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

#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

#606 - Add `preprocessing_opts()`

Issue - State: open - 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

#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

#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

#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

#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

#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

#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