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{simulist} full package review#33

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joshwlambert wants to merge 184 commits intoemptyepiverse-trace/simulist:emptyfrom reviewepiverse-trace/simulist:reviewCopy head branch name to clipboard

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Commits

Commits on Aug 30, 2023

• Automatic readme update

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  committed
  96d0dc9

Commits on Oct 17, 2023

• updated DESCRIPTION with title, description, authors & dependencies

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  88d62fb

• updated .Rbuildignore and .gitignore

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  fcf014b

• added simulist.Rproj

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  ba60494

• added sim_linelist function

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  f419e11

• added internal functions to add info to linelist

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  648640b

• updated NAMESPACE

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  ed3a580

• updated WORDLIST

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  d980d36

• added test for sim_linelist

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  4c314ca

• temporary warnPartialMatchArg = FALSE

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  6875759

• Update CITATION.cff

  

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  dc1c1b7

• added create_contacts WIP function

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  04a2658

• updated .add_hospitalisation and .add_deaths to also handle pop-wide and age-dependent rates

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  1dc4cc3

• updated sim_linelist to handle and check generalised age-dependent rates

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  0b9eb61

• added .check_rate_df function

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  8ea860a

• only call .add_ct if add_ct = TRUE

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  9e4ed4f

• error if include_contacts = TRUE while WIP

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  db9e9e1

• updated .add_names arg in create_contacts

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  22246e4

• temp branch specific install of epiparameter

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  49f7828

• add authors to documentation of sim_linelist

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  b207d36

• use <- assignment throughout

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  4fce2bd

• replace 1:expr with seq_len(expr)

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  7473042

• use TRUE/FALSE over T/F

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  3724fc5

• added nocov and nolint flags to create_contacts while WIP

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  b70b951

• added nocov flags to dev-utils

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  f5556df

• added .create_linelist function for mock testing

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  86a6e41

• added tests for .create_linelist

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  bf650b2

• keep ct in sim_linelist return if add_ct = TRUE

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  0085355

• updated WORDLIST

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  f62ab19

• added sim_linelist tests

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  3f78a4e

• fixed assignment typo in .add_ct

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  3769baa

• join by numerics in .add_names

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  34c2627

• consistent behaviour and side-effects for add_cols functions

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  a0ed143

• added tests for add_cols functions

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  e0e63b3

• added tests for checker functions

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  be508cf

• linting

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  34ee344

• temp nolint flag until removing NSE permanently from pkg

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  480bc40

• added package logo

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  a4a1d80

• updated README (badges, quick start, help and citation)

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  0e03fb2

• updated WORDLIST

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  9f83705

• Automatic readme update

  

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  joshwlambert

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  b396401

Commits on Oct 19, 2023

• only output case names when add_names = TRUE

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  46930ad

• updated sim_linelist tests to include case_name and case_type

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  3a47d77

• added sim_linelist test for add_names = FALSE

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  d658bf0

• updated WORDLIST

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  b227572

• added first draft of getting started vignette

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  9c1db7e

• updates to simulist vignette

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  5327a54

• added bookdown to Suggests

  joshwlambert

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  e84007b

• Update CITATION.cff

  

  actions-user

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  joshwlambert

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  f5c9a4e

• added first draft of age-stratified rates vignette

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  a480e16

• added checks to .check_rate_df for overlapping and non-contiguous age groups

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  ff97e3e

• added tests for .check_rate_df overlapping and non-contiguous age groups

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  2359eba

• add link to age-strat-rates vignette in get started vignette

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  b8e17dc

• updates to age-strat-rates vignette

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  committed
  af6dd79

Commits on Oct 20, 2023

• remove dplyr from Imports

  joshwlambert

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  ebb2cbb

• replaced dplyr with base R joins

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  5f5dd24

• Update CITATION.cff

  

  actions-user

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  6ee8e76

Commits on Oct 23, 2023

• Use vectorized randomNames() call

  

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  5ec9253

• added create_config function

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  8f2a1d4

• added tests for create_config

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  dd842f9

• added config argument to sim_linelist and use config parameters

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  7296764

• updated WORDLIST

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  4d3e42f

• remove genders from create_config

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  d24d830

• allow multiple distributions for .add_date_first_contact, .add_date_last_contact, .add_cit

