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Add changelog (NEWS.md), associated pkgdown styling
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‎DESCRIPTION‎

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Type: Package
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Package: epiprocess
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Title: Tools for basic signal processing in epidemiology
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Version: 1.0.0
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Version: 0.5.0.9999
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Authors@R: c(
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person("Jacob", "Bien", role = "ctb"),
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person("Logan", "Brooks", role = "aut"),

‎NEWS.md‎

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# epiprocess 0.5.0.9999 (dev version)
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## Cleanup:
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* Added a `NEWS.md` file to track changes to the package.
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# epiprocess 0.5.0:
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## Potentially-breaking changes:
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* `epix_slide`, `<epi_archive>$slide` now feed `f` an `epi_df` rather than
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converting to a tibble/`tbl_df` first, allowing use of `epi_df` methods and
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metadata, and often yielding `epi_df`s out of the slide as a result. To obtain
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the old behavior, convert to a tibble within `f`.
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## Improvements:
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* Fixed `epix_merge`, `<epi_archive>$merge` always raising error on `sync="truncate"`
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## Cleanup:
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* Added `Remotes:` entry for `genlasso`, which was removed from CRAN
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* Added `as_epi_archive` tests
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* Added missing `epix_merge` test for `sync="truncate"`
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# epiprocess 0.4.0:
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## Potentially-breaking changes:
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* Fixed `[.epi_df` to not reorder columns, which was incompatible with
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downstream packages.
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* Changed `[.epi_df` decay-to-tibble logic to more coherent with `epi_df`s
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current tolerance of nonunique keys: stopped decaying to a tibble in some
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cases where a unique key wouldn't have been preserved, since we don't
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enforce a unique key elsewhere.
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* Fixed `[.epi_df` to adjust `"other_keys"` metadata when corresponding
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columns are selected out.
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* Fixed `[.epi_df` to raise an error if resulting column names would be
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nonunique.
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* Fixed `[.epi_df` to drop metadata if decaying to a tibble (due to removal
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of essential columns).
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## Improvements:
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* Added check that `epi_df` `additional_metadata` is list.
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* Fixed some incorrect `as_epi_df` examples.
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## Cleanup:
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* Applied rename of upstream package in examples: `delphi.epidata` ->
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`epidatr`.
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* Rounded out `[.epi_df` tests.
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# epiprocess 0.3.0:
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## Breaking changes:
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* `as_epi_archive`, `epi_archive$new`:
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* Compactification (see below) by default may change results if working
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directly with the `epi_archive`'s `DT` field; to disable, pass in
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`compactify=FALSE`.
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* `epi_archive`'s wrappers and R6 methods have been updated to follow these
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rules regarding reference semantics:
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* `epix_<method>` will not mutate input `epi_archive`s, but may alias them
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or alias their fields (which should not be a worry if a user sticks to
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these `epix_*` functions and "regular" R functions with
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copy-on-write-like behavior, avoiding mutating functions `[.data.table`)
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* `x$<method>` may mutate `x`; if it mutates `x`, it will return `x`
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invisibly (where this makes sense), and, for each of its fields, may
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either mutate the object to which it refers or reseat the reference (but
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not both); if `x$<method>` does not mutate `x`, its result may contain
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aliases to `x` or its fields.
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* `epix_merge`, `<epi_archive>$merge`:
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* Removed `...`, `locf`, and `nan` parameters.
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* Changed the default behavior, which now corresponds to using
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`by=key(x$DT)` (but demanding that is the same set of column names as
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`key(y$DT)`), `all=TRUE`, `locf=TRUE`, `nan=NaN` (but with the
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post-filling step fixed to only apply to gaps, and no longer fill over
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`NA`s originating from `x$DT` and `y$DT`).
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* `x` and `y` are no longer allowed to share names of non-`by` columns.
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* `epix_merge` no longer mutates its `x` argument (but `$merge` continues
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to do so).
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* Removed (undocumented) capability of passing a `data.table` as `y`.
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* `epix_slide`:
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* Removed inappropriate/misleading `n=7` default argument (due to
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reporting latency, `n=7` will *not* yield 7 days of data in a typical
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daily-reporting surveillance data source, as one might have assumed).
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## New features:
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* `as_epi_archive`, `epi_archive$new`:
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* New `compactify` parameter allows removal of rows that are redundant for the
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purposes of `epi_archive`'s methods, which use the last version of each
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observation carried forward.
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* New `clobberable_versions_start` field allows marking a range of versions
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that could be "clobbered" (rewritten without assigning new version
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tags); previously, this was hard-coded as `max(<epi_archive>$DT$version)`.
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* New `versions_end` field allows marking a range of versions beyond
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`max(<epi_archive>$DT$version)` that were observed, but contained no
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changes.
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* `epix_merge`, `$merge`:
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* New `sync` parameter controls what to do if `x` and `y` aren't equally
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up to date (i.e., if `x$versions_end` and `y$versions_end` are
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different).
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* New function `epix_fill_through_version`, method
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`<epi_archive>$fill_through_version`: non-mutating & mutating way to
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ensure that an archive contains versions at least through some
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`fill_versions_end`, extrapolating according to `how` if necessary
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* Example archive data object is now constructed on demand from its
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underlying data, so it will be based on the user's version of
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`epi_archive` rather than an outdated R6 implementation from whenever the
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data object was generated.
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# epiprocess 0.2.0:
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## Breaking changes:
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* Removed default `n=7` argument to `epix_slide`.
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## Improvements:
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* Ignore `NA`s when printing `time_value` range for an `epi_archive`.
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* Fixed misleading column naming in `epix_slide` example.
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* Trimmed down `epi_slide` examples.
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* Synced out-of-date docs.
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## Cleanup:
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* Removed dependency of some `epi_archive` tests on an example archive.
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object, and made them more understandable by reading without running.
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* Fixed `epi_df` tests relying on S3 implementation external to `epiprocess`.
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* Added tests for `epi_archive` methods and wrapper functions.
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* Removed some dead code.
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* Made `.{Rbuild,git}ignore` files more comprehensive.
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# epiprocess 0.1.2:
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## New features:
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* New `new_epi_df` function is similar to `as_epi_df`, but (i) recalculates,
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overwrites, and/or drops most metadata of `x` if it has any, (ii) may
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still reorder the columns of `x` even if it's already an `epi_df`, and
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(iii) treats `x` as optional, constructing an empty `epi_df` by default.
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## Improvements:
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* Fixed `geo_type` guessing on alphabetical strings with more than 2
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characters to yield `"custom"`, not US `"nation"`.
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* Fixed `time_type` guessing to actually detect `Date`-class `time_value`s
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regularly spaced 7 days apart as `"week"`-type as intended.
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* Improved printing of `epi_df`s, `epi_archives`s
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* Fixed `as_of` to not cut off any (forecast-like) data with `time_value >
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max_version`.
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* Expanded `epi_df` docs include conversion from `tsibble`/`tbl_ts` objects,
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usage of `other_keys`, and pre-processing objects not following the
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`geo_value`, `time_value` naming scheme.
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* Expanded `epi_slide` examples to show how to use an `f` argument with
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named parameters.
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* Updated examples to print relevant columns given a common 80-column
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terminal width.
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* Added growth rate examples.
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* Improved `as_epi_archive` and `epi_archive$new`/`$initialize`
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documentation, including constructing a toy archive.
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## Cleanup:
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* Added tests for `epi_slide`, `epi_cor`, and internal utility functions.
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* Fixed currently-unused internal utility functions `MiddleL`, `MiddleR` to
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yield correct results on odd-length vectors.
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# epiprocess 0.1.1:
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## New features:
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* New example data objects allow one to quickly experiment with `epi_df`s
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and `epi_archives` without relying/waiting on an API to fetch data.
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## Improvements:
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* Improved `epi_slide` error messaging.
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* Fixed description of the appropriate parameters for an `f` argument to
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`epi_slide`; previous description would give incorrect behavior if `f` had
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named parameters that did not receive values from `epi_slide`'s `...`.
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* Added some examples throughout the package.
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* Using example data objects in vignettes also speeds up vignette compilation.
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* Cleanup:
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* Set up gh-actions CI.
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* Added tests for `epi_df`s.
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# epiprocess 0.1.0
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## Implemented core functionality, vignettes:
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Classes:
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* `epi_df`: specialized `tbl_df` for geotemporal epidemiological time
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series data, with optional metadata recording other key columns (e.g.,
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demographic breakdowns) and `as_of` what time/version this data was
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current/published. Associated functions:
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* `as_epi_df` converts to an `epi_df`, guessing the `geo_type`,
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`time_type`, `other_keys`, and `as_of` if not specified.
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* `as_epi_df.tbl_ts` and `as_tsibble.epi_df` automatically set
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`other_keys` and `key`&`index`, respectively.
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* `epi_slide` applies a user-supplied computation to a sliding/rolling
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time window and user-specified groups, adding the results as new
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columns, and recycling/broadcasting results to keep the result size
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stable. Allows computation to be provided as a function, `purrr`-style
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formula, or tidyeval dots. Uses `slider` underneath for efficiency.
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* `epi_cor` calculates Pearson, Kendall, or Spearman correlations
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between two (optionally time-shifted) variables in an `epi_df` within
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user-specified groups.
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* Convenience function: `is_epi_df`
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* `epi_archive`: R6 class for version (patch) data for geotemporal
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epidemiological time series data sets. Comes with S3 methods and regular
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functions wrappers for those unfamiliar with R6 methods. Associated functions:
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* `as_epi_archive`: prepares an `epi_archive` object from a data frame
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containing snapshots and/or patch data for every available version of
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the data set.
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* `as_of`: extracts a snapshot of the data set as of some requested
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version, in `epi_df` format
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* `epix_slide`, `<epi_archive>$slide`: similar to `epi_slide`, but for
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`epi_archive`s; for each requested `ref_time_value` and group, applies
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a time window and user-specified computation to a snapshot of the data
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as of `ref_time_value`.
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* `epix_merge`, `<epi_archive>$merge`: like `merge` for `epi_archive`s,
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but allowing for the last version of each observation to be carried
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forward to fill in gaps in `x` or `y`.
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* Convenience function: `is_epi_archive`
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Additional functions:
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* `growth_rate`: estimates growth rate of a time series using one of a few
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built-in `method`s based on relative change, linear regression,
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smoothing splines, or trend filtering.
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* `detect_outlr`: applies one or more outlier detection methods to a given
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signal variable, and optionally aggregates the outputs to create a
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consensus result
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* `detect_outlr_rm`: outlier detection function based on a
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rolling-median-based outlier detection function; one of the methods
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included in `detect_outlr`.
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* `detect_outlr_stl`: outlier detection function based on a seasonal-trend
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decomposition using LOESS (STL); one of the methods included in
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`detect_outlr`.

