Ecosyste.ms: Issues

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GitHub / epiforecasts/EpiNow2 issues and pull requests

#512 - Use of choices here and elsewhere should be moved into the argument default

Issue - State: closed - Opened by seabbs 11 months ago - 1 comment
Labels: enhancement, good first issue

#511 - Use more consistent representations in function documentation and hyperlink functions

Pull Request - State: closed - Opened by jamesmbaazam 11 months ago - 3 comments
Labels: documentation

#510 - Consistency in documentation style

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 1 comment
Labels: documentation

#509 - forecast_infections

Issue - State: closed - Opened by seabbs 11 months ago - 1 comment

#507 - Example data set for `estimate_truncation`

Issue - State: closed - Opened by sbfnk 11 months ago

#506 - Documentation of `reported_cases` should not refer to integers

Issue - State: closed - Opened by sbfnk 11 months ago - 1 comment

#505 - Remove references to "confirmed" cases

Issue - State: open - Opened by sbfnk 11 months ago - 2 comments

#504 - distribution interface to `dist_spec`

Pull Request - State: closed - Opened by sbfnk 11 months ago - 45 comments

#503 - deprecate `fixed` argument to `dist_spec`

Pull Request - State: closed - Opened by sbfnk 11 months ago - 2 comments

#502 - fix check for fixed delay distribution

Pull Request - State: closed - Opened by sbfnk 11 months ago - 1 comment

#501 - Fix partial matching

Pull Request - State: closed - Opened by jamesmbaazam 11 months ago - 1 comment

#500 - Support skipping NAs in the likelihood

Issue - State: closed - Opened by seabbs 11 months ago - 2 comments

#499 - Safeguards against partial matching

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 2 comments

#498 - gamma_dist_def: scale is inverse scale?

Issue - State: closed - Opened by seabbs 11 months ago - 1 comment
Labels: bug

#496 - Add section on acknowledging contributions to CONTRIBUTION.md

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 1 comment

#495 - Reporting templates and the `report` package

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 4 comments

#494 - Fix default value for `generation_time` in `regional_epinow()`

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 1 comment
Labels: bug

#493 - Move `secondary_opts()` to `opts.R` for findability

Issue - State: closed - Opened by jamesmbaazam 11 months ago
Labels: refactor

#492 - Update outdated actions

Issue - State: closed - Opened by sbfnk 11 months ago - 1 comment

#491 - Replace `update_list()` with `utils::modifyList()`

Pull Request - State: closed - Opened by jamesmbaazam 11 months ago
Labels: refactor

#490 - Missing PR number in NEWS

Issue - State: closed - Opened by jamesmbaazam 11 months ago

#489 - Rmd check showing as failing in README but actually passing?

Issue - State: closed - Opened by seabbs 11 months ago
Labels: bug

#488 - Is `EpiNow2::update_list()` `utils::modifyList()`?

Issue - State: closed - Opened by jamesmbaazam 11 months ago - 1 comment
Labels: refactor

#487 - Update phi parameterisation

Pull Request - State: closed - Opened by seabbs 12 months ago - 2 comments

#486 - Issue 485: Update the phi parameterisation

Pull Request - State: closed - Opened by seabbs 12 months ago - 6 comments

#485 - phi = 1 / sqrt(sqrt_phi) -> phi = 1 / sqrt_phi ^ 2

Issue - State: closed - Opened by seabbs 12 months ago - 1 comment

#484 - stan model chunks

Pull Request - State: closed - Opened by sbfnk 12 months ago - 11 comments

#483 - revert to use CRAN version of rstan

Pull Request - State: closed - Opened by sbfnk 12 months ago - 1 comment

#482 - Quick start in README vs. workflow vignette

Issue - State: closed - Opened by sbfnk 12 months ago - 21 comments
Labels: documentation

#481 - Replace get functions with examples for delay distributions

Pull Request - State: closed - Opened by sbfnk 12 months ago - 8 comments

#480 - Fix partial matching of dist to distribution in dist_spec()

Pull Request - State: closed - Opened by jamesmbaazam 12 months ago

#478 - Zeta -> Z

Pull Request - State: closed - Opened by seabbs 12 months ago

#477 - Zeta is Z

Issue - State: closed - Opened by seabbs 12 months ago - 1 comment
Labels: bug

#476 - Add input validation

Pull Request - State: closed - Opened by jamesmbaazam 12 months ago - 24 comments

#475 - Tricks to increase development speed

Issue - State: closed - Opened by jamesmbaazam 12 months ago - 1 comment
Labels: discussion

#474 - fix bounds of initial conditions for delays

Pull Request - State: closed - Opened by sbfnk 12 months ago - 1 comment

#472 - cmdstanr version

Pull Request - State: closed - Opened by sbfnk 12 months ago - 1 comment

#471 - Testing using rstan develop branch

Issue - State: closed - Opened by sbfnk 12 months ago - 7 comments

#470 - manually install up-to-date rstan in action

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#469 - testing with updated rstan

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#468 - Clearer distinguish length and max

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#467 - Keep CITATION and `citation.cff` in sync with DESCRIPTION

Pull Request - State: closed - Opened by jamesmbaazam about 1 year ago - 9 comments

#466 - Add workflow to sync citation file with DESCRIPTION.