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  1774592

• updated add_cols tests to test for unaccepted distributions

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  47c25fc

• test for config inputs in sim_linelist

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  7937538

• ensure arg matching in do.call for add_cols functions

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  b01eee7

• update create_config with correct arg name

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  8793e4d

• update and added tests for distribution arg names

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  47df3b0

• linting

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  9698f08

Commits on Oct 25, 2023

• add URL and BugReports fields to DESCRIPTION

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  fb3f1c2

• added Hugo as pkg contributor

  joshwlambert

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  7ce2f9c

• Update CITATION.cff

  

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  joshwlambert

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  a6f9a9e

• Update DESCRIPTION

  Show description for f1e0a7c
  

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  Bisaloo

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  f1e0a7c

• updated create_contacts function to use add_cols functions and added arguments to allow flexibility

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  79763f8

• subset col by name not index in create_contacts

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  82d031d

• added documentation for create_contacts, added dot prefix for internal, removed arg default as internal

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  ff7d0be

• added sim_contacts (exported) function

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  79a13d1

• added tests for sim_contacts

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  b2224bd

• removed including contacts in sim_linelist

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  6a1d616

• removed test that checked include_contacts in sim_linelist

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  0d6cb16

• added info on sim_contacts to README and simulist vignette

  joshwlambert

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  2e9bb4a

• linelist -> line list in text

  joshwlambert

  committed
  091555b

• Update CITATION.cff

  

  actions-user

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  joshwlambert

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  eb7f69d

• updated README

  joshwlambert

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  5dfbf33

• Automatic readme update

  

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  06f8a77

Commits on Oct 26, 2023

• moved replicated sim code into sim_utils functions

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  158321f

• added sim_outbreak (exported) function

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  b509068

• added tests for sim_outbreak

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  1223772

• added age-strat rates test for sim_outbreak

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  08bdcc6

• added sim_outbreak example to README

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  9042004

• added sim_outbreak example to simulist vignette

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  4263afe

• Automatic readme update

  

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  joshwlambert

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  a634771

• linting

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  4ca2e27

Commits on Oct 27, 2023

• remove time_rounded col from internal chain object

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  8203fab

• removed hosp_rounded col from internal chain object

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  6e95e34

• removed death_rounded col from internal chain object

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  8477070

Commits on Oct 30, 2023

• updated .check_rate_df to use new user input rate df

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  committed
  c5977b7

• simplify .add_hospitalisation and .add_deaths based on new rate df

  joshwlambert

  committed
  a90d3bc

• updated sim_linelist documentation for new rate df

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  committed
  b2323d4

• updated age-strat-rates vignette with new rates df

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  d37a300

• use row.names over rownames

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  d71520c

• updated tests for new rate df

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  048ef28

Commits on Nov 1, 2023

• added .check_age_df

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  a5b95a3

• added tests for .check_age_df

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  49cf009

• updated sim_linelist and .sim_bp_linelist to accommodate age structured population

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  3a62cd5

• added test for age structured sim_linelist

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  94482df

• changed age_range argument to population_age

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  42fc87f

• fix case for age-strat rates and population age structure

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  7070761

• added test for age-strat rates and age structure

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  4c2b02f

• updated input checking for age structure in sim_outbreak

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  8a8f077

• updated documentation for population_age

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  cc9d8ca

• fixed sim_outbreak .check_rate_df and added nolint for cyclocomp

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  73ac4a9

• added ggplot2 to Suggests in DESCRIPTION

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  fa4bbf2

• added first draft of age-struct-pop vignette

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  5cfd4fc

• updated simulist vignette to link to age-struct-pop vignette

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  ddef376

• updated WORDLIST

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  dd01f2c

• updated create_contacts to handle age struct data frame

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  4bebfa8

• added sim_outbreak test for age structure

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  d457d64

• Update CITATION.cff

  

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  d298b83

• updated yaml settings and added code folding and figure captions for age-struct-pop vignette

