Issue 250: Move development version to main
#257
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fix line width warnings in ggplot2
* force numeric for prediction and true value when scoring * changes for review
…209) * add epinowcast method examples and tests for summary * add tests for plot.epinowcast * add examples for all plots + fix log default bug * add tests for enw_plot_obs and expand examples * add tests for enw_plot_obs and expand examples * drop log scale tests in wrapper
* add docs for enw_dates_to_factors * add docs for enw_dates_to_factors * add docs for mod_matrix * write docs and tests for enw_design * add docs and tests for enw_effects_metadata * add docs and tests for enw_add_pooling_effect * add docs and tests for enw_add_cumulative_membership * fixed spurious warning for enw_formula tests and shortened snapshot * fix spurious warning in enw_manual_formula snapshot tests * fix spurious warning in enw_formula_as_data_list snapshot tests * clean up test noise from loading data.table * add missing return documentation * inherit documented parameters where possible * add docs and tests for enw_metadata * add add_group internal helper functin * add more robust handling of .group when missing * add docs and tests for enw_assign_group * add docs and tests for enw_add_delay * add docs and tests for enw_add_max_reported * clean up preprocessing examples * add docs for enw_nowcast_summary * add snapshot tests for enw_nowcast_summary * add docs and tests for enw_nowcast_samples * add docs and tests for enw_add_latest_obs_to_nowcast * add use of summary for enw_add_latest_obs_to_nowcast docs and tests' * add missing postprocessing examples and tests * add docs and tets for enw_summarise_samples * add docs and tests for enw_pp_summary * update news * update documentation * fix variable notes * fix formatting issues * add snapshot rounding to account for platform floating point differences * increase rounding threshold to account for inter-platform issues * rounding fixed for quantiles_to_long tests * Update R/preprocess.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * standardise use of data.frame across package * improve tests for add_group * generalise docs for is.Date * use more backticks in titles etc for dates * dont duplicate observed label * rename round_numeric -> round_numerics * doc that dates_to_factors drops everything else * add @pearsonca as reviewer * add_group requires a data.table and won't let you be sassy * catch data.table issue in enw_assign_group * add new check_by internal helper fn * use everywhere * be more DRY in enw_summarise_samples * find and replace backticks * is.Date title correction * improved enw_add_cumulative_membership docs * merge in plot test changes * screaming whilst manually reviewing all the instances of data.frame * Update R/check.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/formula-tools.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-design-tools.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/preprocess.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/preprocess.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/methods.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-module-helpers.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/preprocess.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-modules.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-tools.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-tools.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/model-tools.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/plot.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/plot.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/plot.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/plot.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * update docs --------- Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com>
* depreciate enw_dates_to_factors * add PR number and @adrian-lison as reviewer * Fix typo I think it is called "deprecated"... --------- Co-authored-by: Adrian Lison <alison@ethz.ch>
* remove internal plot helpers * add tests for check_ functions and refactor check_quantiles to work as expected * correct PR number * clean up whitespace * Add check for valid probabilities * Add @adrian-lison as a reviewer. --------- Co-authored-by: Adrian Lison <adrian.lison@bsse.ethz.ch>
* draft change: add_pooling_effect to more generic finder_fn * update documentation for add_pooling_effect * update internal usage of add_pooling_effect * string=>prefix and dangling commas in add_pooling_effect * expand add_pooling_effect tests to ... * update NEWS * format new tests * refine news item and make breaking changes section with other breaking changes from the development version --------- Co-authored-by: Sam <s.e.abbott12@gmail.com>
* Replace lint.yaml by lint-changed-file.yaml Copied from r-lib/actions with some extra bells and whistles copied from lint.yaml - triggered on develop and can be triggered manually - can be skipped with the [ci skip] instruction in the commit message * Try to include all linters * Fix some indents Indents in function argument definition have not been changed because they are an explicit style choice * Add fixed = TRUE to calls with fixed regexes * Add leading zero to double * Use toString() rather than paste(collapse = ", ") * Use anyNA() rather than any(is.na()) * Remove unused variables * Pass function directly to sapply instead of creating lambda * Use dedicated lengths() function * Remove unnecessary library() calls * Use file.path() to construct file paths * Replace unnecessary ifelse() by as.numeric() * Remove unnecessary paste0() in warning() and stop() * Remove unnecessary c() * Use seq_len() rather than : * Use sort() rather than order() * Remove nested if * Disable linters that generate too many false positive or that flag explicit style choices that diverge from default * Run devtools::document() * Add NEWS items * Increment version number * Remove extra trailing whitespace
Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
* Update DESCRIPTION * Add @pratikunterwegs as a contributor * match orcid style * Update DESCRIPTION Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com> --------- Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com>
…specification (#232) * make enw_metadata target_date default be detected from data * typo for news and add @pearsonca as reviewer * improve enw_metadata examples and tests * update news to self-reviewed
