Update main branch with v0.7.0

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$

.github/workflows/R-CMD-check.yaml

@@ -1,10 +1,12 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 
@@ -27,3 +29,5 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        env:
+          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}

.github/workflows/pkgdown.yaml

@@ -1,10 +1,12 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -34,6 +36,8 @@ jobs:
           needs: website
 
       - name: Build site
+        env:
+          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 

DESCRIPTION

@@ -1,11 +1,12 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.5.0.9999
+Version: 0.6.0.9999
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", role = "aut"),
     person("Rafael", "Catoia", role = "ctb"),
+    person("Nat", "DeFries", role = "ctb"),
     person("Daniel", "McDonald", role = "aut"),
     person("Rachel", "Lobay", role = "ctb"),
     person("Ken", "Mawer", role = "ctb"),
@@ -20,13 +21,15 @@ Description: This package introduces a common data structure for epidemiological
     work with revisions to these data sets over time, and offers associated
     utilities to perform basic signal processing tasks.
 License: MIT + file LICENSE
-Imports: 
+Imports:
+    cli,
     data.table,
-    dplyr,
+    dplyr (>= 1.0.0),
     fabletools,
     feasts,
     generics,
     genlasso,
+    lifecycle (>= 1.0.1),
     lubridate,
     magrittr,
     purrr,
@@ -35,18 +38,18 @@ Imports:
     slider,
     tibble,
     tidyr,
-    tidyselect,
+    tidyselect (>= 1.2.0),
     tsibble,
-    utils
+    utils,
+    vctrs
 Suggests:
     covidcast,
     epidatr,
     ggplot2,
     knitr,
     outbreaks,
     rmarkdown,
-    testthat (>= 3.0.0),
-    vctrs,
+    testthat (>= 3.1.5),
     waldo (>= 0.3.1),
     withr
 VignetteBuilder: 
@@ -59,7 +62,22 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 2.10)
 URL: https://cmu-delphi.github.io/epiprocess/
+Collate: 
+    'archive.R'
+    'correlation.R'
+    'data.R'
+    'epi_df.R'
+    'epiprocess.R'
+    'methods-epi_archive.R'
+    'grouped_epi_archive.R'
+    'growth_rate.R'
+    'methods-epi_df.R'
+    'outliers.R'
+    'reexports.R'
+    'slide.R'
+    'utils.R'
+    'utils_pipe.R'

NAMESPACE

@@ -1,24 +1,31 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("[",epi_df)
-S3method(arrange,epi_df)
+S3method("names<-",epi_df)
 S3method(as_epi_df,data.frame)
 S3method(as_epi_df,epi_df)
 S3method(as_epi_df,tbl_df)
 S3method(as_epi_df,tbl_ts)
+S3method(as_tibble,epi_df)
 S3method(as_tsibble,epi_df)
-S3method(filter,epi_df)
+S3method(dplyr_col_modify,col_modify_recorder_df)
+S3method(dplyr_col_modify,epi_df)
+S3method(dplyr_reconstruct,epi_df)
+S3method(dplyr_row_slice,epi_df)
+S3method(epix_truncate_versions_after,epi_archive)
+S3method(epix_truncate_versions_after,grouped_epi_archive)
+S3method(group_by,epi_archive)
 S3method(group_by,epi_df)
+S3method(group_by,grouped_epi_archive)
+S3method(group_by_drop_default,grouped_epi_archive)
 S3method(group_modify,epi_df)
-S3method(mutate,epi_df)
+S3method(groups,grouped_epi_archive)
 S3method(next_after,Date)
 S3method(next_after,integer)
 S3method(print,epi_df)
-S3method(relocate,epi_df)
-S3method(rename,epi_df)
-S3method(slice,epi_df)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
+S3method(ungroup,grouped_epi_archive)
 S3method(unnest,epi_df)
 export("%>%")
 export(archive_cases_dv_subset)
@@ -35,12 +42,14 @@ export(epi_slide)
 export(epix_as_of)
 export(epix_merge)
 export(epix_slide)
+export(epix_truncate_versions_after)
 export(filter)
 export(group_by)
 export(group_modify)
 export(growth_rate)
 export(is_epi_archive)
 export(is_epi_df)
+export(is_grouped_epi_archive)
 export(max_version_with_row_in)
 export(mutate)
 export(new_epi_df)
@@ -60,9 +69,16 @@ importFrom(data.table,key)
 importFrom(data.table,set)
 importFrom(data.table,setkeyv)
 importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,dplyr_col_modify)
+importFrom(dplyr,dplyr_reconstruct)
+importFrom(dplyr,dplyr_row_slice)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_drop_default)
 importFrom(dplyr,group_modify)
+importFrom(dplyr,group_vars)
+importFrom(dplyr,groups)
 importFrom(dplyr,mutate)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
@@ -72,20 +88,37 @@ importFrom(dplyr,ungroup)
 importFrom(lubridate,days)
 importFrom(lubridate,weeks)
 importFrom(magrittr,"%>%")
+importFrom(purrr,map_lgl)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,arg_match)
+importFrom(rlang,caller_arg)
+importFrom(rlang,caller_env)
+importFrom(rlang,check_dots_empty0)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
+importFrom(rlang,env)
+importFrom(rlang,f_env)
+importFrom(rlang,f_rhs)
+importFrom(rlang,global_env)
+importFrom(rlang,is_environment)
+importFrom(rlang,is_formula)
+importFrom(rlang,is_function)
+importFrom(rlang,is_missing)
 importFrom(rlang,is_quosure)
+importFrom(rlang,is_string)
+importFrom(rlang,missing_arg)
+importFrom(rlang,new_function)
 importFrom(rlang,quo_is_missing)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(stats,cor)
 importFrom(stats,median)
+importFrom(tibble,as_tibble)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
+importFrom(utils,tail)

