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Add network model simulation #60

Merged
merged 50 commits into from
Feb 7, 2024
Merged

Add network model simulation #60

merged 50 commits into from
Feb 7, 2024

Commits on Jan 12, 2024

  1. add WIP .sim_network_bp function

    @joshwlambert
    joshwlambert committed Jan 12, 2024
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Commits on Jan 15, 2024

  1. fix sampling contacts and bookkeeping ancestors

    @joshwlambert
    joshwlambert committed Jan 15, 2024
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Commits on Jan 16, 2024

  1. fixed sampling contact distribution with replacement

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  2. increase size of allocated vectors

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  3. fixed issue counting chain length

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  4. simplified vector indexing in .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  5. simplified next_gen_size calculation in .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  6. remove preallocation of id vec and add vector growing to .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  7. remove input checking from .sim_network_bp as it is an internal function

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  8. updated .check_sim_input with new model arguments

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  9. updated .sim_contacts_tbl for new simulation model

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  10. updated exported simulation function to use new model arguments

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  11. updated .sim_bp_linelist to use .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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  12. updated add_cols function to sample infected individuals

    @joshwlambert
    joshwlambert committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. removed contact_distribution from functions that no longer use it

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  2. removed documentation for old arguments and added documentation for n… 

    …ew arguments (mean_contacts, contact_interval, prob_infect)
    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  3. added details to .sim_network_bp documentation

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  4. updated man files for updated functions

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  5. fix typo converting contact_interval to function in sim_contacts

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  6. fixed examples and inherit doc in .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  7. added tests for .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  8. added linelist row filtering to sim_outbreak

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  9. reduced maximum iterations for simulation conditioning

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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  10. updated tests to pass with new arguments

    @joshwlambert
    joshwlambert committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. pass add_names argument to .sim_network_bp

    @joshwlambert
    joshwlambert committed Jan 18, 2024
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  2. update simulation functions to use new arguments in vignettes

    @joshwlambert
    joshwlambert committed Jan 18, 2024
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  3. remove mention of bpmodels from the package

    @joshwlambert
    joshwlambert committed Jan 18, 2024
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  4. Update CITATION.cff

    @actions-user
    actions-user committed Jan 18, 2024
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  5. update README to use new simulation function arguments

    @joshwlambert
    joshwlambert committed Jan 18, 2024
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  6. Automatic readme update

    @actions-user
    actions-user committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. update mean_contacts to contact_distribution

    @joshwlambert
    joshwlambert committed Jan 19, 2024
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  2. update tests to use contact_distribution instead of mean_contacts

    @joshwlambert
    joshwlambert committed Jan 19, 2024
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  3. update vignettes and README to use contact_distribution instead of me… 

    …an_contacts
    @joshwlambert
    joshwlambert committed Jan 19, 2024
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  4. Automatic readme update

    @actions-user
    actions-user committed Jan 19, 2024
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  5. linting

    @joshwlambert
    joshwlambert committed Jan 19, 2024
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Commits on Jan 31, 2024

  1. increase excess degree distribution density upper bound

    @joshwlambert
    joshwlambert committed Jan 31, 2024
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  2. update seed in .sim_network_bp test to pass

    @joshwlambert
    joshwlambert committed Jan 31, 2024
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Commits on Feb 5, 2024

  1. added .sample_names function

    @joshwlambert
    joshwlambert committed Feb 5, 2024
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  2. use .sample_names in .add_names function

    @joshwlambert
    joshwlambert committed Feb 5, 2024
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  3. removed warning and break for large line lists with names in .sim_net… 

    …work_bp
    @joshwlambert
    joshwlambert committed Feb 5, 2024
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  4. linting

    @joshwlambert
    joshwlambert committed Feb 5, 2024
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Commits on Feb 6, 2024

  1. added network option to create_config

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  2. updated create_config tests

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  3. add option to turn off network effect in .sim_network_bp and remove a… 

    …dd_names argument
    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  4. added test for .sim_network_bp without network effect and update othe… 

    …r tests
    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  5. removed add_names argument from .sim_network_bp call in sim_* functions

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  6. removed add_names argument from .sim_bp_linelist

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  7. updated sim_contacts and sim_linelist tests

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  8. added info box to simulist vignette on network effect in model

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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  9. use snapshot tests for regression testing .sim_network_bp

    @joshwlambert
    joshwlambert committed Feb 6, 2024
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