epiverse-trace epichains issues

epiverse-trace / epichains

Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models

https://epiverse-trace.github.io/epichains/

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Rename `ntrees` argument to `index_cases` to clarify meaning

#187 jamesmbaazam closed 9 months ago
1
Rename ntrees in simulate_summary() to index_cases

#186 jamesmbaazam closed 9 months ago
0
Use class() and attr() instead of structure()

#184 jamesmbaazam closed 9 months ago
1
Fix [undesirable_function_linter] error

#183 jamesmbaazam closed 9 months ago
0
Remove `simulate_tree()` and `simulate_tree_from_pop()` and replace usage with `simulate_chains()`

#182 jamesmbaazam closed 9 months ago
5
Remove `simulate_tree()` and `simulate_tree_from_pop()`

#181 jamesmbaazam closed 9 months ago
0
Add .lintr configuration from packagetemplate

#180 jamesmbaazam closed 9 months ago
0
Cyclomatic complexity of `simulate_chains()`

#179 jamesmbaazam closed 9 months ago
5
Allow `simulate_summary()` to deal with finite populations

#178 jamesmbaazam closed 8 months ago
0
Update `.lintr` to `packagetemplate` version

#177 jamesmbaazam closed 9 months ago
0
Add lint-changed-files and dependency-change workflows

#176 jamesmbaazam closed 9 months ago
0
columns in return values of `simulate_tree`

#175 sbfnk closed 5 months ago
1
Improve input checking: prefer checkmate for custom checks

#174 jamesmbaazam closed 9 months ago
1
Add pkgdown reference

#173 jamesmbaazam closed 9 months ago
0
Remove defaults from class constructors and validators

#172 jamesmbaazam closed 9 months ago
1
Combine `simulate_tree()` and `simulate_tree_from_pop()` into `simulate_chains()`.

#171 jamesmbaazam closed 9 months ago
6
Fix getting started vignette

#170 jamesmbaazam closed 10 months ago
0
Fix summary method

#169 jamesmbaazam closed 10 months ago
0
Add a pkgdown reference index

#168 jamesmbaazam closed 9 months ago
0
Consider alternative implementations for the offspring distribution

#167 jamesmbaazam closed 8 months ago
11
General improvements to COVID-19 data raw

#166 jamesmbaazam opened 10 months ago
0
README: Revise Quick Start section

#165 jamesmbaazam closed 7 months ago
0
README: Fix badges

#164 jamesmbaazam closed 10 months ago
0
`rborel()`: suggest renaming argument `infinite` to be more informative, e.g. `stop_sims_after`

#163 jamesmbaazam closed 7 months ago
0
Remove redundant internal checking functions in favour of {checkmate} functions

#162 jamesmbaazam closed 9 months ago
0
Remove default empty vectors in constructors

#161 jamesmbaazam closed 9 months ago
0
Add examples to exported class constructors

#160 jamesmbaazam closed 7 months ago
0
Improve input checking of `<epichains_*>` constructors and validators

#159 jamesmbaazam closed 7 months ago
1
Clarify documentation of `ntrees`

#158 jamesmbaazam closed 9 months ago
0
Improve helper functions

#157 jamesmbaazam closed 9 months ago
0
Spring cleaning (2024)

#156 jamesmbaazam closed 5 months ago
1
Fix wrong index of max `<chain_summary>`

#155 jamesmbaazam closed 10 months ago
0
Improve <epichains_summary> validator

#154 jamesmbaazam closed 10 months ago
1
Contributing.md: Change references to {bpmodels}

#153 jamesmbaazam closed 8 months ago
0
Clarify use of "chain sizes and lengths"

#152 jamesmbaazam closed 7 months ago
0
Set seeds in all cases where stochastic functions are used

#151 jamesmbaazam closed 8 months ago
0
Generate sizeable outbreaks in function documentation examples

#150 jamesmbaazam closed 7 months ago
1
Set all optional arguments to `NULL` rather than missing

#149 jamesmbaazam closed 7 months ago
1
Code optimisation: prefer matrices over data.frames in loops

#148 jamesmbaazam closed 5 months ago
1
Prefer the use of `checkmate::assert_*()` or `stopifnot(checkmate::test_*())` rather than `if(!checkmate::test_*()) stop()`

#147 jamesmbaazam closed 9 months ago
1
Be consistent with the use of `return()`

#146 jamesmbaazam closed 9 months ago
0
Mention the type of all function arguments and returns in function documentations

#145 jamesmbaazam closed 7 months ago
0
Update the WORDLIST and enable R CMD check failure on spelling errors

#144 jamesmbaazam closed 10 months ago
0
Update the WORDLIST and enable R CMD check failure on spelling errors

#143 jamesmbaazam closed 10 months ago
1
Combine `simulate_tree()` and `simulate_tree_from_pop()`

#142 jamesmbaazam closed 9 months ago
0
Improve structure and clarity of wording in Getting Started intro vignette.

#141 jamesmbaazam closed 7 months ago
0
Add "Related Packages" section to README

#140 jamesmbaazam closed 7 months ago
1
Restructure applications literature vignette into themes

#139 jamesmbaazam opened 10 months ago
0
Import `truncdist` properly

#138 jamesmbaazam closed 10 months ago
0
Intervention vignette: Point to analogous analytical intervention examples in superspreading package vignette

#137 jamesmbaazam closed 7 months ago
0

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