From 76e516de064231b2ce7725ebfac4e7cf570b66dd Mon Sep 17 00:00:00 2001
From: Dmitry Shemetov <dshemetov@ucdavis.edu>
Date: Thu, 24 Oct 2024 10:45:34 -0700
Subject: [PATCH 01/39] doc: update from Rachel's comments

---
 R/methods-epi_df.R       |  2 +-
 man/complete.epi_df.Rd   |  4 +++-
 vignettes/epiprocess.Rmd | 10 +++++-----
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index 84a75e46..7d99bd49 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -258,7 +258,7 @@ group_modify.epi_df <- function(.data, .f, ..., .keep = FALSE) {
 
 #' Complete epi_df
 #'
-#' A `tidyr::complete()` analogue for `epi_df`` objects. This function
+#' A `tidyr::complete()` analogue for `epi_df` objects. This function
 #' can be used, for example, to add rows for missing combinations
 #' of `geo_value` and `time_value`, filling other columns with `NA`s.
 #' See the examples for usage details.
diff --git a/man/complete.epi_df.Rd b/man/complete.epi_df.Rd
index 71dbcb38..7645a01f 100644
--- a/man/complete.epi_df.Rd
+++ b/man/complete.epi_df.Rd
@@ -16,7 +16,9 @@
 \item{explicit}{see \code{\link[tidyr:complete]{tidyr::complete}}}
 }
 \description{
-A \code{tidyr::complete()} analogue for \verb{epi_df`` objects. This function can be used, for example, to add rows for missing combinations of }geo_value\code{and}time_value\verb{, filling other columns with }NA`s.
+A \code{tidyr::complete()} analogue for \code{epi_df} objects. This function
+can be used, for example, to add rows for missing combinations
+of \code{geo_value} and \code{time_value}, filling other columns with \code{NA}s.
 See the examples for usage details.
 }
 \examples{
diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd
index 613f9146..b9648e00 100644
--- a/vignettes/epiprocess.Rmd
+++ b/vignettes/epiprocess.Rmd
@@ -86,7 +86,7 @@ edf %>%
 ```
 
 We can compute the 7 day moving average of the confirmed daily cases for each
-geo_value by using the `epi_slide_mean()` function. For a more in-depth guide to
+`geo_value` by using the `epi_slide_mean()` function. For a more in-depth guide to
 sliding, see `vignette("epi_df")`.
 
 ```{r}
@@ -96,7 +96,7 @@ edf %>%
 ```
 
 We can compute the growth rate of the confirmed cumulative cases for each
-geo_value. For a more in-depth guide to growth rates, see `vignette("growth_rate")`.
+`geo_value`. For a more in-depth guide to growth rates, see `vignette("growth_rate")`.
 
 ```{r}
 edf %>%
@@ -104,7 +104,7 @@ edf %>%
   mutate(cases_growth = growth_rate(x = time_value, y = cases_cumulative, method = "rel_change", h = 7))
 ```
 
-Detect outliers in daily reported cases for each geo_value. For a more in-depth
+Detect outliers in daily reported cases for each `geo_value`. For a more in-depth
 guide to outlier detection, see `vignette("outliers")`.
 
 ```{r message=FALSE}
@@ -114,8 +114,8 @@ edf %>%
   ungroup()
 ```
 
-Add a column to the epi_df object with the daily deaths for each geo_value and
-compute the correlations between cases and deaths for each geo_value. For a more
+Add a column to the epi_df object with the daily deaths for each `geo_value` and
+compute the correlations between cases and deaths for each `geo_value`. For a more
 in-depth guide to correlations, see `vignette("correlation")`.
 
 ```{r}

From 63bdc1da6428e1c248445427c865cf963c1c1fb4 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 24 Oct 2024 15:53:37 -0700
Subject: [PATCH 02/39] docs(complete.epi_df): fix backticks, tweak 1-line
 summary

---
 R/methods-epi_df.R     | 4 ++--
 man/complete.epi_df.Rd | 6 ++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index 84a75e46..ffbfa9c5 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -256,9 +256,9 @@ group_modify.epi_df <- function(.data, .f, ..., .keep = FALSE) {
   dplyr::dplyr_reconstruct(NextMethod(), .data)
 }
 
-#' Complete epi_df
+#' Complete an `epi_df` with additional rows for missing key combinations
 #'
-#' A `tidyr::complete()` analogue for `epi_df`` objects. This function
+#' A `tidyr::complete()` analogue for `epi_df` objects. This function
 #' can be used, for example, to add rows for missing combinations
 #' of `geo_value` and `time_value`, filling other columns with `NA`s.
 #' See the examples for usage details.
diff --git a/man/complete.epi_df.Rd b/man/complete.epi_df.Rd
index 71dbcb38..02323a5c 100644
--- a/man/complete.epi_df.Rd
+++ b/man/complete.epi_df.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/methods-epi_df.R
 \name{complete.epi_df}
 \alias{complete.epi_df}
-\title{Complete epi_df}
+\title{Complete an \code{epi_df} with additional rows for missing key combinations}
 \usage{
 \method{complete}{epi_df}(data, ..., fill = list(), explicit = TRUE)
 }
@@ -16,7 +16,9 @@
 \item{explicit}{see \code{\link[tidyr:complete]{tidyr::complete}}}
 }
 \description{
-A \code{tidyr::complete()} analogue for \verb{epi_df`` objects. This function can be used, for example, to add rows for missing combinations of }geo_value\code{and}time_value\verb{, filling other columns with }NA`s.
+A \code{tidyr::complete()} analogue for \code{epi_df} objects. This function
+can be used, for example, to add rows for missing combinations
+of \code{geo_value} and \code{time_value}, filling other columns with \code{NA}s.
 See the examples for usage details.
 }
 \examples{

From c3be3acc34f69c55465b2d272dc49b2a9af5d5c3 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 25 Oct 2024 11:19:18 -0700
Subject: [PATCH 03/39] docs(complete.epi_df): further tweak summary line

