From c8bc7a4adbe7a26c99f1b3e8d96f52f5ba8f6717 Mon Sep 17 00:00:00 2001 From: Dmitry Shemetov Date: Wed, 15 Nov 2023 16:30:15 -0800 Subject: [PATCH] docs(NEWS): fix formatting --- NEWS.md | 163 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 81 insertions(+), 82 deletions(-) diff --git a/NEWS.md b/NEWS.md index df674425..be8b9b56 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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. @@ -19,7 +19,7 @@ inter-release development versions will include an additional ".9999" suffix. g, ) { }` to `f = function(x, g, rt, ) { }`. -## 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 @@ -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" @@ -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+## Breaking changes * Changes to both `epi_slide` and `epix_slide`: * The `n`, `align`, and `before` arguments have been replaced by new `before` @@ -102,7 +102,7 @@ inter-release development versions will include an additional ".9999" suffix.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). @@ -116,7 +116,7 @@ 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`, `$slide` have a new parameter `all_versions`. With `all_versions=TRUE`, `epix_slide` will pass a filtered `epi_archive` to each @@ -124,7 +124,7 @@ inter-release development versions will include an additional ".9999" suffix. pseudoprospective forecasts with a revision-aware forecaster using nested `epix_slide` operations. -## Improvements: +## Improvements * Added `dplyr::group_by` and `dplyr::ungroup` S3 methods for `epi_archive` objects, plus corresponding `$group_by` and `$ungroup` R6 methods. The @@ -134,35 +134,35 @@ inter-release development versions will include an additional ".9999" suffix. requirement (part of [#154](https://github.com/cmu-delphi/epiprocess/issues/154)). -## Cleanup: +## Cleanup * Added a `NEWS.md` file to track changes to the package. * Implemented `?dplyr::dplyr_extending` for `epi_df`s ([#223](https://github.com/cmu-delphi/epiprocess/issues/223)). * Fixed various small documentation issues ([#217](https://github.com/cmu-delphi/epiprocess/issues/217)). -# epiprocess 0.5.0: +# epiprocess 0.5.0 -## Potentially-breaking changes: +## Potentially-breaking changes * `epix_slide`, `$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`, `$merge` always raising error on `sync="truncate"`. -## Cleanup: +## Cleanup * Added `Remotes:` entry for `genlasso`, which was removed from CRAN. * Added `as_epi_archive` tests. * Added missing `epix_merge` test for `sync="truncate"`. -# epiprocess 0.4.0: +# epiprocess 0.4.0 -## Potentially-breaking changes: +## Potentially-breaking changes * Fixed `[.epi_df` to not reorder columns, which was incompatible with downstream packages. @@ -177,20 +177,20 @@ inter-release development versions will include an additional ".9999" suffix. * Fixed `[.epi_df` to drop metadata if decaying to a tibble (due to removal of essential columns). -## Improvements: +## Improvements * Added check that `epi_df` `additional_metadata` is list. * Fixed some incorrect `as_epi_df` examples. -## Cleanup: +## Cleanup * Applied rename of upstream package in examples: `delphi.epidata` -> `epidatr`. * Rounded out `[.epi_df` tests. -# epiprocess 0.3.0: +# epiprocess 0.3.0 -## Breaking changes: +## Breaking changes * `as_epi_archive`, `epi_archive$new`: * Compactification (see below) by default may change results if working @@ -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$new`: * New `compactify` parameter allows removal of rows that are redundant for the @@ -248,20 +248,20 @@ inter-release development versions will include an additional ".9999" suffix. `epi_archive` rather than an outdated R6 implementation from whenever the data object was generated. -# epiprocess 0.2.0: +# epiprocess 0.2.0 -## Breaking changes: +## Breaking changes * Removed default `n=7` argument to `epix_slide`. -## Improvements: +## Improvements * Ignore `NA`s when printing `time_value` range for an `epi_archive`. * Fixed misleading column naming in `epix_slide` example. * Trimmed down `epi_slide` examples. * Synced out-of-date docs. -## Cleanup: +## Cleanup * Removed dependency of some `epi_archive` tests on an example archive. object, and made them more understandable by reading without running. @@ -271,16 +271,16 @@ inter-release development versions will include an additional ".9999" suffix. * Removed some dead code. * Made `.{Rbuild,git}ignore` files more comprehensive. -# epiprocess 0.1.2: +# epiprocess 0.1.2 -## New features: +## New features * New `new_epi_df` function is similar to `as_epi_df`, but (i) recalculates, overwrites, and/or drops most metadata of `x` if it has any, (ii) may still reorder the columns of `x` even if it's already an `epi_df`, and (iii) treats `x` as optional, constructing an empty `epi_df` by default. -## Improvements: +## Improvements * Fixed `geo_type` guessing on alphabetical strings with more than 2 characters to yield `"custom"`, not US `"nation"`. @@ -300,20 +300,20 @@ inter-release development versions will include an additional ".9999" suffix. * Improved `as_epi_archive` and `epi_archive$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 @@ -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`, `$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`, `$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`, `$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`, `$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`.