Update epi_df.Rmd rate aggregation, key_colnames(), revision_summary()
#599
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to ease epipredict transition.
* Produce error rather than default selection when user provides a tidyselection in ... but it selects zero columns. * Change time_within_x_latest to take `values` as a vector * Use `.data` instead of `pick` etc. in some places
So it is not misinterpreted as "the amount of time that it has been near the latest".
and avoid unnecessary `abs()`
* This may fix some behaviors and emit more sensible error messages on yearmonths given yearmonth-incompatible settings. * This should express time differences for weekly data in terms of weeks, and may emit errors given weekly-"incompatible" settings. * This appears to be computationally faster (vs. `as.integer(version) - as.integer(time_value)`).
It's probably best to immediately ungroup after performing grouped operations in our documentation, as leaving things grouped accidentally is a source of errors. Sometime we should consider an overhaul to use `by =` and `.by =` where appropriate (sorting effects not needed) and available (not all operations support this syntax yet). There were already 0s in the example data, so "highlight" with words the effects of completion + note one potential surprise in other applications.
- Note `...` optional in args of slide comp fn. - Push toward computations returning tibbles rather than vanilla data.frames. - Highlight `na.rm = TRUE`'s operation (not the only type of 7dsum/7dav), mention we also show sum. - Immediately ungroup output + save a line using new autogroup-ungroup behavior of epi_slide_opt&co.
So that naming, docs, and implementation all match.
So we can crossref in other internal roxygen without CHECK warning.
* Make `key_colnames.epi_archive` output epikey-time-version rather than just epikey-time. * Make `key_colnames.data.frame` require `other_keys` be provided. * Remove `key_colnames.default`. * Make `key_colnames` forbid passing `exclude` positionally. * Update downstream `revision_summary`.
Fix length -> vec_size. Combining (logical/generic) NA with Dates is apparently slow. Slice with NA_integer_ index instead. Fix docs: dplyr 1.1.0 should also have a generalized dplyr::lag. Removing some dplyr::lag features for speed might be another motivation, but we seem to be faster for some ptypes x sizes and slower for others. Also, don't export this function; we don't need to.
Various iterations of vec_position_lag seem to be trading off performance and whether they beat dplyr::lag for different classes. dplyr::lag appears to be better-performing than many/all variants tested so far for lagging very long Date and character vectors, like we would do during compactification. We might try speeding up compactification by iterating on some of these variants, something inspired by `check_ukey_unique()`, etc., but that's not the present goal, so just use `dplyr::lag()` for now.
e.g., `distribution`s
Plus add some pluralization and capitalization features.
…ample Fix age group rate aggregation example
Rework `key_colnames`
Co-authored-by: David Weber <david.weber2@pm.me>
…ary-age_agg-updates' into lcb/update-key_colnames.epi_archive
…rchive Update `revision_summary`
brookslogan
changed the title
key_colnames(), revision_summary()epi_df.Rmd rate aggregation, key_colnames(), revision_summary()
brookslogan
deleted the
lcb/key_colnames-revision_summary-age_agg-updates
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Checklist
Please:
PR).
brookslogan, nmdefries.
DESCRIPTION. Always incrementthe patch version number (the third number), unless you are making a
release PR from dev to main, in which case increment the minor version
number (the second number).
(backwards-incompatible changes to the documented interface) are noted.
Collect the changes under the next release number (e.g. if you are on
1.7.2, then write your changes under the 1.8 heading).
process.
Change explanations for reviewer
See #591, #592, #540.
Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch
epi_dfcallskey_colnamesincorrectly and aggregates rates incorrectly #587key_colnamesreturns wrong values for archive data #565epi_archive's compactify doesn't support distributions #541revision_summaryif there are multiple valid ones #571