---
 R/methods-epi_df.R     | 2 +-
 man/complete.epi_df.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index ffbfa9c5..6e19f753 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -256,7 +256,7 @@ group_modify.epi_df <- function(.data, .f, ..., .keep = FALSE) {
   dplyr::dplyr_reconstruct(NextMethod(), .data)
 }
 
-#' Complete an `epi_df` with additional rows for missing key combinations
+#' "Complete" an `epi_df`, adding missing rows and/or replacing `NA`s
 #'
 #' A `tidyr::complete()` analogue for `epi_df` objects. This function
 #' can be used, for example, to add rows for missing combinations
diff --git a/man/complete.epi_df.Rd b/man/complete.epi_df.Rd
index 02323a5c..38c9a6fe 100644
--- a/man/complete.epi_df.Rd
+++ b/man/complete.epi_df.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/methods-epi_df.R
 \name{complete.epi_df}
 \alias{complete.epi_df}
-\title{Complete an \code{epi_df} with additional rows for missing key combinations}
+\title{"Complete" an \code{epi_df}, adding missing rows and/or replacing \code{NA}s}
 \usage{
 \method{complete}{epi_df}(data, ..., fill = list(), explicit = TRUE)
 }

From ac12ec185886a294f95bef0d38d9b3587bb5eaa7 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Wed, 6 Nov 2024 03:56:53 -0800
Subject: [PATCH 04/39] refactor(epi_slide_opt): simplify tidyselect

---
 NAMESPACE | 2 --
 R/slide.R | 8 ++------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 1fd65d37..04e8bf61 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -189,7 +189,6 @@ importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,arg_match)
-importFrom(rlang,as_label)
 importFrom(rlang,caller_arg)
 importFrom(rlang,caller_env)
 importFrom(rlang,check_dots_empty)
@@ -207,7 +206,6 @@ importFrom(rlang,is_quosure)
 importFrom(rlang,list2)
 importFrom(rlang,missing_arg)
 importFrom(rlang,new_function)
-importFrom(rlang,quo_get_expr)
 importFrom(rlang,quo_is_missing)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
diff --git a/R/slide.R b/R/slide.R
index f936916e..e7325e66 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -564,7 +564,7 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'  functions).
 #'
 #' @importFrom dplyr bind_rows mutate %>% arrange tibble select all_of
-#' @importFrom rlang enquo quo_get_expr as_label expr_label caller_arg
+#' @importFrom rlang enquo expr_label caller_arg
 #' @importFrom tidyselect eval_select
 #' @importFrom purrr map map_lgl
 #' @importFrom data.table frollmean frollsum frollapply
@@ -714,11 +714,7 @@ epi_slide_opt <- function(
   # positions of user-provided `col_names` into string column names. We avoid
   # using `names(pos)` directly for robustness and in case we later want to
   # allow users to rename fields via tidyselection.
-  if (inherits(quo_get_expr(enquo(.col_names)), "character")) {
-    pos <- eval_select(dplyr::all_of(.col_names), data = .x, allow_rename = FALSE)
-  } else {
-    pos <- eval_select(enquo(.col_names), data = .x, allow_rename = FALSE)
-  }
+  pos <- eval_select(enquo(.col_names), data = .x, allow_rename = FALSE)
   col_names_chr <- names(.x)[pos]
   # Always rename results to "slide_value_<original column name>".
   result_col_names <- paste0("slide_value_", col_names_chr)

From c75de3829a5e07c4858030c987919bbe4ce9e75d Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 7 Nov 2024 14:49:45 -0800
Subject: [PATCH 05/39] Fix typo + adjust naming of sliding median example

---
 R/slide.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index e7325e66..3064b087 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -6,8 +6,8 @@
 #' as follows:
 #'
 #' ```
-#' # Create new column `cases_7dm` that contains a 7-day trailing median of cases
-#' epi_slide(edf, cases_7dav = median(cases), .window_size = 7)
+#' # Create new column `cases_7dmed` that contains a 7-day trailing median of cases
+#' epi_slide(edf, cases_7dmed = median(cases), .window_size = 7)
 #' ```
 #'
 #' For two very common use cases, we provide optimized functions that are much

From a2f2f448c639334767c7fbaa2e28bd7f69b0bd53 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 11 Nov 2024 16:19:58 -0800
Subject: [PATCH 06/39] delphidocs on dev

---
 .github/workflows/pkgdown.yaml | 26 +++----------------
 _pkgdown.yml                   | 46 +++++++++++-----------------------
 2 files changed, 18 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 886055ae..3a1ff927 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -28,7 +28,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -42,32 +42,12 @@ jobs:
           needs: website
 
       - name: Build site
-        # - target_ref gets the ref from a different variable, depending on the event
-        # - override allows us to set the pkgdown mode and version_label
-        #   - mode: release is the standard build mode, devel places the site in /dev
-        #   - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
-        #                    https://bootswatch.com/cosmo/
-        # - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
-        #   https://github.com/r-lib/pkgdown/issues/2257
-        run: |
-          target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
-          override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
-            list(development = list(mode = "release", version_label = "light"))
-          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
-            list(development = list(mode = "devel", version_label = "success"))
-          } else {
-            stop("Unexpected target_ref: ", target_ref)
-          }
-          pkg <- pkgdown::as_pkgdown(".", override = override)
-          cli::cli_rule("Cleaning files from old site...")
-          pkgdown::clean_site(pkg)
-          pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
-          pkgdown:::build_github_pages(pkg)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2214df7c..743adc4b 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,40 +1,25 @@
-# Colors should stay consistent across epipredict, epiprocess, and epidatr,
-# using Carnegie Red
-# https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html
-
-# This is to give a default value to the `mode` parameter in the
-# `pkgdown::build_site` function. This is useful when building the site locally,
-# as it will default to `devel` mode. In practice, this should all be handled
-# dynamically by the CI/CD pipeline.
 development:
-  mode: devel
-  version_label: success
+  mode: auto
 
