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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: 0.7.0
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Version: 0.7.0.9999
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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"),

‎NAMESPACE

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importFrom(data.table,between)
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importFrom(data.table,copy)
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importFrom(data.table,key)
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importFrom(data.table,rbindlist)
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importFrom(data.table,set)
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importFrom(data.table,setDF)
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importFrom(data.table,setkeyv)
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importFrom(dplyr,arrange)
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importFrom(dplyr,bind_rows)
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importFrom(stats,cor)
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importFrom(stats,median)
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importFrom(tibble,as_tibble)
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importFrom(tibble,new_tibble)
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importFrom(tibble,validate_tibble)
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importFrom(tidyr,unnest)
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importFrom(tidyselect,eval_select)
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importFrom(tidyselect,starts_with)

‎NEWS.md

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# epiprocess 0.7.0.9999
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## Improvements
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* Updated vignettes for compatibility with epidatr 1.0.0 in PR #377.
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# epiprocess 0.7.0
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Note that `epiprocess` uses the [Semantic Versioning
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("semver")](https://semver.org/) scheme for all release versions, but any
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inter-release development versions will include an additional ".9999" suffix.
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## Breaking changes:
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## Breaking changes
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* Changes to `epi_slide` and `epix_slide`:
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* If `f` is a function, it is now required to take at least three arguments.
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g, <any other arguments>) { <body> }` to `f = function(x, g, rt, <any
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other arguments>) { <body> }`.
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## New features:
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## New features
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* `epi_slide` and `epix_slide` also make the window data, group key and reference
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time value available to slide computations specified as formulas or tidy
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evaluation expressions, in additional or completely new ways.
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* `epi_slide` and `epix_slide` also make the window data, group key and
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reference time value available to slide computations specified as formulas or
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tidy evaluation expressions, in additional or completely new ways.
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* If `f` is a formula, it can now access the reference time value via `.z` or
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`.ref_time_value`.
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* If `f` is missing, the tidy evaluation expression in `...` can now refer to
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* To keep the old behavior, convert the output of `epix_slide()` to `epi_df`
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when desired and set the metadata appropriately.
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## Improvements:
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## Improvements
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* `epi_slide` and `epix_slide` now support `as_list_col = TRUE` when the slide
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computations output atomic vectors, and output a list column in "chopped"
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format (see `tidyr::chop`).
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* `epi_slide` now works properly with slide computations that output just a
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`Date` vector, rather than converting `slide_value` to a numeric column.
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* Fix `?archive_cases_dv_subset` information regarding modifications of upstream
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data by @brookslogan in (#299).
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* Update to use updated `epidatr` (`fetch_tbl` -> `fetch`) by @brookslogan in
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(#319).
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# epiprocess 0.6.0
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## Breaking changes:
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## Breaking changes
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* Changes to both `epi_slide` and `epix_slide`:
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* The `n`, `align`, and `before` arguments have been replaced by new `before`
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the old behavior, pass in `clobberable_versions_start =
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max_version_with_row_in(x)`.
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## Potentially-breaking changes:
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## Potentially-breaking changes
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* Fixed `[` on grouped `epi_df`s to maintain the grouping if possible when
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dropping the `epi_df` class (e.g., when removing the `time_value` column).
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* `epi_slide` and `epix_slide` now raise an error rather than silently filtering
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out `ref_time_values` that don't meet their expectations.
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## New features:
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## New features
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* `epix_slide`, `<epi_archive>$slide` have a new parameter `all_versions`. With
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`all_versions=TRUE`, `epix_slide` will pass a filtered `epi_archive` to each
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computation rather than an `epi_df` snapshot. This enables, e.g., performing
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pseudoprospective forecasts with a revision-aware forecaster using nested
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`epix_slide` operations.
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## Improvements:
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## Improvements
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* Added `dplyr::group_by` and `dplyr::ungroup` S3 methods for `epi_archive`
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objects, plus corresponding `$group_by` and `$ungroup` R6 methods. The
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requirement (part of
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[#154](https://github.com/cmu-delphi/epiprocess/issues/154)).
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## Cleanup:
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## Cleanup
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* Added a `NEWS.md` file to track changes to the package.
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* Implemented `?dplyr::dplyr_extending` for `epi_df`s
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([#223](https://github.com/cmu-delphi/epiprocess/issues/223)).
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* Fixed various small documentation issues ([#217](https://github.com/cmu-delphi/epiprocess/issues/217)).
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# epiprocess 0.5.0:
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# epiprocess 0.5.0
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## Potentially-breaking changes:
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## Potentially-breaking changes
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* `epix_slide`, `<epi_archive>$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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## 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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## 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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# epiprocess 0.4.0
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## Potentially-breaking changes:
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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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* 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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## 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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## 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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# epiprocess 0.3.0
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## Breaking changes:
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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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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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## 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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`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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# epiprocess 0.2.0
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## Breaking changes:
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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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## 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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## 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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* 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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# epiprocess 0.1.2
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## New features:
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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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## 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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* 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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## 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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# epiprocess 0.1.1
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## New features:
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## New features
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313324
* 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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## Improvements
317328

318329
* Improved `epi_slide` error messaging.
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* Fixed description of the appropriate parameters for an `f` argument to
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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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## Cleanup
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327338
* 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.
348-
* `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 that wrap around this functionality for those unfamiliar with R6
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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`.
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## Implemented core functionality, vignettes
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345+
* 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
349+
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
357+
stable. Allows computation to be provided as a function, `purrr`-style
358+
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
361+
user-specified groups.
362+
* 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
365+
functions that wrap around this functionality for those unfamiliar with R6
366+
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>$slide`: similar to `epi_slide`, but for
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`epi_archive`s; for each requested `ref_time_value` and group, applies
374+
a time window and user-specified computation to a snapshot of the data
375+
as of `ref_time_value`.
376+
* `epix_merge`, `<epi_archive>$merge`: like `merge` for `epi_archive`s,
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but allowing for the last version of each observation to be carried
378+
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,
383+
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
386+
consensus result.
387+
* `detect_outlr_rm`: outlier detection function based on a
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rolling-median-based outlier detection function; one of the methods
389+
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
392+
`detect_outlr`.

‎R/archive.R

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@@ -495,7 +495,10 @@ epi_archive =
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version <= max_version, ] %>%
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unique(by = c("geo_value", "time_value", other_keys),
497497
fromLast = TRUE) %>%
498-
tibble::as_tibble() %>%
498+
tibble::as_tibble() %>%
499+
# (`as_tibble` should de-alias the DT and its columns in any edge
500+
# cases where they are aliased. We don't say we guarantee this
501+
# though.)
499502
dplyr::select(-"version") %>%
500503
as_epi_df(geo_type = self$geo_type,
501504
time_type = self$time_type,

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