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add inference #79

Merged
merged 59 commits into from
Oct 16, 2024
Merged

add inference #79

merged 59 commits into from
Oct 16, 2024

Commits on Feb 23, 2023

  1. Add inference and testing

    @ejd99
    ejd99 committed Feb 23, 2023
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Commits on Feb 24, 2023

  1. remove test/

    @ejd99
    ejd99 committed Feb 24, 2023
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  2. add phylolm

    @ejd99
    ejd99 committed Feb 24, 2023
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Commits on Feb 28, 2023

  1. add inference example

    @ejd99
    ejd99 committed Feb 28, 2023
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Commits on Mar 1, 2023

  1. hopefully will now pass tests

    @ejd99
    ejd99 committed Mar 1, 2023
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  2. include global skipR

    @ejd99
    ejd99 committed Mar 1, 2023
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Commits on Mar 14, 2023

  1. added estimaterates!

    @ejd99
    ejd99 committed Mar 14, 2023
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Commits on Mar 29, 2023

  1. Updated estimaterates, all info is on the tree

    @ejd99
    ejd99 committed Mar 29, 2023
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Commits on Apr 5, 2023

  1. add lambda calcs

    @ejd99
    ejd99 committed Apr 5, 2023
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Commits on Apr 16, 2023

  1. Merge branch 'rr/getnodesfix' into ejd/inference

    @richardreeve
    richardreeve committed Apr 16, 2023
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  2. Merge branch 'rr/getnodesfix' into ejd/inference

    @richardreeve
    richardreeve committed Apr 16, 2023
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  3. Fix inference testing

    @richardreeve
    richardreeve committed Apr 16, 2023
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  4. examples folder needs manifest

    @richardreeve
    richardreeve committed Apr 16, 2023
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  5. Only compare to R if packages are installed

    @richardreeve
    richardreeve committed Apr 16, 2023
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  6. Update workflows

    @richardreeve
    richardreeve committed Apr 16, 2023
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Commits on Apr 23, 2023

  1. Merge branch 'rr/getnodesfix' into ejd/inference

    @richardreeve
    richardreeve committed Apr 23, 2023
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Commits on Apr 24, 2023

  1. Minor fixes to type stability

    @richardreeve
    richardreeve committed Apr 24, 2023
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  2. Switch from Dict to a struct for trait storage

    @richardreeve
    richardreeve committed Apr 24, 2023
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Commits on Apr 26, 2023

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve committed Apr 26, 2023
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Commits on Aug 2, 2023

  1. fix problems with estimaterates and clean examples

    @ejd99
    ejd99 committed Aug 2, 2023
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Commits on Oct 27, 2023

  1. mult lambda

    @ejd99
    ejd99 committed Oct 27, 2023
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  2. manifest and project

    @ejd99
    ejd99 committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve committed Oct 30, 2023
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Commits on Nov 25, 2023

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve committed Nov 25, 2023
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Commits on Dec 7, 2023

  1. Merge branch 'dev' into ejd/inference 

    # Conflicts:
#	Project.toml
#	src/API.jl
    @richardreeve
    richardreeve committed Dec 7, 2023
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  2. Fix authorship list

    @richardreeve
    richardreeve committed Dec 7, 2023
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  3. multi lambda

    @ejd99
    ejd99 committed Dec 7, 2023
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  4. Merge branch 'ejd/inference' of https://github.com/EcoJulia/Phylo.jl … 

    …into ejd/inference
    @ejd99
    ejd99 committed Dec 7, 2023
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  5. fix tests

    @ejd99
    ejd99 committed Dec 7, 2023
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  6. add orcid

    @ejd99
    ejd99 committed Dec 7, 2023
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Commits on Dec 20, 2023

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve authored Dec 20, 2023
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Commits on Jan 6, 2024

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve authored Jan 6, 2024
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Commits on Mar 21, 2024

  1. export traitdata

    @ejd99
    ejd99 committed Mar 21, 2024
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  2. create distribution for bayesian analysis

    @ejd99
    ejd99 committed Mar 21, 2024
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  3. example baysian analysis

    @ejd99
    ejd99 committed Mar 21, 2024
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Commits on Mar 27, 2024

  1. Change Float to Number, add bayes method for signal

    @ejd99
    ejd99 committed Mar 27, 2024
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  2. example for Bayes method to calculate signal

    @ejd99
    ejd99 committed Mar 27, 2024
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  3. include chain and plottinng

    @ejd99
    ejd99 committed Mar 27, 2024
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  4. change to d.tree

    @ejd99
    ejd99 committed Mar 27, 2024
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Commits on Apr 2, 2024

  1. Fixing node data types to allow Duals in a small union

    @richardreeve
    richardreeve committed Apr 2, 2024
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  2. Whitespace and name fixes

    @richardreeve
    richardreeve committed Apr 2, 2024
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  3. Update manifest to Julia 1.10

    @richardreeve
    richardreeve committed Apr 2, 2024
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  4. Update Bayesian inference testing

    @richardreeve
    richardreeve committed Apr 2, 2024
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  5. Whitespace fixes

    @richardreeve
    richardreeve committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. Whitespace fixes

    @richardreeve
    richardreeve committed Apr 3, 2024
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  2. Bugfix in threepoint!() lambda calculation and speed up

    @richardreeve
    richardreeve committed Apr 3, 2024
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  3. Clean up code for Bayesian example

    @richardreeve
    richardreeve committed Apr 3, 2024
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  4. Removed redundant upper calculation

    @richardreeve
    richardreeve committed Apr 3, 2024
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Commits on Apr 6, 2024

  1. Clean demo code

    @richardreeve
    richardreeve committed Apr 6, 2024
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Commits on Jun 11, 2024

  1. Claire Analysis

    @ejd99
    ejd99 committed Jun 11, 2024
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  2. Merge commit '4de1d89bce3f63f1d84ccaa1ba84549636efaa6f' into ejd/infe… 

    …rence
    @richardreeve
    richardreeve committed Jun 11, 2024
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Commits on Jul 18, 2024

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve committed Jul 18, 2024
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  2. Fix case issue

    @richardreeve
    richardreeve committed Jul 18, 2024
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  3. Inference fixes

    @richardreeve
    richardreeve committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. Merge branch 'dev' into ejd/inference

    @richardreeve
    richardreeve committed Jul 22, 2024
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Commits on Oct 13, 2024

  1. Fix for dropping no tips, metadata fix

    @richardreeve
    richardreeve committed Oct 13, 2024
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Commits on Oct 14, 2024

  1. Allow retention of internal nodes with only one outbound connection a… 

    …fter droptips!().
    @richardreeve
    richardreeve committed Oct 14, 2024
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  2. keep_tips!() can have keep argument

    @richardreeve
    richardreeve committed Oct 14, 2024
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  3. Report on whether R ran

    @richardreeve
    richardreeve committed Oct 14, 2024
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