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{simulist} v0.3.0 full package review #117

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{simulist} v0.3.0 full package review #117

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Commits on Jan 9, 2024

  1. Update CITATION.cff

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Commits on Jan 11, 2024

  1. Add DOI to README & CITATION (#56) 

    * Add DOI to README

* Add CITATION file with DOI

* Update CITATION.cff

* Automatic readme update

* Add more info

* Update CITATION.cff

* Fix code syntax

* Update CITATION.cff

* Update CITATION.cff

* Automatic readme update

---------

Co-authored-by: GitHub Action <[email protected]>
    @Bisaloo @actions-user
    Bisaloo and actions-user authored Jan 11, 2024
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Commits on Feb 7, 2024

  1. add WIP .sim_network_bp function

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  2. fix sampling contacts and bookkeeping ancestors

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  3. fixed sampling contact distribution with replacement

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  4. increase size of allocated vectors

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  5. fixed issue counting chain length

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  6. simplified vector indexing in .sim_network_bp

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  7. simplified next_gen_size calculation in .sim_network_bp

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

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

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  10. updated .check_sim_input with new model arguments

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  11. updated .sim_contacts_tbl for new simulation model

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  12. updated exported simulation function to use new model arguments

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  13. updated .sim_bp_linelist to use .sim_network_bp

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  14. updated add_cols function to sample infected individuals

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  15. removed contact_distribution from functions that no longer use it

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  16. removed documentation for old arguments and added documentation for n… 

    …ew arguments (mean_contacts, contact_interval, prob_infect)
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  17. added details to .sim_network_bp documentation

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  18. updated man files for updated functions

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  19. fix typo converting contact_interval to function in sim_contacts

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  20. fixed examples and inherit doc in .sim_network_bp

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  21. added tests for .sim_network_bp

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  22. added linelist row filtering to sim_outbreak

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  23. reduced maximum iterations for simulation conditioning

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  24. updated tests to pass with new arguments

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  25. pass add_names argument to .sim_network_bp

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  26. update simulation functions to use new arguments in vignettes

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  27. remove mention of bpmodels from the package

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  28. Update CITATION.cff

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  29. update README to use new simulation function arguments

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  30. Automatic readme update

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  31. update mean_contacts to contact_distribution

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  32. update tests to use contact_distribution instead of mean_contacts

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  33. update vignettes and README to use contact_distribution instead of me… 

    …an_contacts
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  34. Automatic readme update

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  35. linting

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  36. increase excess degree distribution density upper bound

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  37. update seed in .sim_network_bp test to pass

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  38. added .sample_names function

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  39. use .sample_names in .add_names function

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  40. removed warning and break for large line lists with names in .sim_net… 

    …work_bp
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  41. linting

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  42. added network option to create_config

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  43. updated create_config tests

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  44. add option to turn off network effect in .sim_network_bp and remove a… 

    …dd_names argument
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  45. added test for .sim_network_bp without network effect and update othe… 

    …r tests
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  46. removed add_names argument from .sim_network_bp call in sim_* functions

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  47. removed add_names argument from .sim_bp_linelist

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  48. updated sim_contacts and sim_linelist tests

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  49. added info box to simulist vignette on network effect in model

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  50. use snapshot tests for regression testing .sim_network_bp

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  51. added more info to add_ct argument, closes #59

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Commits on Feb 8, 2024

  1. remove row names before returning linelist and contact table

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  2. updated testdata README with new function arguments

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  3. updated testdata .rds files

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Commits on Feb 9, 2024

  1. use snapshots for regression testing sim_linelist

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  2. use snapshots for regression testing sim_contacts

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  3. use snapshots for regression testing sim_outbreak

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  4. removed old empty create_linelist test file

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Commits on Feb 15, 2024

  1. refactor .sim_bp_linelist, .sim_clinical_linelist, and .sim_contacts_… 

    …tbl into .sim_internal, closes #42
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  2. update sim_outbreak, sim_linelist and sim_contacts to use .sim_intern… 