* Do not use else after stop() * add news entry and update dev package version * correct news typo --------- Co-authored-by: Sam <s.e.abbott12@gmail.com>
* removed no_contrasts variable * fix bug with use of both random walks and random effects * update snapshot tests * Xupdate news - move bugs to top * fix enw_replace_priors bug due to pillars usage * add a test for using a fit object with enw_replace_priors * add an example of using a fit object to update priors to enw_replace_priors docs * update news with examples and test changes * add rw__ prefix for random walk variances to help identify * add support for using the same variable as a random effect and as a random walk + erorr when same used as re and fixed * fix enw_replace_priors example * ignore top leevel figures folder * fixed linting issues * update Germany vignette * update news and description * add tests to cover new input checks * update news and dev version
* update citation * update README * add news item for CITATION update
* update news * catch news issue * update READE
* add generic touchstone setup * add news item for PR * add Github Actons config from EpiNow2 * add custom benchmarks based on package examples * add custom benchmarks based on package examples * remove test.R * don't try and pin touchstone as this happens automatically * update news * try keeping touch stone * Test pin_assets as point of failure * Test pin_assets inst/examples as point of failure * TEMPORARILY DISABLE expensive WORKFLOWS * Test pin_assets touchstone as point of failure * Test workaround touchstone * Add set_cmdstan_path * Fix set cmdstan path * revert changes * correctly revert * try reodering branch_install() * drop pin_assests again * update DESCRIPTION and NEWS dev version * turn expensive workflows back on * update news * resetup touchston after reading docs again * revert to using touchstone from * use forked touchstone * use full path for benchmark scripts * drop use of path pinning * drop pin_assets based on EpiNow2 implementation from @sbfnk * try not sourcing * update PR news * check news * add a custom touchstone action that installs cmdstanr * use the right touchstone version * remove cmdstanr from initial workflow * use correct file structure for a local action * more work on the file system * more file system fighting * try and get the local action from the GitHub repo * flail around wiht pin_assets * pin_assets is definitely a problem * imagine the working directory is in the touchstone folder * make cmdstan install quiet * actually commit the required files * update touchstone script * don' t check preprocessing * drop where am I checks for touchstone custom action * don't pre-compile the model but instead pass in a function call * use n = 3 for all benchmarks * fix for multi-chain use * move model compilation out of benchmark stan side changes will bias * reduce the number of samples called for and switch out some obseration models * get ready for merging into develop * make sure model is being compiled as needed * make use of develop github action ready for merging * add more news detail * add missing line --------- Co-authored-by: Adrian Lison <adrian.lison@bsse.ethz.ch>
Consolidates checking and copying for data-like arguments to assorted functions. --------- Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
* add linelist converter and rename current cnonverters * depreciate data converters * depreciate data converters * update NAMESPACE * add enw_incidence_to_linelist * complete data converters documentation * add snapshot tests for enw_incidence_to_linelist * add snapshot tests for enw_linelist_to_incidence and fix grouping bug picked up by testing * add imported data.table functions * add news item * add @jhellewell14 to news item for new features * added a new argument to enw_complete_dates to make filtering by the meax observed optional * add completion_beyond_max_report pass through * rename arg to include max_report * lint changes with lintr::lint_package() * final linting * add @jhellewell14 as a contributor * add new lines at end of test scripts where needed * rebase and update to include coerce_dt() * tweak news file * deal with linting issues * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * additional suggested changes from @pearsonca * deal with linting issues * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * Update R/data-converters.R Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> --------- Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com>
…latest cmdstan (#255) * correct initial conditions for r intercept + revert CI to latest cmdstan * update NEWS and DESCRIPTION * deal with spare bracket in news * clean up spurious bullet
4 tasks
…256) * update README.Rmd * update contributing guide * add an action to render the README if README.Rmd is touched * add a concurrency check * add Rscript shell arg * update news * update dev version * change README name * touch readme * touch readme * Update README.Rmd Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com> * Automatic readme update * Update README.Rmd Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com> * add spaces around getting started resources * Automatic readme update --------- Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com> Co-authored-by: GitHub Action <action@github.com> Co-authored-by: Carl A. B. Pearson <pearsonca@users.noreply.github.com>
Codecov Report
@@ Coverage Diff @@
## main #257 +/- ##
==========================================
+ Coverage 88.18% 96.82% +8.63%
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Files 14 15 +1
Lines 1490 1574 +84
==========================================
+ Hits 1314 1524 +210
+ Misses 176 50 -126
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if ac6ff7d is merged into main:
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Everything looks good I think. Going to merge into into |
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Description
Following on from #250 this PR shifts our development version onto
main. As we are near release the time to do this is nearly upon us anyway. Also as this release contains important bug fixes it seems key to expose to users as soon as possible.I think this can be passed with minimal review once checks are passing (just to check rebasing etc has gone okay) as we will do pre-release checks very shortly for
0.2.1and this is not a "release" in the sense of previous moves fromdeveloptomain.Checklist
NEWS.mdand theDESCRIPTION.