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Some development for an OU branch rates model #419

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Some development for an OU branch rates model #419

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Commits on Apr 21, 2022

  1. Adding a move to generally sample from the prior

    @hoehna
    hoehna committed Apr 21, 2022
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  2. fixing the MH ratio of the prior sampling move

    @hoehna
    hoehna committed Apr 21, 2022
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Commits on Apr 26, 2022

  1. fixing Jacobian of ln-BM clock model

    @hoehna
    hoehna committed Apr 26, 2022
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  2. code cleaning

    @hoehna
    hoehna committed Apr 26, 2022
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  3. more cleaning

    @hoehna
    hoehna committed Apr 26, 2022
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  4. Adding an ln(OU) relaxed clock model

    @hoehna
    hoehna committed Apr 26, 2022
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  5. Adding new moves to explore better convergence for autocorrelated clo… 

    …ck models
    @hoehna
    hoehna committed Apr 26, 2022
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  6. fixing bug in RateAgeBetaShift move when rates depend on tree

    @hoehna
    hoehna committed Apr 26, 2022
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  7. Adding new features to Rev

    @hoehna
    hoehna committed Apr 26, 2022
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Commits on Apr 28, 2022

  1. New validation script for loguniform distribution

    @hoehna
    hoehna committed Apr 28, 2022
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  2. Fixing simulation of new relaxed clock models

    @hoehna
    hoehna committed Apr 28, 2022
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  3. readability

    @hoehna
    hoehna committed Apr 28, 2022
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  4. make output file extension consistent

    @hoehna
    hoehna committed Apr 28, 2022
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Commits on Apr 18, 2023

  1. Adding a move to generally sample from the prior

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  2. fixing the MH ratio of the prior sampling move

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  3. fixing Jacobian of ln-BM clock model

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  4. code cleaning

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  5. more cleaning

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  6. Adding an ln(OU) relaxed clock model

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  7. Adding new moves to explore better convergence for autocorrelated clo… 

    …ck models
    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  8. fixing bug in RateAgeBetaShift move when rates depend on tree

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  9. Adding new features to Rev

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  10. New validation script for loguniform distribution

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  11. Fixing simulation of new relaxed clock models

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  12. readability

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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  13. make output file extension consistent

    @hoehna @bjoelle
    hoehna authored and bjoelle committed Apr 18, 2023
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Commits on Dec 7, 2023

  1. Merge branch 'development' into dev_clock_rate_mix

    @hoehna
    hoehna committed Dec 7, 2023
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  2. merge

    @hoehna
    hoehna committed Dec 7, 2023
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Commits on Mar 8, 2024

  1. new node vale BM model for ACLN

    @hoehna
    hoehna committed Mar 8, 2024
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  2. Merge commit '21ab167ad3046b7d049dac152089732e0fda08fc' into dev_cloc… 

    …k_rate_mix
    @hoehna
    hoehna committed Mar 8, 2024
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Commits on Mar 12, 2024

  1. new soft bounds

    @hoehna
    hoehna committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. soft bounds also only for one side

    @hoehna
    hoehna committed Mar 13, 2024
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Commits on Mar 18, 2024

  1. fixing value ownership

    @hoehna
    hoehna committed Mar 18, 2024
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  2. fixing value ownership

    @hoehna
    hoehna committed Mar 18, 2024
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Commits on Apr 17, 2024

  1. OU with internal node states

    @hoehna
    hoehna committed Apr 17, 2024
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  2. Merge commit 'ca7c5debe0b2d5b7c0cd1beaefb0340ede2f4c7d' into dev_cloc… 

    …k_rate_mix

# Conflicts:
#	src/core/distributions/TypedDistribution.h
    @hoehna
    hoehna committed Apr 17, 2024
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Commits on Apr 25, 2024

  1. Adding an option to delay moves before using.

    @hoehna
    hoehna committed Apr 25, 2024
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  2. Merge commit '303865ba980b6fb620ba45fb32458c6643fae834' into dev_cloc… 

    …k_rate_mix
    @hoehna
    hoehna committed Apr 25, 2024
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  3. changing all other moves to use the delay too

    @hoehna
    hoehna committed Apr 25, 2024
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  4. fixing forgotten move

    @hoehna
    hoehna committed Apr 25, 2024
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Commits on May 7, 2024

  1. Some more bug fixing who owns the values

    @hoehna
    hoehna committed May 7, 2024
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  2. Merge commit 'bec51c4a9f3581046b7c8af121197e7ef0dae9d4' into dev_cloc… 

    …k_rate_mix

# Conflicts:
#	src/core/distributions/AnalyticalMixtureDistribution.h
    @hoehna
    hoehna committed May 7, 2024
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  3. fixing skygrid output. The setValue was disregarded before.

    @hoehna
    hoehna committed May 7, 2024
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