NEWS.md

@@ -1,12 +1,144 @@
-# epiprocess 0.5.0.9999 (development version)
+# epiprocess 0.7.0
 
 Note that `epiprocess` uses the [Semantic Versioning
-("semver")](https://semver.org/) scheme for all release versions, but not for
-development versions. A ".9999" suffix indicates a development version.
+("semver")](https://semver.org/) scheme for all release versions, but any
+inter-release development versions will include an additional ".9999" suffix.
+
+## Breaking changes:
+
+* Changes to `epi_slide` and `epix_slide`:
+  * If `f` is a function, it is now required to take at least three arguments.
+    `f` must take an `epi_df` with the same column names as the archive's `DT`,
+    minus the `version` column; followed by a one-row tibble containing the
+    values of the grouping variables for the associated group; followed by a
+    reference time value, usually as a `Date` object. Optionally, it can take
+    any number of additional arguments after that, and forward values for those
+    arguments through `epi[x]_slide`'s `...` args.
+    * To make your existing slide computations work, add a third argument to
+      your `f` function to accept this new input: e.g., change `f = function(x,
+      g, <any other arguments>) { <body> }` to `f = function(x, g, rt, <any
+      other arguments>) { <body> }`.
+
+## 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
+  evaluation expressions, in additional or completely new ways.
+  * If `f` is a formula, it can now access the reference time value via `.z` or
+    `.ref_time_value`.
+  * If `f` is missing, the tidy evaluation expression in `...` can now refer to
+    the window data as an `epi_df` or `tibble` with `.x`, the group key with
+    `.group_key`, and the reference time value with `.ref_time_value`. The usual
+    `.data` and `.env` pronouns also work, but`pick()` and `cur_data()` are not;
+    work off of `.x` instead.
+* `epix_slide` has been made more like `dplyr::group_modify`. It will no longer
+  perform element/row recycling for size stability, accepts slide computation
+  outputs containing any number of rows, and no longer supports `all_rows`.
+  * To keep the old behavior, manually perform row recycling within `f`
+    computations, and/or `left_join` a data frame representing the desired
+    output structure with the current `epix_slide()` result to obtain the
+    desired repetitions and completions expected with `all_rows = TRUE`.
+* `epix_slide` will only output grouped or ungrouped tibbles. Previously, it
+  would sometimes output `epi_df`s, but not consistently, and not always with
+  the metadata desired. Future versions will revisit this design, and consider
+  more closely whether/when/how to output an `epi_df`.
+  * To keep the old behavior, convert the output of `epix_slide()` to `epi_df`
+    when desired and set the metadata appropriately.
+
+## 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"
+  format (see `tidyr::chop`).
+* `epi_slide` now works properly with slide computations that output just a
+  `Date` vector, rather than converting `slide_value` to a numeric column.
+
+# epiprocess 0.6.0
+
+## Breaking changes:
+
+* Changes to both `epi_slide` and `epix_slide`:
+  * The `n`, `align`, and `before` arguments have been replaced by new `before`
+    and `after` arguments. To migrate to the new version, replace these
+    arguments in every `epi_slide` and `epix_slide` call. If you were only using
+    the `n` argument, then this means replacing `n = <n value>` with `before =
+    <n value> - 1`.
+    * `epi_slide`'s time windows now extend `before` time steps before and
+      `after` time steps after the corresponding `ref_time_values`. See
+      `?epi_slide` for details on matching old alignments.
