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Bayes #23

Closed
wants to merge 68 commits into from
Closed

Bayes #23

wants to merge 68 commits into from

Commits on Sep 22, 2023

  1. Add files for listing children and subtrees

    @laukeller
    laukeller committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. added simulation of trees and comparison plots (not correct yet)

    @laukeller
    laukeller committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. removed plots and warmup directory, added plotting/csv related files … 

    …& _simulate.py
    @laukeller
    laukeller committed Sep 26, 2023
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Commits on Sep 27, 2023

  1. Merge branch 'main' into warmup

    @pawel-czyz
    pawel-czyz authored Sep 27, 2023
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  2. changed _simulate.py, write_csv.py and created a few unit tests

    @laukeller
    laukeller committed Sep 27, 2023
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  3. Merge branch 'warmup' of github.com:cbg-ethz/pMHN into warmup

    @laukeller
    laukeller committed Sep 27, 2023
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  4. changed comment in _simulate.py

    @laukeller
    laukeller committed Sep 27, 2023
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  5. minor changes

    @laukeller
    laukeller committed Sep 27, 2023
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Commits on Sep 28, 2023

  1. moved files to warmup dir

    @laukeller
    laukeller committed Sep 28, 2023
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  2. remove not needed files

    @laukeller
    laukeller committed Sep 28, 2023
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  3. change: draw new sampling time if tree is discarded, mean_sampling_ti… 

    …me now passed as an argument
    @laukeller
    laukeller committed Sep 28, 2023
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  4. reformatted files with black

    @laukeller
    laukeller committed Sep 28, 2023
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  5. changed unit tests

    @laukeller
    laukeller committed Sep 28, 2023
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Commits on Sep 29, 2023

  1. reformat with black

    @laukeller
    laukeller committed Sep 29, 2023
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  2. Merge branch 'main' of github.com:cbg-ethz/pMHN 

    PR approved?
    @laukeller
    laukeller committed Sep 29, 2023
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  3. Merge branch 'warmup' 

    PR approved?
    @laukeller
    laukeller committed Sep 29, 2023
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Commits on Sep 30, 2023

  1. Remove poetry.lock

    @pawel-czyz
    pawel-czyz committed Sep 30, 2023
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  2. fixed ruff errors

    @laukeller
    laukeller committed Sep 30, 2023
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  3. fixed ruff errors

    @laukeller
    laukeller committed Sep 30, 2023
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  4. Merge branch 'warmup' of github.com:cbg-ethz/pMHN into warmup

    @laukeller
    laukeller committed Sep 30, 2023
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  5. Merge branch 'warmup' 

    all errors should be fixed now.
    @laukeller
    laukeller committed Sep 30, 2023
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  6. pyright fixed

    @laukeller
    laukeller committed Sep 30, 2023
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  7. Merge branch 'warmup'

    @laukeller
    laukeller committed Sep 30, 2023
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Commits on Oct 4, 2023

  1. modified _backend and added _tree_utils, created unit tests for both

    @laukeller
    laukeller committed Oct 4, 2023
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Commits on Oct 7, 2023

  1. added files for likelihood comparison, changed absolute paths to rela… 

    …tive paths, created modified_io, added 1e-10 to return value of likelihood function
    @laukeller
    laukeller committed Oct 7, 2023
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  2. small change

    @laukeller
    laukeller committed Oct 7, 2023
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Commits on Oct 8, 2023

  1. added likelihood tests, modified test_tree_utils.py

    @laukeller
    laukeller committed Oct 8, 2023
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Commits on Oct 9, 2023

  1. minor changes

    @laukeller
    laukeller committed Oct 9, 2023
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  2. minor change

    @laukeller
    laukeller committed Oct 9, 2023
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Commits on Oct 12, 2023

  1. implemented 2 new versions of the likelihood calculation which relies… 

    … on _tree_utils_new.py
    @laukeller
    laukeller committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. memoization for finding all subtrees