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  0c828ef

• updated wording of external links for age pyramids in age-struct-pop vignette

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  ac61728

• normalise sample weights for age sampling

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  9229dbe

• added test to check simulated proportion of ages matches input for sim_linelist

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  08adc77

• brackets do not need be escaped in vignette

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  ad40bcd

• renamed .create_contacts with .sim_contacts

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  4418f90

Commits on Nov 2, 2023

• include death_date col in line list

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  6fa521a

• updated tests to include death_date col

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  ecb82dd

• added complete reprex to .create_linelist doc

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  76ab692

• updated WORDLIST

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  4717c9f

• added first draft of visualisation vignette

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  d52dc7c

• added interval = "daily" instead of rounding and death_dates in plot to vis-linelist vignette

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  d29c0aa

• added min version of incidence2 to DESCRIPTION

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  a519a03

• Update CITATION.cff

  

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  a5d929a

Commits on Nov 3, 2023

• added .check_sim_input function

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  af28cee

• replaced input checking with .check_sim_input in sim_* functions

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  037e4d6

• updated .check_sim_input documentation

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  0afecb9

• moved population_age check to all sims in .check_sim_input

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  d707faf

• added tests for .check_sim_input

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  6144131

Commits on Nov 7, 2023

• added epicontacts to Suggests in DESCRIPTION

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  b7ef5a0

• renamed part_name and contact_name vars in contact table to from and to for epicontacts integration

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  681d3d4

• updated tests with new contacts col names

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  ba68ed7

• added first draft of visualising contacts data section to vis-linelist vignette

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  429812b

• Update CITATION.cff

  

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  ab8165e

• changed output engine in vis-linelist vignette to rmarkdown::html_vignette

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  3739d9c

• minor edits to vis-linelist vignette and added fig.cap labels

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  2e6cf9e

• updated WORDLIST and fixed typos in vis-linelist vignette

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  2bc35d8

• linting

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  2d4a62b

Commits on Nov 9, 2023

• added first draft of design-principles vignette

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  b8be92d

• updated WORDLIST

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  a7ce825

• updated website formatting in _pkgdown.yml

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  6951145

• edits to design-principles vignette

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  6b94cc1

Commits on Nov 10, 2023

• match {linelist} tag names to line list col names

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  9ba5d37

• add design decision on linelist tags in design-principles vignette

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  01b69fb

• updated WORDLIST

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  e66cfa8

• renamed .sim_contacts to .sim_contacts_tbl and updated sim_outbreak and sim_contacts

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  5e9cc20

• {styler} run

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  3e3ddf2

• Automatic readme update

  

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  d3b05d7

Commits on Nov 29, 2023

• remove branch-specific remote install of epiparameter

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  41967d4

Commits on Nov 30, 2023

• added .check_func_req_args

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  0fe0eba

• added Pratik as contributor

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  d4421c6

• convert <epidist> to function in exported functions

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  da851e5

• check for functions not epidist in checkers

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  1958122

• updated internal functions to use distribution functions

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  d42d3ba

• added package documentation with func to remove unused imports check note

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  43740a8

• updated WORDLIST

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  9bc2c1c

• updated tests of internal functions to convert epidist to func

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  4c3f0df

• add option of anonymous function to function documentation

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  2139308

• added section to simulist.Rmd vignette on using anonymous functions

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  5afa173

• added dependency tracker GHA workflow

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  9a9fef3

• fixed typo in sim_linelist tests and rm whitespace from test-sim_contacts

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  e7aff53

Commits on Dec 5, 2023

• updated GHA workflows with merge_groups, error on notes and rebasing

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  c1c33f2

• added link to package documentation file

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  52af940

• added nolint flag check to release_bullets

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  b0b51d7

• added helper state check to tests and turned off stop_on_warning

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  bd77c21

• added check.env file

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  c0e76a7

• added tools to .Rbuildignore

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  2a3b6a1

• run tests in parallel

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  e1331ce

• updated copyright holder in license files

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  349a804

• updated .lintr

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  240e766

• updated WORDLIST

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  6c89a7a

• added nolint flag for mapply call

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  533b1d1

• added NEWS.md and draft of v0.1.0 release notes

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  4e6748d

• Automatic readme update

  

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