 template:
-  bootstrap: 5
-  bootswatch: cosmo
-  bslib:
-    font_scale: 1.0
-    primary: "#C41230"
-    success: "#B4D43C"
-    link-color: "#C41230"
-
-navbar:
-  bg: primary
-  type: light
+  package: delphidocs
 
 url: https://cmu-delphi.github.io/epiprocess/
 
 home:
   links:
-    - text: Introduction to Delphi's Tooling Work
-      href: https://cmu-delphi.github.io/delphi-tooling-book/
-    - text: Get the epipredict R package
+    - text: The epipredict package
       href: https://cmu-delphi.github.io/epipredict/
-    - text: Get the epidatr R package
-      href: https://github.com/cmu-delphi/epidatr
-    - text: Get the epidatasets R package
-      href: https://cmu-delphi.github.io/epidatasets/
+  sidebar:
+    structure: [links, license, community, citation, authors, dev, related]
+    components:
+      related:
+        title: Delphi packages and resources
+        text: |
+          * [The epidatr package](https://github.com/cmu-delphi/epidatr/)
+          * [The epipredict package](https://cmu-delphi.github.io/epipredict/)
+          * [The epidatasets package](https://cmu-delphi.github.io/epidatasets/)
+          * [Introduction to Delphi's Tooling Work](https://cmu-delphi.github.io/delphi-tooling-book/)
 
 articles:
   - title: Using the package
@@ -54,10 +39,9 @@ articles:
 
 repo:
   url:
-    home: https://github.com/cmu-delphi/epiprocess/tree/main/
-    source: https://github.com/cmu-delphi/epiprocess/blob/main/
+    home: https://github.com/cmu-delphi/epiprocess/
+    source: https://github.com/cmu-delphi/epiprocess/
     issue: https://github.com/cmu-delphi/epiprocess/issues
-    user: https://github.com/
 
 reference:
   - title: "`epi_df` basics"

From fab1c088e22cc68562aac0182941eff3639db050 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Wed, 6 Nov 2024 04:22:53 -0800
Subject: [PATCH 07/39] feat(epi_slide_opt)!: add `.prefix =, .suffix =,
 .new_col_names =`

- BREAKING CHANGE: adjust default output column naming scheme, disallow
  overwriting columns.
---
 NAMESPACE                       |   5 +
 R/epi_df.R                      |  11 +-
 R/epiprocess-package.R          |   3 +
 R/slide.R                       | 172 +++++++++++++++++++++++++-------
 R/utils.R                       |  67 ++++++++++++-
 README.Rmd                      |   3 +-
 README.md                       |   3 +-
 man/epi_slide.Rd                |   4 +-
 man/epi_slide_opt.Rd            |  57 +++++++++--
 man/time_delta_to_n_steps.Rd    |  31 ++++++
 tests/testthat/test-epi_slide.R | 155 ++++++++++++++++++++++++++--
 11 files changed, 439 insertions(+), 72 deletions(-)
 create mode 100644 man/time_delta_to_n_steps.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 04e8bf61..e044739b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -114,6 +114,7 @@ importFrom(checkmate,assert_list)
 importFrom(checkmate,assert_logical)
 importFrom(checkmate,assert_numeric)
 importFrom(checkmate,assert_scalar)
+importFrom(checkmate,assert_string)
 importFrom(checkmate,checkInt)
 importFrom(checkmate,check_atomic)
 importFrom(checkmate,check_data_frame)
@@ -176,6 +177,7 @@ importFrom(dplyr,summarize)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(ggplot2,autoplot)
+importFrom(glue,glue)
 importFrom(lifecycle,deprecated)
 importFrom(lubridate,as.period)
 importFrom(lubridate,days)
@@ -198,6 +200,7 @@ importFrom(rlang,env)
 importFrom(rlang,expr_label)
 importFrom(rlang,f_env)
 importFrom(rlang,f_rhs)
+importFrom(rlang,is_bare_integerish)
 importFrom(rlang,is_environment)
 importFrom(rlang,is_formula)
 importFrom(rlang,is_function)
@@ -206,6 +209,7 @@ importFrom(rlang,is_quosure)
 importFrom(rlang,list2)
 importFrom(rlang,missing_arg)
 importFrom(rlang,new_function)
+importFrom(rlang,quo_get_env)
 importFrom(rlang,quo_is_missing)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
@@ -230,3 +234,4 @@ importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
 importFrom(utils,capture.output)
 importFrom(utils,tail)
+importFrom(vctrs,vec_data)
diff --git a/R/epi_df.R b/R/epi_df.R
index bcf9e56f..5cf379e2 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -232,7 +232,6 @@ as_epi_df.tbl_df <- function(
     as_of,
     other_keys = character(),
     ...) {
-  # possible standard substitutions for time_value
   x <- rename(x, ...)
   x <- guess_column_name(x, "time_value", time_column_names())
   x <- guess_column_name(x, "geo_value", geo_column_names())
@@ -282,11 +281,11 @@ as_epi_df.tbl_df <- function(
     cli_abort("as_epi_df: `other_keys` can't include \".time_value_counts\"")
   }
 