+    * `epix_slide`'s time windows now extend `before` time steps before the
+      corresponding `ref_time_values` all the way through the latest data
+      available at the corresponding `ref_time_values`.
+  * Slide functions now keep any grouping of `x` in their results, like
+    `mutate` and `group_modify`.
+    * To obtain the old behavior, `dplyr::ungroup` the slide results immediately.
+* Additional `epi_slide` changes:
+  * When using `as_list_col = TRUE` together with `ref_time_values` and
+    `all_rows=TRUE`, the marker for excluded computations is now a `NULL` entry
+    in the list column, rather than a `NA`; if you are using `tidyr::unnest()`
+    afterward and want to keep these missing data markers, you will need to
+    replace the `NULL` entries with `NA`s. Skipped computations are now more
+    uniformly detectable using `vctrs` methods.
+* Additional`epix_slide` changes:
+  * `epix_slide`'s `group_by` argument has been replaced by `dplyr::group_by` and
+    `dplyr::ungroup` S3 methods. The `group_by` method uses "data masking" (also
+    referred to as "tidy evaluation") rather than "tidy selection".
+    * Old syntax:
+      * `x %>% epix_slide(<other args>, group_by=c(col1, col2))`
+      * `x %>% epix_slide(<other args>, group_by=all_of(colname_vector))`
+    * New syntax:
+      * `x %>% group_by(col1, col2) %>% epix_slide(<other args>)`
+      * `x %>% group_by(across(all_of(colname_vector))) %>% epix_slide(<other args>)`
+  * `epix_slide` no longer defaults to grouping by non-`time_value`, non-`version`
+    key columns, instead considering all data to be in one big group.
+    * To obtain the old behavior, precede each `epix_slide` call lacking a
+      `group_by` argument with an appropriate `group_by` call.
+  * `epix_slide` now guesses `ref_time_values` to be a regularly spaced sequence
+    covering all the `DT$version` values and the `version_end`, rather than the
+    distinct `DT$time_value`s. To obtain the old behavior, pass in
+    `ref_time_values = unique(<ungrouped archive>$DT$time_value)`.
+* `epi_archive`'s `clobberable_versions_start`'s default is now `NA`, so there
+  will be no warnings by default about potential nonreproducibility. To obtain
+  the old behavior, pass in `clobberable_versions_start =
+  max_version_with_row_in(x)`.
+
+## 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).
+* Fixed `epi_df` operations to be more consistent about decaying into
+  non-`epi_df`s when the result of the operation doesn't make sense as an
+  `epi_df` (e.g., when removing the `time_value` column).
+* Changed `bind_rows` on grouped `epi_df`s to not drop the `epi_df` class. Like
+  with ungrouped `epi_df`s, the metadata of the result is still simply taken
+  from the first result, and may be inappropriate
+  ([#242](https://github.com/cmu-delphi/epiprocess/issues/242)).
+* `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:
+
+* `epix_slide`, `<epi_archive>$slide` have a new parameter `all_versions`. With
+  `all_versions=TRUE`, `epix_slide` will pass a filtered `epi_archive` to each
+  computation rather than an `epi_df` snapshot. This enables, e.g., performing
+  pseudoprospective forecasts with a revision-aware forecaster using nested
+  `epix_slide` operations.
+
+## Improvements:
+
+* Added `dplyr::group_by` and `dplyr::ungroup` S3 methods for `epi_archive`
+  objects, plus corresponding `$group_by` and `$ungroup` R6 methods. The
+  `group_by` implementation supports the `.add` and `.drop` arguments, and
+  `ungroup` supports partial ungrouping with `...`.
+* `as_epi_archive`, `epi_archive$new` now perform checks for the key uniqueness
+  requirement (part of
+  [#154](https://github.com/cmu-delphi/epiprocess/issues/154)).
 
 ## 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: