Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / epiforecasts/EpiNow2 issues and pull requests
#615 - `estimate_secondary` doesn't use seeding time
Issue -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#614 - add within-model profiling
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 4 comments
#613 - Prior(s) for R
Issue -
State: closed - Opened by sbfnk 7 months ago
- 2 comments
Labels: bug
#612 - add 1 before fitting final week when creating shifted cases
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#611 - Non-mechanistic model with shifted cases can create explosive exponential growth
Issue -
State: closed - Opened by sbfnk 7 months ago
Labels: bug
#610 - Directly calculated growth
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 4 comments
#609 - NOT FOR MERGING: use organisation PAT instead of github token
Pull Request -
State: closed - Opened by sbfnk 7 months ago
#608 - Add `filter_leading_zeros` and `zero_threshold` to `estimate_secondary()` and `estimate_truncation()`
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
- 2 comments
#607 - Deprecate `obs`, `reports`, and `reported_cases` in favour of `data`
Issue -
State: closed - Opened by jamesmbaazam 7 months ago
#606 - Add `preprocessing_opts()`
Issue -
State: open - Opened by jamesmbaazam 7 months ago
#605 - Add `filter_leading_zeros` and `zero_threshold` arguments to `estimate_secondary()` and `estimate_truncation()`
Issue -
State: closed - Opened by jamesmbaazam 7 months ago
#604 - Remove reporting templates
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
- 1 comment
#603 - use inv_square instead of 1/pow(..., 2)
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#602 - precompile: loop over orig files
Pull Request -
State: closed - Opened by sbfnk 7 months ago
#601 - fold secondary options into observation model
Issue -
State: open - Opened by sbfnk 7 months ago
- 1 comment
#600 - Time-varying parameters (i.e. conversion to latent variables)
Issue -
State: open - Opened by sbfnk 7 months ago
- 2 comments
#599 - Architecture diagram for the package
Issue -
State: open - Opened by jamesmbaazam 7 months ago
#598 - streamline deprecation warnings
Issue -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#597 - Deprecate `adjust_infection_to_report()`, `report_cases()`, and `sample_approx_dist()`
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
- 4 comments
#596 - Links in package README not going to website
Issue -
State: open - Opened by athowes 7 months ago
- 2 comments
#595 - Remove tune_inv_gamma function after deprecation
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
#594 - Change expected type of `reported_cases` argument to `numeric`
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
#593 - Internal functions
Issue -
State: closed - Opened by sbfnk 7 months ago
#592 - remove author tags
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#591 - Simulate secondary
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 4 comments
#590 - Only set seeds in testing when needed.
Pull Request -
State: closed - Opened by sbfnk 7 months ago
#589 - Only set one seed in tests
Pull Request -
State: closed - Opened by sbfnk 7 months ago
#588 - fix estimate_secondary without delays
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 1 comment
#587 - `estimate_secondary` fails without delays
Issue -
State: closed - Opened by sbfnk 7 months ago
Labels: bug
#586 - don't install pandoc in synthetic validation
Pull Request -
State: closed - Opened by sbfnk 7 months ago
- 3 comments
#585 - Synthetic validation action is failing
Issue -
State: closed - Opened by sbfnk 7 months ago
#584 - Move data creation for `estimate_truncation()` to `data_raw`
Pull Request -
State: closed - Opened by jamesmbaazam 7 months ago
- 8 comments
#583 - Group deprecated functions together in `pkgdown` Reference Page
Issue -
State: closed - Opened by jamesmbaazam 7 months ago
- 2 comments
#581 - `dist_spec()` in the `@dist-interface` branch still works for "lognormal" but does not for "gamma"
Issue -
State: closed - Opened by avallecam 7 months ago
- 1 comment
#580 - `Gamma()` can not use `shape` and `scale` as combined parameters.
Issue -
State: closed - Opened by avallecam 7 months ago
- 2 comments
#579 - `EpiNow2::discretise` is masking `epiparameter::discretise`
Issue -
State: closed - Opened by avallecam 7 months ago
- 2 comments
#578 - Move up version for deprecation warnings
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
- 3 comments
#577 - Fix render readme
Pull Request -
State: closed - Opened by sbfnk 8 months ago
#576 - Render readme github action is failing
Issue -
State: closed - Opened by sbfnk 8 months ago
#575 - replace purrr::map_dfc call
Pull Request -
State: closed - Opened by sbfnk 8 months ago
#574 - R CMD check failures
Issue -
State: closed - Opened by sbfnk 8 months ago
#573 - Update deprecation warnings
Issue -
State: closed - Opened by sbfnk 8 months ago
#572 - Deprecate `init_cumulative_fit()`
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
- 1 comment
#571 - Clarify how infections are estimated
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
- 1 comment
Labels: documentation
#570 - Move secondary_opts to opts.R
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
- 1 comment
#569 - Fix default values for `generation_time` argument
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
#568 - Add missing PR # in NEWS.md
Pull Request -
State: closed - Opened by jamesmbaazam 8 months ago
#567 - Remove `tune_inv_gamma`
Issue -
State: closed - Opened by sbfnk 8 months ago
Labels: good first issue
#566 - deprecate `update_secondary_args`
Issue -
State: closed - Opened by sbfnk 8 months ago
- 2 comments
Labels: question
#565 - warn about generation time default
Issue -
State: closed - Opened by sbfnk 8 months ago
Labels: good first issue
#564 - create `gt_opts` as an alias for `generation_time_opts`
Issue -
State: closed - Opened by sbfnk 8 months ago
- 4 comments
Labels: question
#563 - stan model implementation of `simulate_secondary`
Issue -
State: closed - Opened by sbfnk 8 months ago
- 2 comments
#562 - Replace all `1/pow(..., 2)` calls in stan with `inv_square`
Issue -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#561 - Author function tags
Issue -
State: closed - Opened by seabbs 8 months ago
- 1 comment
Labels: question, low priority, develop
#560 - Fixed rep phi
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#559 - Bundle repeated checks
Issue -
State: open - Opened by sbfnk 8 months ago
- 1 comment
#558 - Setting seeds in tests
Issue -
State: closed - Opened by sbfnk 8 months ago
- 6 comments
#557 - Simulate infections
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 3 comments
#556 - update touchstone actions to use original source
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 7 comments
#555 - Possibility to generalise probability distribution interface?
