Commits

Branch selector

 main

User selector

All users

Datepicker

All time

Commit History

Commits on Jan 6, 2025

• Merge pull request #9 from mtrsl/some_tidying

  Show description for f880427
  jhellewell14

  authored
  f880427

  Copy full SHA for f880427

Commits on Dec 19, 2024

• Simplify random_vector

  mtrsl

  committed
  83e0839

  Copy full SHA for 83e0839

• Remove unneeded type annotations; remove some u...

  Show description for 543d004
  mtrsl

  committed
  543d004

  Copy full SHA for 543d004

• Use nice ndarray type aliases instead of full type names

  mtrsl

  committed
  0236549

  Copy full SHA for 0236549

Commits on Dec 16, 2024

• Huge changes as I tried to make tree moves use an iterator, broke everything, fixed it again finally

  jhellewell14

  committed
  702ad73

  Copy full SHA for 702ad73

Commits on Dec 4, 2024

• Was not using rate matrix values after it had potentially been updated by a TreeMove

  jhellewell14

  committed
  f1fdbdf

  Copy full SHA for f1fdbdf

• Rewrote move apply method for TreeState as an implementation of an Iterator

  jhellewell14

  committed
  476a28c

  Copy full SHA for 476a28c

Commits on Dec 2, 2024

• Added a branchlength move

  jhellewell14

  committed
  cca6fe3

  Copy full SHA for cca6fe3

Commits on Nov 29, 2024

• Lots of cleaning up old code and fixing clippy suggestions

  jhellewell14

  committed
  cadebdc

  Copy full SHA for cadebdc

• All Topology moves now have the TreeMove trait

  jhellewell14

  committed
  22ead15

  Copy full SHA for 22ead15

• Integrating new TreeState struct and TreeMove trait into code

  jhellewell14

  committed
  d1edf0b

  Copy full SHA for d1edf0b

• Wrote a load of code in lib.rs that generalises applying move functions to work with moves on the topoology and the rate matrix

  jhellewell14

  committed
  49e0bb4

  Copy full SHA for 49e0bb4

Commits on Nov 27, 2024

• fixing tests

  jhellewell14

  committed
  add74da

  Copy full SHA for add74da

• Added rate matrix update move, need to think more on how moves should propose new parameters

  jhellewell14

  committed
  8fcad35

  Copy full SHA for 8fcad35

Commits on Nov 26, 2024

• Added implemention for RateMatrix trait that does a matrix move for evolutionary model inference

  jhellewell14

  committed
  7aa644b

  Copy full SHA for 7aa644b

Commits on Nov 21, 2024

• Fixed child swap move code. Was not updating node depths in the subtrees that were moved. This was then producing incorrect Newick Strings that could not be converted to a new integer tree vector

  jhellewell14

  committed
  44624fc

  Copy full SHA for 44624fc

Commits on Nov 20, 2024

• Half way through adding new Topology move type that I think makes more sense than nearest neighbour for binary trees. I choose a node and swap one of its children with the node's parent

  jhellewell14

  committed
  d5ac120

  Copy full SHA for d5ac120

Commits on Nov 15, 2024

• Fixing discrepancies between number of sequences and resulting genetic data structure size

  jhellewell14

  committed
  1071f17

  Copy full SHA for 1071f17

Commits on Nov 12, 2024

• Fixed likelihood tests for new data format. Added a function that creates random dummy genetic data

  jhellewell14

  committed
  09d046f

  Copy full SHA for 09d046f

Commits on Oct 31, 2024

• initial go at nearest neighbour interchange MoveFn in new data structure

  jhellewell14

  committed
  cf08062

  Copy full SHA for cf08062

• Fixed optimisation code in lib.rs

  jhellewell14

  committed
  d30e1ad

  Copy full SHA for d30e1ad

• Added peturb vector MoveFn, put moves in their own file

  jhellewell14

  committed
  fe55757

  Copy full SHA for fe55757

• Wrote functions to apply move functions (with corresponding trait)

  jhellewell14

  committed
  9b82761

  Copy full SHA for 9b82761

Commits on Oct 28, 2024

• Huge underlying changes to data structure. Separated tree topology into Topology struct and corresponding iterators over the tree. Genetic data now in a 3d array indexed by [sample, loci, likelihoo…

  Show description for 4542e03
  jhellewell14

  committed
  4542e03

  Copy full SHA for 4542e03

Commits on Oct 10, 2024

• Build was failing because I hadn't pushed Cargo.toml changes

  jhellewell14

  committed
  19d5926

  Copy full SHA for 19d5926

Commits on Oct 9, 2024

• Added Tree method to do NNI. At the moment it just does a NNI. What I really need is for it to suggest a NNI, calculate the likelihood, and then accept or reject it

  jhellewell14

  committed
  fbbe614

  Copy full SHA for fbbe614

Commits on Oct 1, 2024

• Added Tree method to get all branch lengths in an nalgebra Vector so that it can be used with an optimiser

  jhellewell14

  committed
  3468ab3

  Copy full SHA for 3468ab3

Commits on Sep 27, 2024

• Added JC69 evolution model

  jhellewell14

  committed
  0623118

  Copy full SHA for 0623118

Commits on Sep 26, 2024

• Introduced a RateMatrix trait that will allow us to define multiple nucleotide evolution models

  jhellewell14

  committed
  c8790d6

  Copy full SHA for c8790d6

Commits on Sep 25, 2024

• The Tree struct now has a RateParam struct that can be used to update a rate_matrix. Trees initialise with a default RateParams. Likelihood functions no longer require an external rate matrix and n…

  Show description for 362e3db
  jhellewell14

  committed
  362e3db

  Copy full SHA for 362e3db

Commits on Sep 24, 2024

• Wrote function that creates GTR rate matrix from parameters. Can eventually become Tree method

  jhellewell14

  committed
  0f2387c

  Copy full SHA for 0f2387c

Commits on Jul 26, 2024

• Fixed main and checked that cargo test and run are working

  jhellewell14

  committed
  b5cb135

  Copy full SHA for b5cb135

• Pushing local changes that I can't remember

  jhellewell14

  committed
  ed3b6a8

  Copy full SHA for ed3b6a8

Commits on May 27, 2024

• Added common likelihood calculations to a HashMap with an ill-advised hash function

  jhellewell14

  committed
  ecda594

  Copy full SHA for ecda594

• Added method to test Mutation equality

  jhellewell14

  committed
  4fc1c6d

  Copy full SHA for 4fc1c6d

Pagination

Previous

Next