Update simulation functions #44

joshwlambert · 2024-01-04T14:14:28Z

This PR updates the simulation functions, both exported and internal, given suggestions from the full package review (#33).

Updates include:

Rename min_chain_size argument to min_outbreak_size
Remove ... and chkDots() from exported simulation functions
Stricter input checking on delay distributions that can be either anonymous functions or <epidist> objects
Column deletion is done by name rather than by position
sim_linelist() documentation is updated
add_ct now defaults to TRUE
Maximum iteration limit is added to while loop when simulation branching process

Tests are updated in accordance with function updates, vignettes are updated with new argument names.

Co-authored-by: Adam Kucharski <[email protected]> Co-authored-by: Hugo Gruson <[email protected]>

…functions

Co-authored-by: Hugo Gruson <[email protected]>

joshwlambert and others added 11 commits January 4, 2024 10:12

update sim_linelist documentation

bee12c2

Co-authored-by: Adam Kucharski <[email protected]> Co-authored-by: Hugo Gruson <[email protected]>

changed default add_ct to TRUE for sim_linelist and sim_outbreak

93939ca

updated sim_linelist and sim_outbreak for new add_ct argument default

a5ceeff

better input checking for delay distributions in exported simulation …

13d9ee1

…functions

renamed min_chain_size to min_outbreak_size

5cc4b1c

added stop criteria for chain sim loop

a377c2e

added test for exceeding max iterations for chain sim

cad3795

removed dots from exported simulation functions

4c990cf

fixed partial arg match in sim_contacts

1d76df2

Co-authored-by: Hugo Gruson <[email protected]>

remove col by name rather than position in .sim_contacts_tbl

df922da

reduce cyclocomp of delay distribution input checking

07fa8e3

joshwlambert merged commit e8bbbfa into main Jan 4, 2024
8 checks passed

joshwlambert deleted the updt_sim_funcs branch January 4, 2024 14:36

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