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add inference#79

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richardreeve merged 59 commits intodevEcoJulia/Phylo.jl:devfrom ejd/inferenceEcoJulia/Phylo.jl:ejd/inferenceCopy head branch name to clipboardOct 16, 2024

+7,412-50

Commits

Commits on Feb 23, 2023

• Add inference and testing

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Commits on Feb 24, 2023

• remove test/

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• add phylolm

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Commits on Feb 28, 2023

• add inference example

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Commits on Mar 1, 2023

• hopefully will now pass tests

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• include global skipR

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Commits on Mar 14, 2023

• added estimaterates!

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Commits on Mar 29, 2023

• Updated estimaterates, all info is on the tree

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Commits on Apr 5, 2023

• add lambda calcs

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Commits on Apr 16, 2023

• Merge branch 'rr/getnodesfix' into ejd/inference

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• Merge branch 'rr/getnodesfix' into ejd/inference

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• Fix inference testing

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• examples folder needs manifest

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• Only compare to R if packages are installed

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• Update workflows

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Commits on Apr 23, 2023

• Merge branch 'rr/getnodesfix' into ejd/inference

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Commits on Apr 24, 2023

• Minor fixes to type stability

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• Switch from Dict to a struct for trait storage

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Commits on Apr 26, 2023

• Merge branch 'dev' into ejd/inference

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Commits on Aug 2, 2023

• fix problems with estimaterates and clean examples

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Commits on Oct 27, 2023

• mult lambda

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• manifest and project

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Commits on Oct 30, 2023

• Merge branch 'dev' into ejd/inference

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Commits on Nov 25, 2023

• Merge branch 'dev' into ejd/inference

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Commits on Dec 7, 2023

• Merge branch 'dev' into ejd/inference

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• Fix authorship list

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• multi lambda

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• Merge branch 'ejd/inference' of https://github.com/EcoJulia/Phylo.jl into ejd/inference

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  46e8efe

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• fix tests

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• add orcid

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Commits on Dec 20, 2023

• Merge branch 'dev' into ejd/inference

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Commits on Jan 6, 2024

• Merge branch 'dev' into ejd/inference

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Commits on Mar 21, 2024

• export traitdata

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• create distribution for bayesian analysis

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• example baysian analysis

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Commits on Mar 27, 2024

• Change Float to Number, add bayes method for signal

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• example for Bayes method to calculate signal

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• include chain and plottinng

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• change to d.tree

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Commits on Apr 2, 2024

• Fixing node data types to allow Duals in a small union

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• Whitespace and name fixes

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• Update manifest to Julia 1.10

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  57d3ff7

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• Update Bayesian inference testing

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• Whitespace fixes

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Commits on Apr 3, 2024

• Whitespace fixes

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• Bugfix in threepoint!() lambda calculation and speed up

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• Clean up code for Bayesian example

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• Removed redundant upper calculation

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Commits on Apr 6, 2024

• Clean demo code

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Commits on Jun 11, 2024

• Claire Analysis

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• Merge commit '4de1d89bce3f63f1d84ccaa1ba84549636efaa6f' into ejd/inference

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Commits on Jul 18, 2024

• Merge branch 'dev' into ejd/inference

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  b3c139a

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• Fix case issue

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• Inference fixes

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Commits on Jul 22, 2024

• Merge branch 'dev' into ejd/inference

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Commits on Oct 13, 2024

• Fix for dropping no tips, metadata fix

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Commits on Oct 14, 2024

• Allow retention of internal nodes with only one outbound connection after droptips!().

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• keep_tips!() can have keep argument

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• Report on whether R ran

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