Commits · 9aaf878a7f6f30fdbaa7bbbcc16f25ab022ba0b1 · VEBER Philippe / codepi

02 Dec, 2020 1 commit
- prc: added visual checks · 9aaf878a
  Philippe Veber authored Dec 02, 2020
  
  9aaf878a
01 Dec, 2020 1 commit
- prc: improved average_precision implementation and fixed tests · dd0615ff
  Philippe Veber authored Nov 30, 2020
  
  dd0615ff
30 Nov, 2020 1 commit
- prc: new (and wrong) implementation of average_position + tests · 0857d270
  Philippe Veber authored Nov 30, 2020
  
  0857d270
29 Nov, 2020 1 commit
- prc: reorganized API · a7f58c54
  Philippe Veber authored Nov 29, 2020
  
  a7f58c54
27 Nov, 2020 1 commit
- prc: more bibliographic references · 9806a257
  Philippe Veber authored Nov 27, 2020
  
  9806a257
26 Nov, 2020 2 commits
- started a note on multinomial · 6c4222e4
  Philippe Veber authored Nov 26, 2020
  
  6c4222e4
- prc: revamped + added interface · 943edcc8
  Philippe Veber authored Nov 26, 2020
  
  943edcc8
25 Nov, 2020 1 commit
- README: updated install instructions · c0ca7c3c
  Philippe Veber authored Nov 25, 2020
  
  c0ca7c3c
24 Nov, 2020 2 commits
- renamed Tamuri into Tdg09 · 9dc0b844
  Philippe Veber authored Nov 24, 2020
  
  9dc0b844
- added in house implementation of TDG09 · 9d0a474a
  Philippe Veber authored Nov 24, 2020
  
  9d0a474a
23 Nov, 2020 6 commits
- moved pair_tree workflow definition to simulation dataset · a8a7d82a
  Philippe Veber authored Nov 23, 2020
  
  a8a7d82a
- tk: moved pair_tree generation to Convergence_tree · aff077d9
  Philippe Veber authored Nov 23, 2020
  
  aff077d9
- tk/Convergence_tree.leaves: leave it be more general to be useful for more tree variants · 09144976
  Philippe Veber authored Nov 23, 2020
  
  09144976
- tk/Candidate_site: equivalent but more strictly typed reformulation · 8471965d
  Philippe Veber authored Nov 23, 2020
  
  8471965d
- Simulation_dataset: added nhx_of_convergence_tree · c2c0c1e0
  Philippe Veber authored Nov 23, 2020
  
  c2c0c1e0
- tk/Tdg09: expose default implementation · f3ec331f
  Philippe Veber authored Nov 22, 2020
  
  f3ec331f
22 Nov, 2020 6 commits
- renaming · 87b4f2e6
  Philippe Veber authored Nov 22, 2020
  
  87b4f2e6
- tk: import Tdg09 from phylogenetics · c3de289d
  Philippe Veber authored Nov 22, 2020
  
  c3de289d
- import Profile_tsv and drop dep on phylogenetics.convergence · c9ac8bf2
  Philippe Veber authored Nov 22, 2020
  
  c9ac8bf2
- tk: move all range-related functions in its module · 317e7ede
  Philippe Veber authored Nov 22, 2020
  
  317e7ede
- app/Lmm_benchmark: upgrade wrt lib · 03742957
  Philippe Veber authored Nov 22, 2020
  
  03742957
- tk/Multinomial_test: added a permutation test · 6815030e
  Philippe Veber authored Nov 22, 2020
  
  6815030e
21 Nov, 2020 8 commits
- tk/Multinomial_test.chisq: heuristic for sparse counts · 5b2db384
  Philippe Veber authored Nov 21, 2020
  
  5b2db384
- tk/Multinomial_test.uniformity_test: opt to reject sites with single AA · a90765e5
  Philippe Veber authored Nov 21, 2020
  
  a90765e5
- tk/Multinomial_test: fixed data non-zero count · 33746acc
  Philippe Veber authored Nov 21, 2020
  
  33746acc
- whitespacecommit · 6546c73e
  Philippe Veber authored Nov 21, 2020
  
  6546c73e
- dune: declare codepi and codepitk as public · 2b8b8142
  Philippe Veber authored Nov 21, 2020
  
  2b8b8142
- tk/Multinomial_test: added chi-squared test implementation · d8691ea5
  Philippe Veber authored Nov 21, 2020
  
  d8691ea5
- update dune version · efa16120
  Philippe Veber authored Nov 21, 2020
  
  efa16120
- tk/Multinomial_test: added a degree of freedom correction heuristic for lrt · 6b3eecf2
  Philippe Veber authored Nov 20, 2020
```
it is based on the assumption of Wilks theorem that the maximum
likelihood estimate shouldn't lie at the border of the parameter
space.
```
  6b3eecf2
20 Nov, 2020 2 commits
- dune-project: add Louis to author list · bc7ef385
  Philippe Veber authored Nov 20, 2020
  
  bc7ef385
- update wrt bistro · 69e06469
  Philippe Veber authored Nov 20, 2020
  
  69e06469
19 Nov, 2020 5 commits
- renamed tk/Multinomial into Multinomial_test · 47ecba26
  Philippe Veber authored Nov 19, 2020
  
  47ecba26
- included multinomial test from phylogenetics_convergence · 8f0cb4f6
  Philippe Veber authored Nov 19, 2020
  
  8f0cb4f6
- multinomial: refactoring · f9f89f6e
  Philippe Veber authored Nov 19, 2020
  
  f9f89f6e
- new tk/Multinomial module · eb3f23a1
  Philippe Veber authored Nov 19, 2020
  
  eb3f23a1
- update wrt phylogenetics · 5ea7464a
  Philippe Veber authored Nov 19, 2020
  
  5ea7464a
17 Nov, 2020 3 commits
- Merge branch 'simulation-dataset-refactoring' · 1ece636f
  Philippe Veber authored Nov 17, 2020
  
  1ece636f
- Multinomial: fixed labels of CPT file · 5eba3f41
  Philippe Veber authored Nov 17, 2020
  
  5eba3f41
- removed buggy version of multinomial · e594f2a8
  Philippe Veber authored Nov 17, 2020
  
  e594f2a8