Issue -
State: open - Opened by joshwlambert 8 months ago
- 1 comment
#554 - add Issue and PR templates
Pull Request -
State: closed - Opened by sbfnk 8 months ago
#553 - `<dist_spec>` is superclass of `list`
Issue -
State: closed - Opened by joshwlambert 8 months ago
- 2 comments
#552 - CRAN release
Issue -
State: closed - Opened by seabbs 8 months ago
- 7 comments
#551 - install cmdstanr in touchdown
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 3 comments
#550 - Enable fixed observation scaling
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 6 comments
#549 - Allow for fixed observation scaling and overdispersion
Issue -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#548 - Efficiency of accumulating NAs
Issue -
State: open - Opened by sbfnk 8 months ago
#547 - Distinguish NA (missing) from NA (accumulated)
Issue -
State: open - Opened by sbfnk 8 months ago
- 8 comments
#546 - Move to `{cli}` for messaging
Issue -
State: closed - Opened by sbfnk 8 months ago
- 2 comments
#545 - Case study on reconstructing infections for COVID and Ebola
Pull Request -
State: closed - Opened by adamkucharski 8 months ago
- 3 comments
#544 - rename simulate_infections -> forecast_infections
Pull Request -
State: closed - Opened by sbfnk 8 months ago
#543 - Not all vignettes are precompiled in the corresponding script
Issue -
State: closed - Opened by sbfnk 8 months ago
#542 - remove unused figures
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#541 - Deprecate `init_cumulative_fit`
Issue -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#540 - Fix tests
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
#539 - snapshots require update due to data.table printing change
Issue -
State: closed - Opened by sbfnk 8 months ago
#538 - repo size
Issue -
State: closed - Opened by sbfnk 8 months ago
- 12 comments
#537 - Cmdstanr option
Pull Request -
State: closed - Opened by sbfnk 8 months ago
- 4 comments
#536 - new infections are reported as confirmed cases
Issue -
State: closed - Opened by sbfnk 8 months ago
- 1 comment
Labels: good first issue
#534 - Add option to accumulate observations
Pull Request -
State: closed - Opened by sbfnk 9 months ago
- 7 comments
#533 - specify tolerance instead of max for distributions
Issue -
State: closed - Opened by sbfnk 9 months ago
- 2 comments
#532 - `adjust_infection_report` return data frame with `confirm` column
Issue -
State: closed - Opened by sbfnk 9 months ago
- 2 comments
Labels: enhancement, good first issue
#531 - Accumulate observations where data are NAs
Issue -
State: closed - Opened by sbfnk 9 months ago
#530 - Infection based damping
Pull Request -
State: closed - Opened by seabbs 9 months ago
#528 - Add support for missing NAs in estimate_infection() model
Pull Request -
State: closed - Opened by seabbs 10 months ago
- 4 comments
#527 - Bump actions/upload-artifact from 3 to 4
Pull Request -
State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies
#526 - Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0
Pull Request -
State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies
#525 - Change all priors to new dist interface, not just delays
Issue -
State: open - Opened by sbfnk 10 months ago
- 3 comments
#524 - Replace superseded purrr::transpose() with purrr::list_transpose()
Pull Request -
State: closed - Opened by jamesmbaazam 10 months ago
#523 - Change "back-calculation" to "non-mechanistic" infection model throughout
Issue -
State: open - Opened by jamesmbaazam 10 months ago
#522 - Clarify how infections are treated in README summary
Issue -
State: closed - Opened by jamesmbaazam 10 months ago
Labels: documentation
#521 - Restructure README and add Getting Started vignette
Pull Request -
State: closed - Opened by jamesmbaazam 11 months ago
- 3 comments
Labels: documentation
#520 - Deprecate `report_cases`, `sample_approx_dist` and `adjust_infection_report`
Issue -
State: closed - Opened by sbfnk 11 months ago
- 2 comments
#519 - `weigh_delay_priors` should be an option to `generation_time_opts`, `delay_opts` and `truncation_opts`
Issue -
State: closed - Opened by sbfnk 11 months ago
#518 - Discretise with two-day censoring windows
Pull Request -
State: closed - Opened by sbfnk 11 months ago
- 6 comments
#517 - Bump actions/checkout from 2 to 4
Pull Request -
State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies
#516 - Bump JamesIves/github-pages-deploy-action from 4.1.4 to 4.4.3
Pull Request -
State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies
#515 - Bump actions/upload-artifact from 2 to 3
Pull Request -
State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies
#514 - Bump r-lib/actions from 1 to 2
Pull Request -
State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies
#513 - add dependabot for github actions updates
Pull Request -
State: closed - Opened by sbfnk 11 months ago