-  duplicated_time_values <- x %>%
-    group_by(across(all_of(c("geo_value", "time_value", other_keys)))) %>%
-    filter(dplyr::n() > 1) %>%
-    ungroup()
-  if (nrow(duplicated_time_values) > 0) {
+  if (anyDuplicated(x[c("geo_value", "time_value", other_keys)])) {
+    duplicated_time_values <- x %>%
+      group_by(across(all_of(c("geo_value", "time_value", other_keys)))) %>%
+      filter(dplyr::n() > 1) %>%
+      ungroup()
     bad_data <- capture.output(duplicated_time_values)
     cli_abort(
       "as_epi_df: some groups in the data have duplicated time values. epi_df requires a unique time_value per group.",
diff --git a/R/epiprocess-package.R b/R/epiprocess-package.R
index e28cec0f..b640a0b5 100644
--- a/R/epiprocess-package.R
+++ b/R/epiprocess-package.R
@@ -6,6 +6,7 @@
 #' @importFrom checkmate anyInfinite anyMissing assert assert_character
 #' @importFrom checkmate assert_class assert_data_frame assert_int assert_list
 #' @importFrom checkmate assert_logical assert_numeric assert_scalar checkInt
+#' @importFrom checkmate assert_string
 #' @importFrom checkmate check_atomic check_data_frame expect_class test_int
 #' @importFrom checkmate check_names
 #' @importFrom checkmate test_subset test_set_equal vname
@@ -16,6 +17,8 @@
 #' @importFrom dplyr select
 #' @importFrom lifecycle deprecated
 #' @importFrom rlang %||%
+#' @importFrom rlang is_bare_integerish
+#' @importFrom vctrs vec_data
 ## usethis namespace: end
 NULL
 
diff --git a/R/slide.R b/R/slide.R
index 3064b087..9d383446 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -537,7 +537,7 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'
 #' @template basic-slide-params
 #' @param .col_names <[`tidy-select`][dplyr_tidy_select]> An unquoted column
-#'   name(e.g., `cases`), multiple column names (e.g., `c(cases, deaths)`),
+#'   name (e.g., `cases`), multiple column names (e.g., `c(cases, deaths)`),
 #'   [other tidy-select expression][tidyselect::language], or a vector of
 #'   characters (e.g. `c("cases", "deaths")`). Variable names can be used as if
 #'   they were positions in the data frame, so expressions like `x:y` can be
@@ -559,13 +559,40 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'  `epi_slide_mean` and `epi_slide_sum`) take care of window completion
 #'  automatically to prevent associated errors.
 #' @param ... Additional arguments to pass to the slide computation `.f`, for
-#'  example, `algo` or `na.rm` in data.table functions. You don't need to
-#'  specify `.x`, `.window_size`, or `.align` (or `before`/`after` for slider
-#'  functions).
+#'   example, `algo` or `na.rm` in data.table functions. You don't need to
+#'   specify `.x`, `.window_size`, or `.align` (or `before`/`after` for slider
+#'   functions).
+#' @param .prefix Optional [`glue::glue`] format string; name the slide result
+#'   column(s) by attaching this prefix to the corresponding input column(s).
+#'   Some shorthand is supported for basing the output names on `.window_size`
+#'   or other arguments; see "Prefix and suffix shorthand" below.
+#' @param .suffix Optional [`glue::glue`] format string; like `.prefix`. The
+#'   default naming behavior is equivalent to `.suffix =
+#'   "_{.n}{.time_unit_abbr}{.align_abbr}{.f_abbr}"`. Can be used in combination
+#'   with `.prefix`.
+#' @param .new_col_names Optional character vector with length matching the
+#'   number of input columns from `.col_names`; name the slide result column(s)
+#'   with these names. Cannot be used in combination with `.prefix` and/or
+#'   `.suffix`.
+#'
+#' @section Prefix and suffix shorthand:
+#'
+#' [`glue::glue`] format strings specially interpret content within curly
+#' braces. E.g., `glue::glue("ABC{2 + 2}")` evaluates to `"ABC4"`. For `.prefix`
+#' and `.suffix`, we provide `glue` with some additional variable bindings:
+#'
+#' - `{.n}` will be the number of time steps in the computation
+#'    corresponding to the `.window_size`.
+#' - `{.time_unit_abbr}` will be a lower-case letter corresponding to the
+#'     `time_type` of `.x`
+#' - `{.align_abbr}` will be `""` if `.align` is the default of `"right"`;
+#'    otherwise, it will be the first letter of `.align`
+#' - `{.f_abbr}` will be a short string based on what `.f`
 #'
 #' @importFrom dplyr bind_rows mutate %>% arrange tibble select all_of
-#' @importFrom rlang enquo expr_label caller_arg
+#' @importFrom rlang enquo expr_label caller_arg quo_get_env
 #' @importFrom tidyselect eval_select
+#' @importFrom glue glue
 #' @importFrom purrr map map_lgl
 #' @importFrom data.table frollmean frollsum frollapply
 #' @importFrom lubridate as.period
@@ -577,8 +604,7 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #' # Compute a 7-day trailing average on cases.
 #' cases_deaths_subset %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+#'   epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7)
 #'
 #' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 #' # to allow partially-missing windows.
@@ -588,11 +614,11 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'     cases,
 #'     .f = data.table::frollmean, .window_size = 7,
 #'     algo = "exact", hasNA = TRUE, na.rm = TRUE
-#'   ) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+#'   )
 epi_slide_opt <- function(
     .x, .col_names, .f, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
+    .prefix = NULL, .suffix = NULL, .new_col_names = NULL,
     .ref_time_values = NULL, .all_rows = FALSE) {
   assert_class(.x, "epi_df")
 
@@ -620,7 +646,7 @@ epi_slide_opt <- function(
   if ("new_col_name" %in% provided_args || ".new_col_name" %in% provided_args) {
     cli::cli_abort(
       "epi_slide_opt: the argument `new_col_name` is not supported for `epi_slide_opt`. If you want to customize
-      the output column names, use `dplyr::rename` after the slide.",
+      the output column names, use `.prefix =`, `.suffix =`, or `.new_col_**names** =`.",
       class = "epiprocess__epi_slide_opt__new_name_not_supported"
     )
   }
@@ -644,21 +670,37 @@ epi_slide_opt <- function(
     )
   }
 
+  # The position of a given column can be differ between input `.x` and
+  # `.data_group` since the grouping step by default drops grouping columns.
+  # To avoid rerunning `eval_select` for every `.data_group`, convert
+  # positions of user-provided `col_names` into string column names. We avoid
+  # using `names(pos)` directly for robustness and in case we later want to
+  # allow users to rename fields via tidyselection.
+  col_names_quo <- enquo(.col_names)
+  pos <- eval_select(col_names_quo, data = .x, allow_rename = FALSE)
+  col_names_chr <- names(.x)[pos]
+
   # Check that slide function `.f` is one of those short-listed from
   # `data.table` and `slider` (or a function that has the exact same
   # definition, e.g. if the function has been reexported or defined
   # locally).
-  if (any(map_lgl(
-    list(frollmean, frollsum, frollapply),
-    ~ identical(.f, .x)
-  ))) {
-    f_from_package <- "data.table"
-  } else if (any(map_lgl(
-    list(slide_sum, slide_prod, slide_mean, slide_min, slide_max, slide_all, slide_any),
-    ~ identical(.f, .x)
-  ))) {
-    f_from_package <- "slider"
-  } else {
+  f_possibilities <-
+    tibble::tribble(
+      ~f, ~package, ~abbr,
+      frollmean, "data.table", "av",
+      frollsum, "data.table", "sum",
+      frollapply, "data.table", "slide",
+      slide_sum, "slider", "sum",
+      slide_prod, "slider", "prod",
+      slide_mean, "slider", "av",
+      slide_min, "slider", "min",
+      slide_max, "slider", "max",
+      slide_all, "slider", "all",
+      slide_any, "slider", "any",
+    )
+  f_info <- f_possibilities %>%
+    filter(map_lgl(.data$f, ~ identical(.f, .x)))
+  if (nrow(f_info) == 0L) {
     # `f` is from somewhere else and not supported
     cli_abort(
       c(
@@ -672,6 +714,7 @@ epi_slide_opt <- function(
       epiprocess__f = .f
     )
   }
+  f_from_package <- f_info$package
 
   user_provided_rtvs <- !is.null(.ref_time_values)
   if (!user_provided_rtvs) {
@@ -702,22 +745,72 @@ epi_slide_opt <- function(
   validate_slide_window_arg(.window_size, time_type)
   window_args <- get_before_after_from_window(.window_size, .align, time_type)
 
+  # Handle output naming
+  if ((!is.null(.prefix) || !is.null(.suffix)) && !is.null(.new_col_names)) {
+    cli_abort(
+      "Can't use both .prefix/.suffix and .new_col_names at the same time.",
+      class = "epiprocess__epi_slide_opt_incompatible_naming_args"
+    )
+  }
+  assert_string(.prefix, null.ok = TRUE)
+  assert_string(.suffix, null.ok = TRUE)
+  assert_character(.new_col_names, len = length(col_names_chr), null.ok = TRUE)
+  if (is.null(.prefix) && is.null(.suffix) && is.null(.new_col_names)) {
+    .suffix <- "_{.n}{.time_unit_abbr}{.align_abbr}{.f_abbr}"
+    # ^ does not account for any arguments specified to underlying functions via
+    # `...` such as `na.rm =`, nor does it distinguish between functions from
+    # different packages accomplishing the same type of computation. Those are
+    # probably only set one way per task, so this probably produces cleaner
+    # names without clashes (though maybe some confusion if switching between
+    # code with different settings).
+  }
+  if (!is.null(.prefix) || !is.null(.suffix)) {
+    .prefix <- .prefix %||% ""
+    .suffix <- .suffix %||% ""
+    if (identical(.window_size, Inf)) {
+      n <- "running_"
+      time_unit_abbr <- ""
+      align_abbr <- ""
+    } else {
+      n <- time_delta_to_n_steps(.window_size, time_type)
+      time_unit_abbr <- time_type_unit_abbr(time_type)
+      align_abbr <- c(right = "", center = "c", left = "l")[[.align]]
+    }
+    glue_env <- rlang::env(
+      .n = n,
+      .time_unit_abbr = time_unit_abbr,
+      .align_abbr = align_abbr,
+      .f_abbr = f_info$abbr,
+      quo_get_env(col_names_quo)
+    )
+    .new_col_names <- unclass(
+      glue(.prefix, .envir = glue_env) +
+        col_names_chr +
+        glue(.suffix, .envir = glue_env)
+    )
+  } else {
+    # `.new_col_names` was provided by user; we don't need to do anything.
+  }
+  if (any(.new_col_names %in% names(.x))) {
+    cli_abort(c(
+      "Naming conflict between new columns and existing columns",
+      "x" = "Overlapping names: {format_varnames(intersect(.new_col_names, names(.x)))}"
+    ), class = "epiprocess__epi_slide_opt_old_new_name_conflict")
+  }
+  if (anyDuplicated(.new_col_names)) {
+    cli_abort(c(
+      "New column names contain duplicates",
+      "x" = "Duplicated names: {format_varnames(unique(.new_col_names[duplicated(.new_col_names)]))}"
+    ), class = "epiprocess__epi_slide_opt_new_name_duplicated")
+  }
+  result_col_names <- .new_col_names
+
   # Make a complete date sequence between min(.x$time_value) and max(.x$time_value).
   date_seq_list <- full_date_seq(.x, window_args$before, window_args$after, time_type)
   all_dates <- date_seq_list$all_dates
   pad_early_dates <- date_seq_list$pad_early_dates
   pad_late_dates <- date_seq_list$pad_late_dates
 
