Create a base class for the two-level model #84
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added 2 commits
September 21, 2023 09:51
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Ik heb een bescrijving (zo goed mogelijk) van het two-level-model toegevoegd. |
wowtor
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Oct 25, 2023
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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Base class structure/outline for the two-level model.