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docs(NEWS): fix formatting
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@dshemetov
dshemetov committed Nov 16, 2023
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Expand Up @@ -4,7 +4,7 @@ Note that `epiprocess` uses the [Semantic Versioning
("semver")](https://semver.org/) scheme for all release versions, but any
inter-release development versions will include an additional ".9999" suffix.

## Breaking changes:
## Breaking changes

* Changes to `epi_slide` and `epix_slide`:
* If `f` is a function, it is now required to take at least three arguments.
Expand All @@ -19,7 +19,7 @@ inter-release development versions will include an additional ".9999" suffix.
g, <any other arguments>) { <body> }` to `f = function(x, g, rt, <any
other arguments>) { <body> }`.

## New features:
## New features

* `epi_slide` and `epix_slide` also make the window data, group key and reference
time value available to slide computations specified as formulas or tidy
Expand All @@ -45,7 +45,7 @@ inter-release development versions will include an additional ".9999" suffix.
* To keep the old behavior, convert the output of `epix_slide()` to `epi_df`
when desired and set the metadata appropriately.

## Improvements:
## Improvements

* `epi_slide` and `epix_slide` now support `as_list_col = TRUE` when the slide
computations output atomic vectors, and output a list column in "chopped"
Expand All @@ -55,7 +55,7 @@ inter-release development versions will include an additional ".9999" suffix.

# epiprocess 0.6.0

## Breaking changes:
## Breaking changes

* Changes to both `epi_slide` and `epix_slide`:
* The `n`, `align`, and `before` arguments have been replaced by new `before`
Expand Down Expand Up @@ -102,7 +102,7 @@ inter-release development versions will include an additional ".9999" suffix.
the old behavior, pass in `clobberable_versions_start =
max_version_with_row_in(x)`.

## Potentially-breaking changes:
## Potentially-breaking changes

* Fixed `[` on grouped `epi_df`s to maintain the grouping if possible when
dropping the `epi_df` class (e.g., when removing the `time_value` column).
Expand All @@ -116,15 +116,15 @@ inter-release development versions will include an additional ".9999" suffix.
* `epi_slide` and `epix_slide` now raise an error rather than silently filtering
out `ref_time_values` that don't meet their expectations.

## New features:
## New features

* `epix_slide`, `<epi_archive>$slide` have a new parameter `all_versions`. With
`all_versions=TRUE`, `epix_slide` will pass a filtered `epi_archive` to each
computation rather than an `epi_df` snapshot. This enables, e.g., performing
pseudoprospective forecasts with a revision-aware forecaster using nested
`epix_slide` operations.

## Improvements:
## Improvements

* Added `dplyr::group_by` and `dplyr::ungroup` S3 methods for `epi_archive`
objects, plus corresponding `$group_by` and `$ungroup` R6 methods. The
Expand All @@ -134,35 +134,35 @@ inter-release development versions will include an additional ".9999" suffix.
requirement (part of
[#154](https://github.com/cmu-delphi/epiprocess/issues/154)).

## Cleanup:
## Cleanup

* Added a `NEWS.md` file to track changes to the package.
* Implemented `?dplyr::dplyr_extending` for `epi_df`s
([#223](https://github.com/cmu-delphi/epiprocess/issues/223)).
* Fixed various small documentation issues ([#217](https://github.com/cmu-delphi/epiprocess/issues/217)).

# epiprocess 0.5.0:
# epiprocess 0.5.0

## Potentially-breaking changes:
## Potentially-breaking changes

* `epix_slide`, `<epi_archive>$slide` now feed `f` an `epi_df` rather than
converting to a tibble/`tbl_df` first, allowing use of `epi_df` methods and
metadata, and often yielding `epi_df`s out of the slide as a result. To obtain
the old behavior, convert to a tibble within `f`.

## Improvements:
## Improvements

* Fixed `epix_merge`, `<epi_archive>$merge` always raising error on `sync="truncate"`.

## Cleanup:
## Cleanup

* Added `Remotes:` entry for `genlasso`, which was removed from CRAN.
* Added `as_epi_archive` tests.
* Added missing `epix_merge` test for `sync="truncate"`.

# epiprocess 0.4.0:
# epiprocess 0.4.0

## Potentially-breaking changes:
## Potentially-breaking changes

* Fixed `[.epi_df` to not reorder columns, which was incompatible with
downstream packages.
Expand All @@ -177,20 +177,20 @@ inter-release development versions will include an additional ".9999" suffix.
* Fixed `[.epi_df` to drop metadata if decaying to a tibble (due to removal
of essential columns).

