Code

Add network model simulation#60

Code

Merged

joshwlambert merged 50 commits intomainepiverse-trace/simulist:mainfrom sim_network_bpepiverse-trace/simulist:sim_network_bpCopy head branch name to clipboardFeb 7, 2024

+1,110-694

Commits

Commits on Jan 12, 2024

• add WIP .sim_network_bp function

  joshwlambert

  committed
  4674431

Commits on Jan 15, 2024

• fix sampling contacts and bookkeeping ancestors

  joshwlambert

  committed
  c01e77e

Commits on Jan 16, 2024

• fixed sampling contact distribution with replacement

  joshwlambert

  committed
  69e99c9

• increase size of allocated vectors

  joshwlambert

  committed
  8a1d3b5

• fixed issue counting chain length

  joshwlambert

  committed
  4907363

• simplified vector indexing in .sim_network_bp

  joshwlambert

  committed
  6122f9b

• simplified next_gen_size calculation in .sim_network_bp

  joshwlambert

  committed
  36da388

• remove preallocation of id vec and add vector growing to .sim_network_bp

  joshwlambert

  committed
  aabab0e

• remove input checking from .sim_network_bp as it is an internal function

  joshwlambert

  committed
  5dc439c

• updated .check_sim_input with new model arguments

  joshwlambert

  committed
  a401eef

• updated .sim_contacts_tbl for new simulation model

  joshwlambert

  committed
  4f6fd61

• updated exported simulation function to use new model arguments

  joshwlambert

  committed
  ae79da1

• updated .sim_bp_linelist to use .sim_network_bp

  joshwlambert

  committed
  049a6ec

• updated add_cols function to sample infected individuals

  joshwlambert

  committed
  fa35b39

Commits on Jan 17, 2024

• removed contact_distribution from functions that no longer use it

  joshwlambert

  committed
  0b629ef

• removed documentation for old arguments and added documentation for new arguments (mean_contacts, contact_interval, prob_infect)

  joshwlambert

  committed
  30e7bfb

• added details to .sim_network_bp documentation

  joshwlambert

  committed
  42b5496

• updated man files for updated functions

  joshwlambert

  committed
  1f0d2c8

• fix typo converting contact_interval to function in sim_contacts

  joshwlambert

  committed
  6de6d13

• fixed examples and inherit doc in .sim_network_bp

  joshwlambert

  committed
  02abe5f

• added tests for .sim_network_bp

  joshwlambert

  committed
  bdcbff7

• added linelist row filtering to sim_outbreak

  joshwlambert

  committed
  4b1ca9d

• reduced maximum iterations for simulation conditioning

  joshwlambert

  committed
  8d09db7

• updated tests to pass with new arguments

  joshwlambert

  committed
  8f6dd78

Commits on Jan 18, 2024

• pass add_names argument to .sim_network_bp

  joshwlambert

  committed
  735ec13

• update simulation functions to use new arguments in vignettes

  joshwlambert

  committed
  c9f8bc5

• remove mention of bpmodels from the package

  joshwlambert

  committed
  dfae23d

• Update CITATION.cff

  actions-user

  committed
  2106172

• update README to use new simulation function arguments

  joshwlambert

  committed
  e19b496

• Automatic readme update

  actions-user

  committed
  9970476

Commits on Jan 19, 2024

• update mean_contacts to contact_distribution

  joshwlambert

  committed
  0d2cf1d

• update tests to use contact_distribution instead of mean_contacts

  joshwlambert

  committed
  2156fcb

• update vignettes and README to use contact_distribution instead of mean_contacts

  joshwlambert

  committed
  3888aeb

• Automatic readme update

  actions-user

  committed
  282057a

• linting

  joshwlambert

  committed
  b428d1c

Commits on Jan 31, 2024

• increase excess degree distribution density upper bound

  joshwlambert

  committed
  bb141f8

• update seed in .sim_network_bp test to pass

  joshwlambert

  committed
  cd5fe64

Commits on Feb 5, 2024

• added .sample_names function

  joshwlambert

  committed
  4315035

• use .sample_names in .add_names function

  joshwlambert

  committed
  d767163

• removed warning and break for large line lists with names in .sim_network_bp

  joshwlambert

  committed
  69ff03f

• linting

  joshwlambert

  committed
  fb5e435

Commits on Feb 6, 2024

• added network option to create_config

  joshwlambert

  committed
  e60bdf7

• updated create_config tests

  joshwlambert

  committed
  2985b39

• add option to turn off network effect in .sim_network_bp and remove add_names argument

  joshwlambert

  committed
  173a855

• added test for .sim_network_bp without network effect and update other tests

  joshwlambert

  committed
  be49848

• removed add_names argument from .sim_network_bp call in sim_* functions

  joshwlambert

  committed
  baeb283

• removed add_names argument from .sim_bp_linelist

  joshwlambert

  committed
  91f77ff

• updated sim_contacts and sim_linelist tests

  joshwlambert

  committed
  5d83edc

• added info box to simulist vignette on network effect in model

  joshwlambert

  committed
  297d713

• use snapshot tests for regression testing .sim_network_bp

  joshwlambert

  committed
  bdac6de