Issue - State: closed - Opened by jamesmbaazam about 1 year ago - 1 comment

#465 - James Azam -> author

Pull Request - State: closed - Opened by seabbs about 1 year ago - 1 comment

#464 - Improve contribution guide

Pull Request - State: closed - Opened by jamesmbaazam about 1 year ago

#463 - Explain precompiled vignettes in contribution guide

Issue - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#462 - update versions in docker action

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#461 - attribute news item

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#460 - remove references to forecast_infections

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#459 - Remove examples with long runtimes

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 3 comments

#458 - workflow/options vignettes

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 3 comments

#457 - fix gt pmf dimensions for non-parametric model

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#456 - Prepare 1.4.0 CRAN release

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#455 - Improve deprecation

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#454 - avoid very narrow initial truncation distributions

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#453 - Update deprecated syntax for future rstan compatibility

Pull Request - State: closed - Opened by andrjohns about 1 year ago - 7 comments

#452 - make estimate_truncation return a dist_spec

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#451 - streamline S3 classes

Issue - State: open - Opened by sbfnk about 1 year ago - 6 comments

#450 - move prior weights to model arguments

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#449 - `estimate_truncation` should return a call to `dist_spec`

Issue - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#448 - use `delay_lp` in `estimate_truncation`

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 3 comments

#447 - Default values of `prior_weight`

Issue - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#446 - bug fix: make simulated delay mean unbounded

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#445 - move synthetic validation to macos

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#444 - Synthetic validation jobs fail

Issue - State: closed - Opened by sbfnk about 1 year ago

#443 - Fix 442

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#442 - `estimate_secondary` fails with `prior_weight = 0`

Issue - State: closed - Opened by sbfnk about 1 year ago - 1 comment
Labels: bug

#441 - Issue 440: Added CSTE workshop as a case study

Pull Request - State: closed - Opened by seabbs about 1 year ago
Labels: documentation

#440 - Add a link to new case studies/walkthroughs

Issue - State: closed - Opened by seabbs about 1 year ago
Labels: documentation

#439 - update estimate truncation vignette

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#438 - allow snapshots shorter than trunc_max

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 7 comments

#437 - style change in response to lintr warnings

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#436 - fix regional summary in case of 0/0

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#435 - fix logmean bound

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#434 - Forecast error bands seem potentially implausible

Issue - State: closed - Opened by dajmcdon about 1 year ago - 3 comments

#433 - disable verbosity for failing chains

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 1 comment

#432 - don't defer negative binomial to Poisson at low levels of overdispersion

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 4 comments

#431 - Identifiability issues due to approximation to negative binomial

Issue - State: closed - Opened by sbfnk about 1 year ago

#430 - Long example run times

Issue - State: closed - Opened by sbfnk about 1 year ago - 7 comments

#429 - Failing samplers during tests

Issue - State: closed - Opened by sbfnk about 1 year ago

#428 - Intermittent segfaults on Ubuntu

Issue - State: closed - Opened by sbfnk about 1 year ago - 3 comments

#427 - downgrade StanHeaders

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#426 - qualify internal functions in tests

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#425 - update R CMD check action

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#424 - Action warnings

Issue - State: closed - Opened by sbfnk about 1 year ago

#423 - EpiNow2 2.0.0 roadmap

Issue - State: closed - Opened by sbfnk about 1 year ago - 4 comments

#422 - Tests fail with standard library loading

Issue - State: closed - Opened by sbfnk about 1 year ago

#421 - Try older version

Pull Request - State: closed - Opened by sbfnk about 1 year ago

#420 - Failing tests on Windows

Issue - State: closed - Opened by sbfnk about 1 year ago - 10 comments

#419 - Revert "initialise vectors to zero"

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#418 - test on windows action

Pull Request - State: closed - Opened by sbfnk about 1 year ago - 2 comments

#416 - speed up generation of infections

Pull Request - State: closed - Opened by sbfnk over 1 year ago - 4 comments

#415 - Not for merging: benchmarking generate infections

Pull Request - State: closed - Opened by sbfnk over 1 year ago - 2 comments

#414 - Benchmarking skeleton

Pull Request - State: closed - Opened by sbfnk over 1 year ago

#413 - shorten seeding time

Pull Request - State: closed - Opened by sbfnk over 1 year ago - 2 comments

#412 - Performance

Issue - State: open - Opened by sbfnk over 1 year ago

#411 - Discretisation

Issue - State: closed - Opened by sbfnk over 1 year ago - 4 comments

#410 - Distribution max is really the length

Issue - State: closed - Opened by sbfnk over 1 year ago