## Improvements:
## Improvements

* Added check that `epi_df` `additional_metadata` is list.
* Fixed some incorrect `as_epi_df` examples.

## Cleanup:
## Cleanup

* Applied rename of upstream package in examples: `delphi.epidata` ->
`epidatr`.
* Rounded out `[.epi_df` tests.

# epiprocess 0.3.0:
# epiprocess 0.3.0

## Breaking changes:
## Breaking changes

* `as_epi_archive`, `epi_archive$new`:
* Compactification (see below) by default may change results if working
Expand Down Expand Up @@ -223,7 +223,7 @@ inter-release development versions will include an additional ".9999" suffix.
reporting latency, `n=7` will *not* yield 7 days of data in a typical
daily-reporting surveillance data source, as one might have assumed).

## New features:
## New features

* `as_epi_archive`, `epi_archive$new`:
* New `compactify` parameter allows removal of rows that are redundant for the
Expand All @@ -248,20 +248,20 @@ inter-release development versions will include an additional ".9999" suffix.
`epi_archive` rather than an outdated R6 implementation from whenever the
data object was generated.

# epiprocess 0.2.0:
# epiprocess 0.2.0

## Breaking changes:
## Breaking changes

* Removed default `n=7` argument to `epix_slide`.

## Improvements:
## Improvements

* Ignore `NA`s when printing `time_value` range for an `epi_archive`.
* Fixed misleading column naming in `epix_slide` example.
* Trimmed down `epi_slide` examples.
* Synced out-of-date docs.

## Cleanup:
## Cleanup

* Removed dependency of some `epi_archive` tests on an example archive.
object, and made them more understandable by reading without running.
Expand All @@ -271,16 +271,16 @@ inter-release development versions will include an additional ".9999" suffix.
* Removed some dead code.
* Made `.{Rbuild,git}ignore` files more comprehensive.

# epiprocess 0.1.2:
# epiprocess 0.1.2

## New features:
## New features

* New `new_epi_df` function is similar to `as_epi_df`, but (i) recalculates,
overwrites, and/or drops most metadata of `x` if it has any, (ii) may
still reorder the columns of `x` even if it's already an `epi_df`, and
(iii) treats `x` as optional, constructing an empty `epi_df` by default.

## Improvements:
## Improvements

* Fixed `geo_type` guessing on alphabetical strings with more than 2
characters to yield `"custom"`, not US `"nation"`.
Expand All @@ -300,20 +300,20 @@ inter-release development versions will include an additional ".9999" suffix.
* Improved `as_epi_archive` and `epi_archive$new`/`$initialize`
documentation, including constructing a toy archive.

## Cleanup:
## Cleanup

* Added tests for `epi_slide`, `epi_cor`, and internal utility functions.
* Fixed currently-unused internal utility functions `MiddleL`, `MiddleR` to
yield correct results on odd-length vectors.

# epiprocess 0.1.1:
# epiprocess 0.1.1

## New features:
## New features

* New example data objects allow one to quickly experiment with `epi_df`s
and `epi_archives` without relying/waiting on an API to fetch data.

## Improvements:
## Improvements

* Improved `epi_slide` error messaging.
* Fixed description of the appropriate parameters for an `f` argument to
Expand All @@ -322,61 +322,60 @@ inter-release development versions will include an additional ".9999" suffix.
* Added some examples throughout the package.
* Using example data objects in vignettes also speeds up vignette compilation.

## Cleanup:
## Cleanup

* Set up gh-actions CI.
* Added tests for `epi_df`s.