    …al, relates #42
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  3. reduced cyclomatic complexity of .sim_internal

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  4. updated design principles vignette to mention .sim_internal instead o… 

    …f .sim_bp_linelist
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  5. updated sim_contacts and sim_outbreak snapshots

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  6. renamed sim_utils file utils as simulation utility functions have bee… 

    …n removed
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  7. added NULL argument defaults to .sim_internal for arguments not alway… 

    …s specified
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  8. added simulist architecture diagram

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  9. added architecture diagram to design principles vignette

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  10. reduce cyclomatic complexity of .check_sim_input and remove nolint flag

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  11. add lint-changed-files GHA workflow as no longer run from .github org… 

    … repo
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Commits on Feb 16, 2024

  1. added plotting transmission chain to vis-linelist vignette

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  2. added dplyr as suggested dependency for vignette

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  3. updated WORDLIST

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  4. Update CITATION.cff

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  5. turn off library_call_linter due to tabset vignette

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  6. Add v0.2.0 release notes to NEWS (#71) 

    * updated NEWS.md with changes for v0.2.0 release

* updated WORDLIST

* updated NEWS.md for v0.2.0 release

* updated WORDLIST
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  7. removed empty create_linelist.R file

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Commits on Feb 19, 2024

  1. Update DESCRIPTION

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Commits on Feb 21, 2024

  1. put expr as first argument of tryCatch 

    Co-authored-by: Chris Hartgerink <[email protected]>
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  2. add comment when defining infections 

    Co-authored-by: Chris Hartgerink <[email protected]>
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Commits on Feb 22, 2024

  1. use sex instead of gender in .sim_internal and .sample_names

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  2. update snapshot tests from column header renaming

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  3. update vignettes from column header renaming

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  4. added NEWS item on renaming gender to sex

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  5. updated testdata after column renaming

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  6. normalise DESCRIPTION

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  7. Update CITATION.cff

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  8. fixed bug for age structured contacts

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  9. added test for age structured contacts

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  10. added sim_contacts snapshot

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  11. name population_age vector

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  12. remove defining age_range in sim_contacts as it is not used

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Commits on Feb 23, 2024

  1. add NULL default to outbreak_start_date in .add_date_contact

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  2. add comment to .add_hospitalisation

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  3. add comment on sample implicit rounding

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  4. use typed NA in add_cols functions

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  5. added lower and upper bounds to case_type_probs assertion

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  6. added lower and upper bound to contact_tracing_status_probs assertion

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  7. improve create_config function documentation

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  8. optimise .sim_network_bp by moving contact distribution density outsi… 

    …de loop
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  9. added @chartgerink and @pratikunterwegs as package reviewers

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  10. NEWS.md updates from v0.2.0 package review

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  11. Update CITATION.cff

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  12. update MIT badge URL

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  13. Automatic readme update

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  14. increment minor version

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  15. Update CITATION.cff

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Commits on Mar 11, 2024

  1. bump to dev version

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  2. Update CITATION.cff

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  3. fixed simulation index allocation bug, closes #89

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Commits on Mar 21, 2024

  1. updated min_outbreak_size to outbreak_size argument

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  2. updated tests with outbreak_size and added new tests for simulation w… 

    …arning
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  3. updated vignettes to use outbreak_size instead of min_outbreak_size

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  4. lowered maximum outreak size to 10,000

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  5. restructured simulist vignette to give more info on reproduction number

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  6. added warning about reproduction number to README

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  7. Automatic readme update

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  8. fixes bug in contact time delay in .sim_network_bp, closes #92

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  9. update test snapshots for simulation after contact delay bug fix, rel… 

    …ates #92
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Commits on Mar 22, 2024

  1. add url to _pkgdown

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Commits on Apr 5, 2024

  1. updated .sim_network_bp to use infectious period instead of contact i… 

    …nterval, closes #61
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  2. updated functions to use infectious period, relates #61

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  3. updated tests and snapshots with infectious period

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  4. updated vignettes to use infectious period, relates #61