-  # The position of a given column can be differ between input `.x` and
-  # `.data_group` since the grouping step by default drops grouping columns.
-  # To avoid rerunning `eval_select` for every `.data_group`, convert
-  # positions of user-provided `col_names` into string column names. We avoid
-  # using `names(pos)` directly for robustness and in case we later want to
-  # allow users to rename fields via tidyselection.
-  pos <- eval_select(enquo(.col_names), data = .x, allow_rename = FALSE)
-  col_names_chr <- names(.x)[pos]
-  # Always rename results to "slide_value_<original column name>".
-  result_col_names <- paste0("slide_value_", col_names_chr)
   slide_one_grp <- function(.data_group, .group_key, ...) {
     missing_times <- all_dates[!(all_dates %in% .data_group$time_value)]
     # `frollmean` requires a full window to compute a result. Add NA values
@@ -827,8 +920,7 @@ epi_slide_opt <- function(
 #' # Compute a 7-day trailing average on cases.
 #' cases_deaths_subset %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_mean(cases, .window_size = 7) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+#'   epi_slide_mean(cases, .window_size = 7)
 #'
 #' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 #' # to allow partially-missing windows.
@@ -838,11 +930,11 @@ epi_slide_opt <- function(
 #'     cases,
 #'     .window_size = 7,
 #'     na.rm = TRUE, algo = "exact", hasNA = TRUE
-#'   ) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+#'   )
 epi_slide_mean <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
+    .prefix = NULL, .suffix = NULL, .new_col_names = NULL,
     .ref_time_values = NULL, .all_rows = FALSE) {
   # Deprecated argument handling
   provided_args <- rlang::call_args_names(rlang::call_match())
@@ -885,6 +977,9 @@ epi_slide_mean <- function(
     ...,
     .window_size = .window_size,
     .align = .align,
+    .prefix = .prefix,
+    .suffix = .suffix,
+    .new_col_names = .new_col_names,
     .ref_time_values = .ref_time_values,
     .all_rows = .all_rows
   )
@@ -899,11 +994,11 @@ epi_slide_mean <- function(
 #' # Compute a 7-day trailing sum on cases.
 #' cases_deaths_subset %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_sum(cases, .window_size = 7) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7dsum = slide_value_cases)
+#'   epi_slide_sum(cases, .window_size = 7)
 epi_slide_sum <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
+    .prefix = NULL, .suffix = NULL, .new_col_names = NULL,
     .ref_time_values = NULL, .all_rows = FALSE) {
   # Deprecated argument handling
   provided_args <- rlang::call_args_names(rlang::call_match())
@@ -945,6 +1040,9 @@ epi_slide_sum <- function(
     ...,
     .window_size = .window_size,
     .align = .align,
+    .prefix = .prefix,
+    .suffix = .suffix,
+    .new_col_names = .new_col_names,
     .ref_time_values = .ref_time_values,
     .all_rows = .all_rows
   )
diff --git a/R/utils.R b/R/utils.R
index 1bfd2129..06876f08 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -640,7 +640,7 @@ guess_time_type <- function(time_value, time_value_arg = rlang::caller_arg(time_
     return("day")
   } else if (inherits(time_value, "yearmonth")) {
     return("yearmonth")
-  } else if (rlang::is_integerish(time_value)) {
+  } else if (is_bare_integerish(time_value)) {
     return("integer")
   }
 
@@ -1109,3 +1109,68 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
     )
   }
 }
+
+
+#' Convert a time delta to a compatible integerish number of steps between time values
+#'
+#' @param time_delta a vector that can be added to time values of time type
+#'   `time_type` to arrive at other time values of that time type, or
+#'   `r lifecycle::badge("experimental")` such a vector with Inf/-Inf entries mixed
+#'   in, if supported by the class of `time_delta`, even if `time_type` doesn't
+#'   necessarily support Inf/-Inf entries. Basically a slide window arg but
+#'   without sign and length restrictions.
+#' @param time_type as in [`validate_slide_window_arg`]
+#' @return [bare integerish][rlang::is_integerish] vector (with possible
+#'   infinite values) that produces the same result as `time_delta` when added
+#'   to time values of time type `time_type`. If the given time type does not
+#'   support infinite values, then it should produce +Inf or -Inf for analogous
+#'   entries of `time_delta`, and match the addition result match the addition
+#'   result for non-infinite values, and product +Inf / -Inf when match the sign
+#'   and of `time_delta`.
+#'
+#' @keywords internal
+time_delta_to_n_steps <- function(time_delta, time_type) {
+  # could be S3 if we're willing to export
+  if (inherits(time_delta, "difftime")) {
+    output_units <- switch(time_type,
+      day = "days",
+      week = "weeks",
+      cli_abort("difftime objects not supported for time_type {format_chr_with_quotes(time_type)}")
+    )
+    units(time_delta) <- output_units # converts number to represent same duration; not just attr<-
+    n_steps <- vec_data(time_delta)
+    if (!is_bare_integerish(n_steps)) {
+      cli_abort("`time_delta` did not appear to contain only integerish numbers
+                 of steps between time values of time type {format_chr_with_quotes(time_type)}")
+    }
+    n_steps
+  } else if (is_bare_integerish(time_delta)) { # (allows infinite values)
+    switch(time_type,
+      day = ,
+      week = ,
+      yearmonth = ,
+      integer = time_delta,
+      cli_abort("Invalid or unsupported time_type {format_chr_with_quotes(time_type)}")
+    )
+  } else {
+    cli_abort("Invalid or unsupported kind of `time_delta`")
+  }
+}
+
+# Using these unit abbreviations happens to make our automatic slide output
+# naming look like taking ISO-8601 duration designations, removing the P, and
+# lowercasing any characters. Fortnightly or sub-daily time types would need an
+# adjustment to remain consistent.
+time_type_unit_abbrs <- c(
+  day = "d",
+  week = "w",
+  yearmonth = "m"
+)
+
+time_type_unit_abbr <- function(time_type) {
+  maybe_unit_abbr <- time_type_unit_abbrs[time_type]
+  if (is.na(maybe_unit_abbr)) {
+    cli_abort("Cannot determine the units of time type {format_chr_with_quotes(time_type)}")
+  }
+  maybe_unit_abbr
+}
diff --git a/README.Rmd b/README.Rmd
index 82d60fc7..0e8756d3 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -113,8 +113,7 @@ Compute the 7 day moving average of the confirmed daily cases for each geo_value
 ```{r}
 edf <- edf %>%
   group_by(geo_value) %>%
-  epi_slide_mean(cases_daily, .window_size = 7, na.rm = TRUE) %>%
-  rename(smoothed_cases_daily = slide_value_cases_daily)
+  epi_slide_mean(cases_daily, .window_size = 7, na.rm = TRUE, .prefix = "smoothed_")
 edf
 ```
 
