 96fa48c
Merge: 6a29a8c 14dbc2c
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 15:03:16 2023 +0200

    Merged TLM branch into means_z branch.

commit 14dbc2c
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 11:58:54 2023 +0200

    Incorporated the mean_covariance_within function and the test in the TLM class. Removed previous files.

commit 84c6102
Merge: d3b5fd0 e617afb
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 11:33:36 2023 +0200

    Merge branch 'TLM' into MSwithin

commit d3b5fd0
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 11:31:40 2023 +0200

    added testdata in Routput folder

commit 992f88e
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 26 11:30:43 2023 +0200

    Resolved some comments, added comments, made it more generic and changed function name.

commit 53c4a0f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 10:56:44 2023 +0200

    added testdata in input folder

commit 5316a0f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 10:25:01 2023 +0200

    refined some comments

commit e617afb
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 09:45:05 2023 +0200

    refined some comments

commit caeb251
Merge: bd09fdd b74bafd
Author: vergep <65766436+vergep@users.noreply.github.com>
Date:   Tue Sep 26 09:38:44 2023 +0200

    Merge pull request #84 from NetherlandsForensicInstitute/feature/tlm_base_class

    Create a base class for the two-level model

commit b74bafd
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 26 09:37:39 2023 +0200

    added predict_proba

commit dd04940
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:54:11 2023 +0200

    added line break

commit 76ac4d5
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:53:29 2023 +0200

    added some more comments in TLM_calc_log_10_LR

commit 6eee46a
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:49:24 2023 +0200

    revised some lines in TLM_calc_ln_den_term

commit 7a8bece
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:47:49 2023 +0200

    minor change in comment

commit 6bffdbe
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:47:21 2023 +0200

    changed some divisions to additions through log in TLM_calc_log10_LR. And added some more comments

commit 95f70e2
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:46:00 2023 +0200

    changed some divisions to additions through log

commit ce5b0ab
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:39:02 2023 +0200

    updated some comments

commit 1b5258c
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:37:27 2023 +0200

    updated some comments and run.py

commit 44c76b9
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:33:33 2023 +0200

    made predict LLR function and test for all pairs

commit a838c8b
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 15:05:06 2023 +0200

    caculated and tested first log10_LR comparison, and removed redundant split of two denominator terms since algebra for the two terms is identical

commit 7c88e96
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 14:38:22 2023 +0200

    added calculation and test for natural log of right denominator term of LR in Bolck et al. (natural log of den in R script)

commit 8ae5206
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 14:31:43 2023 +0200

    added calculation and test for natural log of left denominator term of LR in Bolck et al. (natural log of num2 in R script)

commit bc3c3f4
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 14:25:09 2023 +0200

    added calculation and test for natural log of numerator of LR in Bolck et al. (natural log of num1 in R script)

commit 2fafb14
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 12:54:45 2023 +0200

    added calculation of mu_h and test

commit b3a60f1
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 12:53:49 2023 +0200

    added calculation of mu_h

commit 7bdd07d
Merge: 66f3918 ef05093
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 10:37:10 2023 +0200

    Merge branch 'predict_U' of https://github.com/NetherlandsForensicInstitute/lir into predict_U

commit e3d9f94
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 09:08:39 2023 +0200

    added a model description

commit 66f3918
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 25 08:49:35 2023 +0200

    changed some comment

commit d981210
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Sep 21 15:36:03 2023 +0200

    fix test

commit d650016
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Sep 21 15:30:12 2023 +0200

    remove sklearn inheritance and replace predict_proba by transform

commit 77f9e4c
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Sep 21 13:51:53 2023 +0200

    add basic properties

commit a2cb3be
Author: Kim de Bie (DBS) <kim@7zj9vz2-l.holmes.nl>
Date:   Thu Sep 21 09:51:44 2023 +0200

    create branch

commit ef05093
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Wed Sep 20 14:21:34 2023 +0200

    Update comments

commit a8dbec4
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Wed Sep 20 14:14:08 2023 +0200

    Add calculations and test for U_hn. Plus transformed T0 to numpy instead of pandas for consistency.

commit 6052cdf
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Wed Sep 20 12:21:11 2023 +0200

    Added tests for U_h0 and U_hx.

commit 6810345
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 17:10:49 2023 +0200

    added intermediate 'predict' results from R

commit e8ebed5
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 16:54:48 2023 +0200

    calculation of U_h0 and U_hx

commit aa0401e
Author: Camille van Dijk <c.van.dijk@nfi.nl>
Date:   Tue Sep 19 15:50:52 2023 +0200

    Set up of calculations of U0 and UU for the predict part.

commit 4168c5f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 15:47:14 2023 +0200

    input data en R-output data added to git

commit 21e0498
Merge: 8d3a11f 7064b1b
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 14:13:05 2023 +0200

    Merge branch 'h' into T0

    # Conflicts:
    #	lir/classifiers.py
    #	tests/run.py
    #	tests/test_TLM.py

commit 8d3a11f
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 13:56:55 2023 +0200

    script and test for T0

commit 7064b1b
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 10:00:46 2023 +0200

    added some comments

commit 33cabd9
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Tue Sep 19 09:58:17 2023 +0200

    script and test for h^2 calculation

commit 9cd21bd
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 17:00:31 2023 +0200

    work in progress to write function for T0

commit b17b482
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 15:44:06 2023 +0200

    added some comments

commit 1f826aa
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 15:41:09 2023 +0200

    code and test for kappa

commit 6a29a8c
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 13:50:39 2023 +0200

    removed 'z' from calc_means_z

commit f956225
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 13:49:57 2023 +0200

    changed names of columns of covars df to more generic names

commit a2ea89c
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 13:43:45 2023 +0200

    added code for calculation and test of means_z

commit 5725935
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Mon Sep 18 13:34:37 2023 +0200

    removed some unused code in test_TLM.py

commit 9deb3ed
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Fri Sep 15 16:07:33 2023 +0200

    1. Creation of run.py, which contains main script used for debugging.
    2. Script that calculates MSWithin + test script.

commit 37c7416
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 14 15:48:24 2023 +0200

    test geschreven voor MSwithin

commit bd09fdd
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 14 10:08:31 2023 +0200

    werkt dit?

commit 6ea6a44
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 14 10:04:34 2023 +0200

    nieuwe test

commit 0f2d543
Author: Peter Vergeer <p.vergeer@nfi.nl>
Date:   Thu Sep 14 10:02:59 2023 +0200

    dummy file to initialize TLM branch
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2 participants
@vergep @akaIDIOT