# epiprocess 0.1.0

## Implemented core functionality, vignettes:

Classes:
* `epi_df`: specialized `tbl_df` for geotemporal epidemiological time
series data, with optional metadata recording other key columns (e.g.,
demographic breakdowns) and `as_of` what time/version this data was
current/published. Associated functions:
* `as_epi_df` converts to an `epi_df`, guessing the `geo_type`,
`time_type`, `other_keys`, and `as_of` if not specified.
* `as_epi_df.tbl_ts` and `as_tsibble.epi_df` automatically set
`other_keys` and `key`&`index`, respectively.
* `epi_slide` applies a user-supplied computation to a sliding/rolling
time window and user-specified groups, adding the results as new
columns, and recycling/broadcasting results to keep the result size
stable. Allows computation to be provided as a function, `purrr`-style
formula, or tidyeval dots. Uses `slider` underneath for efficiency.
* `epi_cor` calculates Pearson, Kendall, or Spearman correlations
between two (optionally time-shifted) variables in an `epi_df` within
user-specified groups.
* Convenience function: `is_epi_df`.
* `epi_archive`: R6 class for version (patch) data for geotemporal
epidemiological time series data sets. Comes with S3 methods and regular
functions that wrap around this functionality for those unfamiliar with R6
methods. Associated functions:
* `as_epi_archive`: prepares an `epi_archive` object from a data frame
containing snapshots and/or patch data for every available version of
the data set.
* `as_of`: extracts a snapshot of the data set as of some requested
version, in `epi_df` format.
* `epix_slide`, `<epi_archive>$slide`: similar to `epi_slide`, but for
`epi_archive`s; for each requested `ref_time_value` and group, applies
a time window and user-specified computation to a snapshot of the data
as of `ref_time_value`.
* `epix_merge`, `<epi_archive>$merge`: like `merge` for `epi_archive`s,
but allowing for the last version of each observation to be carried
forward to fill in gaps in `x` or `y`.
* Convenience function: `is_epi_archive`.

Additional functions:
* `growth_rate`: estimates growth rate of a time series using one of a few
built-in `method`s based on relative change, linear regression,
smoothing splines, or trend filtering.
* `detect_outlr`: applies one or more outlier detection methods to a given
signal variable, and optionally aggregates the outputs to create a
consensus result.
* `detect_outlr_rm`: outlier detection function based on a
rolling-median-based outlier detection function; one of the methods
included in `detect_outlr`.
* `detect_outlr_stl`: outlier detection function based on a seasonal-trend
decomposition using LOESS (STL); one of the methods included in
`detect_outlr`.
## Implemented core functionality, vignettes

* Classes:
* `epi_df`: specialized `tbl_df` for geotemporal epidemiological time
series data, with optional metadata recording other key columns (e.g.,
demographic breakdowns) and `as_of` what time/version this data was
current/published. Associated functions:
* `as_epi_df` converts to an `epi_df`, guessing the `geo_type`,
`time_type`, `other_keys`, and `as_of` if not specified.
* `as_epi_df.tbl_ts` and `as_tsibble.epi_df` automatically set
`other_keys` and `key`&`index`, respectively.
* `epi_slide` applies a user-supplied computation to a sliding/rolling
time window and user-specified groups, adding the results as new
columns, and recycling/broadcasting results to keep the result size
stable. Allows computation to be provided as a function, `purrr`-style
formula, or tidyeval dots. Uses `slider` underneath for efficiency.
* `epi_cor` calculates Pearson, Kendall, or Spearman correlations
between two (optionally time-shifted) variables in an `epi_df` within
user-specified groups.
* Convenience function: `is_epi_df`.
* `epi_archive`: R6 class for version (patch) data for geotemporal
epidemiological time series data sets. Comes with S3 methods and regular
functions that wrap around this functionality for those unfamiliar with R6
methods. Associated functions:
* `as_epi_archive`: prepares an `epi_archive` object from a data frame
containing snapshots and/or patch data for every available version of
the data set.
* `as_of`: extracts a snapshot of the data set as of some requested
version, in `epi_df` format.
* `epix_slide`, `<epi_archive>$slide`: similar to `epi_slide`, but for
`epi_archive`s; for each requested `ref_time_value` and group, applies
a time window and user-specified computation to a snapshot of the data
as of `ref_time_value`.
* `epix_merge`, `<epi_archive>$merge`: like `merge` for `epi_archive`s,
but allowing for the last version of each observation to be carried
forward to fill in gaps in `x` or `y`.
* Convenience function: `is_epi_archive`.
* Additional functions:
* `growth_rate`: estimates growth rate of a time series using one of a few
built-in `method`s based on relative change, linear regression,
smoothing splines, or trend filtering.
* `detect_outlr`: applies one or more outlier detection methods to a given
signal variable, and optionally aggregates the outputs to create a
consensus result.
* `detect_outlr_rm`: outlier detection function based on a
rolling-median-based outlier detection function; one of the methods
included in `detect_outlr`.
* `detect_outlr_stl`: outlier detection function based on a seasonal-trend
decomposition using LOESS (STL); one of the methods included in
`detect_outlr`.

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