‎pkgdown/extra.scss‎

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/* The news/changelog in pkgdown 2.0.6 is squashed relative to 1.6.1, and
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secondary headings are too prominent when using ## (but we can't change to
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### without impacting side navbar). Just trying a couple of bootswatches
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didn't seem to help, and nice template packages might be limited for use by
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particular own groups (e.g., tidytemplate).
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*/
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/* Current approach: add some spacing with CSS, and change ## -> ### in the .md
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to get smaller fonts more easily.
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*/
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/* General structure: div.template-news wraps everything of interest regarding
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the rendered NEWS.md. Within that, div.level2's wrap the each package version
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+ the changes for that version. (Within those,) h2.pkg-version's label the
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versions.
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*/
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/* Matches the first-listed version's section. (This is written as a general
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rule, but the adjacent sibling rule with override it for non-first versions'
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sections. Using :first-child probably wouldn't work as a sibling
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div.page-header precedes the first div.level2.) */
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div.template-news div.level2 {
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margin-top: 1.5em;
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}
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/* Matches subsequent versions' sections. Places more vspace between these
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sections than before the first section.
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*/
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div.template-news div.level2 + div.level2 {
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margin-top: 2.5em;
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}
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/* Place some additional vspace after each version number heading; currently,
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the immediately following content is always a secondary heading, which looks
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weird with the default spacing.
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*/
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div.template-news h2.pkg-version {
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margin-bottom: 0.5em;
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}
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/* Use `h4` styling for `h3`s (the ## headings); this is the only thing we need
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.scss for, and we could really just copy-paste in the appropriate value if
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needed: */
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div.template-news h3 {
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@extend h4;
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}
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/* Original approach, to be removed at some later time: try adding hrules before
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and after primary headings (version numbers). The initial "hrule" (actually a
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border) after the "Source:" pointer has a different color from natural
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hrules, so we need some custom CSS styling to get these colors to match and
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look okay:
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*/
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/* .template-news .page-header { */
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/* /\* 1px solid to match original *\/ */
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/* /\* (original color was something like --bs-default which seemed to be set to */
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/* --bs-gray-300) *\/ */
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/* border-bottom: 1px solid var(--bs-secondary); */
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/* } */
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/* .template-news hr { */
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/* height: 1px; /\* defensive *\/ */
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/* background-color: var(--bs-secondary); */
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/* opacity: 1; /\* counteracts a 0.25 setting somewhere *\/ */
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/* } */

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