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  5. updated README with infectious period, relates #61

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  6. Automatic readme update

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  7. updated testdata and testdata README

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  8. updated RoxygenNote in DESCRIPTION

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  9. added is_na function

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  10. added tests for is_na function

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  11. fixed link in is_na documentation

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  12. added .cross_check_sim_input and allow NA risks in .check_sim_input

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  13. updated .add_hospitalisation and .add_death to allow NA risks

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  14. updated sim_linelist and sim_outbreak to use .cross_check_sim_input a… 

    …nd convert NA to closures
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  15. updated documentation on risks

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  16. added tests for .cross_check_sim_input and .check_sim_input with NA r… 

    …isks
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  17. updated sim_linelist test to use outbreak_size to ensure linelist is … 

    …large enough
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  18. updated sim_linelist and sim_outbreak snapshots due to number of rand… 

    …om samples increasing from .cross_check_sim_input
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  19. Update CITATION.cff

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  20. added sim_linelist tests for onset-to-event and risk NAs

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  21. move some input checking and conversion from sim_linelist and sim_out… 

    …break into new as_function function (DRYer)
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  22. fixed .cross_check_sim_input when onset-to-event dist produces NA

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  23. added sim_linelist tests that columns are NA when onset-to-event dist… 

    … is NA
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  24. Automatic readme update

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  25. linting checking and utility functions

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  26. added simulating without hospitalisation and/or death to simulist vig… 

    …nette
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Commits on Apr 25, 2024

  1. added onset_to_recovery to sim_linelist and sim_outbreak, WIP #36

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  2. added onset_to_recovery to as_function, WIP #36

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  3. renamed and updated .add_deaths to .add_outcome, WIP #36

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  4. updated .sim_internal to call .add_outcome and use outcome columns, WIP 

    #36
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  5. added onset_to_recovery to .check_sim_input and updated .cross_check_… 

    …sim_input to return compound warnings or errors, WIP #36
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  6. add tidyr to Suggests in DESCRIPTION

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  7. added data reshaping (base R and tidyverse) to fix vis-linelist vignette

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  8. Update CITATION.cff

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  9. updated testdata and testdata README

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  10. updated tests and snapshots with onset-to-recovery, relates #36

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  11. linting

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  12. added time_varying_death_risk to create_config, WIP #36

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  13. updated create_config tests

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  14. updated .add_outcome to use time-varying death risk if specified in c… 

    …onfig, WIP #36
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  15. updated .add_outcome tests

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  16. added config argument to .add_outcome call in .sim_internal

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  17. added bullet point on type checking the config list to the design-pri… 

    …nciples vignette
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  18. updated create_config documentation

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  19. updated wording of input checking for create_config point in design-p… 

    …rinciples vignette
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  20. added first draft of time-varying-cfr vignette, relates #36

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  21. added time-varying-cfr vignette to _pkgdown.yml reference

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  22. updated WORDLIST

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  23. updated hosp_death_risk and non_hosp_death_risk documentation to incl… 

    …ude time-varying rates, relates #36
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  24. updated time-varying-cfr vignette figure captions, code folding and w… 

    …ording
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  25. fix .add_outcome test by adding config argument

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  26. updating .add_outcome to include time-varying cfr for age-strat risks… 

    … and fixing indexing bug
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  27. linting

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  28. ensure .check_func_req_args errors with incorrect function argument n… 

    …umber
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  29. added tests for .check_func_req_args

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  30. fixed time-varying death idx sampling

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  31. updated WORDLIST

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  32. added nolint flags and echo expression to time-varying-cfr vignette i… 

    …felse
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  33. added sim_linelist tests for time-varying cfr

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  34. updated snapshots for sim_linelist tests

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  35. added comments to .add_outcome

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  36. update time_varying_death_risk default in create_config to NULL

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  37. explicitly add number of required args in .check.func_req_args call i… 

    …n time_varying_risk
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  38. simplify time-varying cfr and remove time_varying_risk internal function

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  39. add lower and upper bound checks for *_risk arguments

