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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 on Aug 30, 2023

• Automatic readme update

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Commits on Oct 17, 2023

• updated DESCRIPTION with title, description, authors & dependencies

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• updated .Rbuildignore and .gitignore

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• added simulist.Rproj

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• added sim_linelist function

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• added internal functions to add info to linelist

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• updated NAMESPACE

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• updated WORDLIST

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• added test for sim_linelist

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• temporary warnPartialMatchArg = FALSE

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• Update CITATION.cff

  

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• added create_contacts WIP function

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

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

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• added .check_rate_df function

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• only call .add_ct if add_ct = TRUE

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• error if include_contacts = TRUE while WIP

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• updated .add_names arg in create_contacts

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• temp branch specific install of epiparameter

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• add authors to documentation of sim_linelist

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• use <- assignment throughout

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• replace 1:expr with seq_len(expr)

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• use TRUE/FALSE over T/F

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• added nocov and nolint flags to create_contacts while WIP

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• added nocov flags to dev-utils

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• added .create_linelist function for mock testing

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• added tests for .create_linelist

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• keep ct in sim_linelist return if add_ct = TRUE

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• updated WORDLIST

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• added sim_linelist tests

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• fixed assignment typo in .add_ct

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• join by numerics in .add_names

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• consistent behaviour and side-effects for add_cols functions

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• added tests for add_cols functions

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• added tests for checker functions

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• linting

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• temp nolint flag until removing NSE permanently from pkg

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• added package logo

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

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• updated WORDLIST

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• Automatic readme update

  

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Commits on Oct 19, 2023

• only output case names when add_names = TRUE

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• updated sim_linelist tests to include case_name and case_type

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• added sim_linelist test for add_names = FALSE

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• updated WORDLIST

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• added first draft of getting started vignette

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• updates to simulist vignette

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• added bookdown to Suggests

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• Update CITATION.cff

  

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• added first draft of age-stratified rates vignette

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

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

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

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• updates to age-strat-rates vignette

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Commits on Oct 20, 2023

• remove dplyr from Imports

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• replaced dplyr with base R joins

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• Update CITATION.cff

  

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Commits on Oct 23, 2023

• Use vectorized randomNames() call

  

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• added create_config function

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• added tests for create_config

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• added config argument to sim_linelist and use config parameters

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• updated WORDLIST

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• remove genders from create_config

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

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• updated add_cols tests to test for unaccepted distributions

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• test for config inputs in sim_linelist

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• ensure arg matching in do.call for add_cols functions

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• update create_config with correct arg name

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• update and added tests for distribution arg names

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• linting

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Commits on Oct 25, 2023

• add URL and BugReports fields to DESCRIPTION

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• added Hugo as pkg contributor

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• Update CITATION.cff

  

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• Update DESCRIPTION

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  f1e0a7c

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

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• subset col by name not index in create_contacts

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

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• added sim_contacts (exported) function

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• added tests for sim_contacts

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• removed including contacts in sim_linelist

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• removed test that checked include_contacts in sim_linelist

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• added info on sim_contacts to README and simulist vignette

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• linelist -> line list in text

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• Update CITATION.cff

  

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• updated README

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• Automatic readme update

  

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Commits on Oct 26, 2023

• moved replicated sim code into sim_utils functions

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• added sim_outbreak (exported) function

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• added tests for sim_outbreak

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• added age-strat rates test for sim_outbreak

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• added sim_outbreak example to README

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• added sim_outbreak example to simulist vignette

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• Automatic readme update

  

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• linting

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Commits on Oct 27, 2023

• remove time_rounded col from internal chain object

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• removed hosp_rounded col from internal chain object

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• removed death_rounded col from internal chain object

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Commits on Oct 30, 2023

• updated .check_rate_df to use new user input rate df

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

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• updated sim_linelist documentation for new rate df

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

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• use row.names over rownames

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• updated tests for new rate df

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Commits on Nov 1, 2023

• added .check_age_df

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• added tests for .check_age_df

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• updated sim_linelist and .sim_bp_linelist to accommodate age structured population

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• added test for age structured sim_linelist

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• changed age_range argument to population_age

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

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• added test for age-strat rates and age structure

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• updated input checking for age structure in sim_outbreak

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• updated documentation for population_age

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• fixed sim_outbreak .check_rate_df and added nolint for cyclocomp

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• added ggplot2 to Suggests in DESCRIPTION

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• added first draft of age-struct-pop vignette

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

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• updated WORDLIST

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• updated create_contacts to handle age struct data frame

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• added sim_outbreak test for age structure

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• Update CITATION.cff

  

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

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

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• normalise sample weights for age sampling

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

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• brackets do not need be escaped in vignette

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• renamed .create_contacts with .sim_contacts

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Commits on Nov 2, 2023

• include death_date col in line list

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• updated tests to include death_date col

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• added complete reprex to .create_linelist doc

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• updated WORDLIST

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• added first draft of visualisation vignette

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

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• added min version of incidence2 to DESCRIPTION

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• Update CITATION.cff

  

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Commits on Nov 3, 2023

• added .check_sim_input function

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• replaced input checking with .check_sim_input in sim_* functions

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• updated .check_sim_input documentation

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• moved population_age check to all sims in .check_sim_input

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• added tests for .check_sim_input

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Commits on Nov 7, 2023

• added epicontacts to Suggests in DESCRIPTION

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

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• updated tests with new contacts col names

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

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• Update CITATION.cff

  

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

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

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• updated WORDLIST and fixed typos in vis-linelist vignette

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• linting

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Commits on Nov 9, 2023

• added first draft of design-principles vignette

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• updated WORDLIST

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• updated website formatting in _pkgdown.yml

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• edits to design-principles vignette

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Commits on Nov 10, 2023

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

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

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• updated WORDLIST

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

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• {styler} run

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• Automatic readme update

  

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Commits on Nov 29, 2023

• remove branch-specific remote install of epiparameter

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Commits on Nov 30, 2023

• added .check_func_req_args

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• added Pratik as contributor

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• convert <epidist> to function in exported functions

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• check for functions not epidist in checkers

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• updated internal functions to use distribution functions

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

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• updated WORDLIST

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• updated tests of internal functions to convert epidist to func

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• add option of anonymous function to function documentation

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

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• added dependency tracker GHA workflow

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

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Commits on Dec 5, 2023

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

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• added link to package documentation file

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• added nolint flag check to release_bullets

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• added helper state check to tests and turned off stop_on_warning

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• added check.env file

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• added tools to .Rbuildignore

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• run tests in parallel

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• updated copyright holder in license files

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• updated .lintr

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• updated WORDLIST

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• added nolint flag for mapply call

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

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• Automatic readme update

  

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