    @laukeller
    laukeller committed Oct 13, 2023
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  2. implemented suggestions from pawel

    @laukeller
    laukeller committed Oct 13, 2023
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  3. merge

    @laukeller
    laukeller committed Oct 13, 2023
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Commits on Oct 16, 2023

  1. minor changes

    @laukeller
    laukeller committed Oct 16, 2023
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  2. small change

    @laukeller
    laukeller committed Oct 16, 2023
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  3. small change

    @laukeller
    laukeller committed Oct 16, 2023
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Commits on Oct 17, 2023

  1. small change

    @laukeller
    laukeller committed Oct 17, 2023
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  2. small change

    @laukeller
    laukeller committed Oct 17, 2023
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  3. small change

    @laukeller
    laukeller committed Oct 17, 2023
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Commits on Oct 18, 2023

  1. changed io file and unit tests for it

    @laukeller
    laukeller committed Oct 18, 2023
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Commits on Oct 20, 2023

  1. genotype

    @laukeller
    laukeller committed Oct 20, 2023
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Commits on Oct 21, 2023

  1. small change

    @laukeller
    laukeller committed Oct 21, 2023
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  2. small change

    @laukeller
    laukeller committed Oct 21, 2023
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Commits on Oct 22, 2023

  1. small change in _tree_utils_geno.py

    @laukeller
    laukeller committed Oct 22, 2023
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  2. small change in diag_entry

    @laukeller
    laukeller committed Oct 22, 2023
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  3. small change in diag_entry function

    @laukeller
    laukeller committed Oct 22, 2023
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  4. small change in _tree_utils.py (memoization not needed)

    @laukeller
    laukeller committed Oct 22, 2023
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  5. small change

    @laukeller
    laukeller committed Oct 22, 2023
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Commits on Oct 23, 2023

  1. implemented pawel's suggestions

    @laukeller
    laukeller committed Oct 23, 2023
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  2. resolve conflicts

    @laukeller
    laukeller committed Oct 23, 2023
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  3. resolve conflicts

    @laukeller
    laukeller committed Oct 23, 2023
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Commits on Oct 25, 2023

  1. Merge branch 'main' into likelihood_optimized

    @laurenzkeller
    laurenzkeller authored Oct 25, 2023
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  2. resolve conflicts

    @laukeller
    laukeller committed Oct 25, 2023
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  3. created treemhn-bayes.smk, added method loglikelihood_tree_list to _b… 

    …ackend_geno, created _treemhn.py file which contains the TreeMHNLoglikelihood class
    @laukeller
    laukeller committed Oct 25, 2023
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Commits on Oct 27, 2023

  1. generated a few plots, modified treemhn-bayes.smk

    @laukeller
    laukeller committed Oct 27, 2023
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Commits on Oct 28, 2023

  1. add files

    @laukeller
    laukeller committed Oct 28, 2023
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  2. add data

    @laukeller
    laukeller committed Oct 28, 2023
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  3. add data

    @laukeller
    laukeller committed Oct 28, 2023
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  4. 1 chain instead of

    @laukeller
    laukeller committed Oct 28, 2023
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  5. deleted config.yaml

    @laukeller
    laukeller committed Oct 28, 2023
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Commits on Oct 30, 2023

  1. plots for 10 patients, 10 mutations

    @laukeller
    laukeller committed Oct 30, 2023
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  2. created summary statistics and trace plots

    @laukeller
    laukeller committed Oct 30, 2023
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  3. added plots

    @laukeller
    laukeller committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. added plots

    @laukeller
    laukeller committed Oct 31, 2023
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  2. plots

    @laukeller
    laukeller committed Oct 31, 2023
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  3. modified treemhn_bayes_v3

    @laukeller
    laukeller committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. add current version of bayes branch

    @laukeller
    laukeller committed Nov 1, 2023
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  2. small change

    @laukeller
    laukeller committed Nov 1, 2023
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