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  40. updated time-varying-cfr vignette to use new time_varying_death_risk … 

    …function signature
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  41. updated sim_linelist tests and snapshots for updated time-varying cfr

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  42. updated sim_outbreak snapshots for updated time-varying cfr

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  43. update .check_func_req_args to check arg names and give more informat… 

    …ive error messages
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  44. updated .check_func_req_args tests

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  45. updated .check_func_req_args call in .add_outcome

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  46. vectorise time-varying cfr in apply_death_risk

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  47. update sim_linelist and sim_outbreak tests and snapshots

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  48. Update CITATION.cff

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Commits on Apr 29, 2024

  1. remove add_ct argument from functions, WIP #41

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  2. remove add_ct argument from tests, WIP #41

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  3. added wrangling-linelist vignette

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  4. added bullet point to design-principles vignette on simulation argume… 

    …nt to parameterise and not change dimensions of data
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  5. updated _pkgdown.yml articles

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  6. linted wrangling-linelist vignette

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  7. updated WORDLIST

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  8. Use negation for base R col subsetting 

    Co-authored-by: Hugo Gruson <[email protected]>
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  9. Use != in base R subsetting 

    Co-authored-by: Hugo Gruson <[email protected]>
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  10. removed eval=FALSE code from wrangling-linelist vignette 

    Co-authored-by: Hugo Gruson <[email protected]>
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Commits on May 3, 2024

  1. added .anonymise function, WIP #41

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  2. added tests for .anonymise

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  3. updated .add_names to use .anonymise, WIP #41

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  4. replace add_names argument with anonymise, WIP #41

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  5. add anonymise argument to sim_contacts

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  6. updated documentation for anonymise

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  7. added test for .add_names with anonymise

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  8. updated tests and snapshots using add_names to anonymise

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  9. updated Anonymous line list section in simulist.Rmd

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  10. updated WORDLIST

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  11. add CODECOV_TOKEN to test-coverage yaml

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Commits on May 7, 2024

  1. removed is_na function and replace with rlang::is_lgl_na

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  2. use *_lgl_idx naming

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  3. add bullet point to design-principles vignette on *_idx and *_lgl_idx… 

    … naming
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  4. update WORDLIST

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Commits on May 20, 2024

  1. started drafting Related projects section of README

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  2. Automatic readme update

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  3. Automatic readme update

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  4. first draft of related projects section in README, relates #21

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  5. updated WORDLIST

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  6. Automatic readme update

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  7. add generative-nowcasting to related projects in README, closes #16

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  8. Automatic readme update

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  9. update WORDLIST

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  10. fix wrangling-linelist VignetteIndexEntry

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  11. add section on related packages that do not simulate line list data t… 

    …o README
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  12. the 2 step simulation for LLsim is added to README

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  13. add footnotes to explain feature table fields in README

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  14. fix footnotes in README feature table

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  15. Automatic readme update

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  16. Update {epidict} info in README 

    Co-authored-by: CarmenTamayo <[email protected]>
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  17. Automatic readme update

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  18. updated WORDLIST

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  19. update spelling and WORDLIST

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  20. Automatic readme update

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  21. add pkgdown favicons to resolve pkgdown CI failure

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Commits on May 21, 2024

  1. update package architecture figure

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    joshwlambert committed May 21, 2024
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Commits on May 22, 2024

  1. update NEWS.md with v0.3.0 changes

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    joshwlambert committed May 22, 2024
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  2. update WORDLIST

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    joshwlambert committed May 22, 2024
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  3. reduce image size of package architecture diagram

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    joshwlambert committed May 22, 2024
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  4. update GHA workflows

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    joshwlambert committed May 22, 2024
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  5. add update-copyright-year workflow

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    joshwlambert committed May 22, 2024
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  6. add contributor point to release_bullets

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    joshwlambert committed May 22, 2024
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  7. update check.env

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    joshwlambert committed May 22, 2024
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  8. update .gitignore

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    joshwlambert committed May 22, 2024
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