diff --git a/README.md b/README.md
index 7c14443d..af8c24e9 100644
--- a/README.md
+++ b/README.md
@@ -136,8 +136,7 @@ geo\_value
 ``` r
 edf <- edf %>%
   group_by(geo_value) %>%
-  epi_slide_mean(cases_daily, .window_size = 7, na.rm = TRUE) %>%
-  rename(smoothed_cases_daily = slide_value_cases_daily)
+  epi_slide_mean(cases_daily, .window_size = 7, na.rm = TRUE, .prefix = "smoothed_")
 edf
 #> An `epi_df` object, 2,808 x 5 with metadata:
 #> * geo_type  = state
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index 10d38957..1c399d35 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -99,8 +99,8 @@ This is useful for computations like rolling averages. The function supports
 many ways to specify the computation, but by far the most common use case is
 as follows:
 
-\if{html}{\out{<div class="sourceCode">}}\preformatted{# Create new column `cases_7dm` that contains a 7-day trailing median of cases
-epi_slide(edf, cases_7dav = median(cases), .window_size = 7)
+\if{html}{\out{<div class="sourceCode">}}\preformatted{# Create new column `cases_7dmed` that contains a 7-day trailing median of cases
+epi_slide(edf, cases_7dmed = median(cases), .window_size = 7)
 }\if{html}{\out{</div>}}
 
 For two very common use cases, we provide optimized functions that are much
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index cd293ee1..7f250cf4 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -13,6 +13,9 @@ epi_slide_opt(
   ...,
   .window_size = NULL,
   .align = c("right", "center", "left"),
+  .prefix = NULL,
+  .suffix = NULL,
+  .new_col_names = NULL,
   .ref_time_values = NULL,
   .all_rows = FALSE
 )
@@ -23,6 +26,9 @@ epi_slide_mean(
   ...,
   .window_size = NULL,
   .align = c("right", "center", "left"),
+  .prefix = NULL,
+  .suffix = NULL,
+  .new_col_names = NULL,
   .ref_time_values = NULL,
   .all_rows = FALSE
 )
@@ -33,6 +39,9 @@ epi_slide_sum(
   ...,
   .window_size = NULL,
   .align = c("right", "center", "left"),
+  .prefix = NULL,
+  .suffix = NULL,
+  .new_col_names = NULL,
   .ref_time_values = NULL,
   .all_rows = FALSE
 )
@@ -43,7 +52,7 @@ columns in \code{other_keys}. If grouped, we make sure the grouping is by
 \code{geo_value} and \code{other_keys}.}
 
 \item{.col_names}{<\code{\link[=dplyr_tidy_select]{tidy-select}}> An unquoted column
-name(e.g., \code{cases}), multiple column names (e.g., \code{c(cases, deaths)}),
+name (e.g., \code{cases}), multiple column names (e.g., \code{c(cases, deaths)}),
 \link[tidyselect:language]{other tidy-select expression}, or a vector of
 characters (e.g. \code{c("cases", "deaths")}). Variable names can be used as if
 they were positions in the data frame, so expressions like \code{x:y} can be
@@ -96,6 +105,20 @@ window will be asymmetric and have one more value before the reference time
 than after.
 }}
 
+\item{.prefix}{Optional \code{\link[glue:glue]{glue::glue}} format string; name the slide result
+column(s) by attaching this prefix to the corresponding input column(s).
+Some shorthand is supported for basing the output names on \code{.window_size}
+or other arguments; see "Prefix and suffix shorthand" below.}
+
+\item{.suffix}{Optional \code{\link[glue:glue]{glue::glue}} format string; like \code{.prefix}. The
+default naming behavior is equivalent to \code{.suffix = "_{.n}{.time_unit_abbr}{.align_abbr}{.f_abbr}"}. Can be used in combination
+with \code{.prefix}.}
+
+\item{.new_col_names}{Optional character vector with length matching the
+number of input columns from \code{.col_names}; name the slide result column(s)
+with these names. Cannot be used in combination with \code{.prefix} and/or
+\code{.suffix}.}
+
 \item{.ref_time_values}{The time values at which to compute the slides
 values. By default, this is all the unique time values in \code{.x}.}
 
@@ -119,12 +142,28 @@ These functions tend to be much faster than \code{epi_slide()}. See
 
 \code{epi_slide_sum} is a wrapper around \code{epi_slide_opt} with \code{.f = datatable::frollsum}.
 }
+\section{Prefix and suffix shorthand}{
+
+
+\code{\link[glue:glue]{glue::glue}} format strings specially interpret content within curly
+braces. E.g., \code{glue::glue("ABC{2 + 2}")} evaluates to \code{"ABC4"}. For \code{.prefix}
+and \code{.suffix}, we provide \code{glue} with some additional variable bindings:
+\itemize{
+\item \code{{.n}} will be the number of time steps in the computation
+corresponding to the \code{.window_size}.
+\item \code{{.time_unit_abbr}} will be a lower-case letter corresponding to the
+\code{time_type} of \code{.x}
+\item \code{{.align_abbr}} will be \code{""} if \code{.align} is the default of \code{"right"};
+otherwise, it will be the first letter of \code{.align}
+\item \code{{.f_abbr}} will be a short string based on what \code{.f}
+}
+}
+
 \examples{
 # Compute a 7-day trailing average on cases.
 cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+  epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7)
 
 # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 # to allow partially-missing windows.
@@ -134,13 +173,11 @@ cases_deaths_subset \%>\%
     cases,
     .f = data.table::frollmean, .window_size = 7,
     algo = "exact", hasNA = TRUE, na.rm = TRUE
-  ) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+  )
 # Compute a 7-day trailing average on cases.
 cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_mean(cases, .window_size = 7) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+  epi_slide_mean(cases, .window_size = 7)
 
 # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 # to allow partially-missing windows.
@@ -150,13 +187,11 @@ cases_deaths_subset \%>\%
     cases,
     .window_size = 7,
     na.rm = TRUE, algo = "exact", hasNA = TRUE
-  ) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7dav = slide_value_cases)
+  )
 # Compute a 7-day trailing sum on cases.
 cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_sum(cases, .window_size = 7) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7dsum = slide_value_cases)
+  epi_slide_sum(cases, .window_size = 7)
 }
 \seealso{
 \code{\link{epi_slide}} for the more general slide function
diff --git a/man/time_delta_to_n_steps.Rd b/man/time_delta_to_n_steps.Rd
new file mode 100644
index 00000000..0f9325be
--- /dev/null
+++ b/man/time_delta_to_n_steps.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{time_delta_to_n_steps}
+\alias{time_delta_to_n_steps}
+\title{Convert a time delta to a compatible integerish number of steps between time values}
+\usage{
+time_delta_to_n_steps(time_delta, time_type)
+}
+\arguments{
+\item{time_delta}{a vector that can be added to time values of time type
+\code{time_type} to arrive at other time values of that time type, or
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} such a vector with Inf/-Inf entries mixed
+in, if supported by the class of \code{time_delta}, even if \code{time_type} doesn't
+necessarily support Inf/-Inf entries. Basically a slide window arg but
+without sign and length restrictions.}
+
+\item{time_type}{as in \code{\link{validate_slide_window_arg}}}
+}
+\value{
+\link[rlang:is_integerish]{bare integerish} vector (with possible
+infinite values) that produces the same result as \code{time_delta} when added
+to time values of time type \code{time_type}. If the given time type does not
+support infinite values, then it should produce +Inf or -Inf for analogous
+entries of \code{time_delta}, and match the addition result match the addition
+result for non-infinite values, and product +Inf / -Inf when match the sign
+and of \code{time_delta}.
+}
+\description{
+Convert a time delta to a compatible integerish number of steps between time values
+}
+\keyword{internal}
diff --git a/tests/testthat/test-epi_slide.R b/tests/testthat/test-epi_slide.R
index f658bcf4..e8c318c7 100644
--- a/tests/testthat/test-epi_slide.R
+++ b/tests/testthat/test-epi_slide.R
@@ -300,34 +300,48 @@ for (p in (param_combinations %>% transpose())) {
       concatenate_list_params(p)
     ),
     {
-      out_sum <- rlang::inject(epi_slide(test_data, ~ sum(.x$value), !!!slide_args)) %>%
-        rename(slide_value_value = slide_value)
-      out_mean <- rlang::inject(epi_slide(test_data, ~ mean(.x$value), !!!slide_args)) %>%
-        rename(slide_value_value = slide_value)
+      out_sum <- rlang::inject(epi_slide(test_data, ~ sum(.x$value), !!!slide_args))
+      out_mean <- rlang::inject(epi_slide(test_data, ~ mean(.x$value), !!!slide_args))
 
       expect_equal(
         out_sum,
-        rlang::inject(epi_slide_opt(test_data, value, .f = data.table::frollsum, !!!slide_args))
+        rlang::inject(epi_slide_opt(test_data, value,
+          .f = data.table::frollsum, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
       expect_equal(
         out_sum,
-        rlang::inject(epi_slide_opt(test_data, value, .f = slider::slide_sum, !!!slide_args))
+        rlang::inject(epi_slide_opt(test_data, value,
+          .f = slider::slide_sum, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
       expect_equal(
         out_sum,
-        rlang::inject(epi_slide_sum(test_data, value, !!!slide_args))
+        rlang::inject(epi_slide_sum(test_data, value, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
       expect_equal(
         out_mean,
-        rlang::inject(epi_slide_opt(test_data, value, .f = data.table::frollmean, !!!slide_args))
+        rlang::inject(epi_slide_opt(test_data, value,
+          .f = data.table::frollmean, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
       expect_equal(
         out_mean,
-        rlang::inject(epi_slide_opt(test_data, value, .f = slider::slide_mean, !!!slide_args))
+        rlang::inject(epi_slide_opt(test_data, value,
+          .f = slider::slide_mean, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
       expect_equal(
         out_mean,
-        rlang::inject(epi_slide_mean(test_data, value, !!!slide_args))
+        rlang::inject(epi_slide_mean(test_data, value, !!!slide_args,
+          .new_col_names = "slide_value"
+        ))
       )
     }
   )
@@ -730,7 +744,7 @@ test_that("no dplyr warnings from selecting multiple columns", {
   )
   expect_equal(
     names(multi_slid),
-    c("geo_value", "time_value", "value", "value2", "slide_value_value", "slide_value_value2")
+    c("geo_value", "time_value", "value", "value2", "value_7dav", "value2_7dav")
   )
   expect_no_warning(
     multi_slid_select <- epi_slide_mean(multi_columns, c(value, value2), .window_size = 7)
@@ -741,3 +755,122 @@ test_that("no dplyr warnings from selecting multiple columns", {
   )
   expect_equal(multi_slid_select, multi_slid)
 })
+
+test_that("epi_slide_opt output naming features", {
+  multi_columns <- dplyr::bind_rows(
+    dplyr::tibble(geo_value = "ak", time_value = test_date + 1:200, value = 1:200, value2 = -1:-200),
+    dplyr::tibble(geo_value = "al", time_value = test_date + 1:5, value = -(1:5), value2 = 1:5)
+  ) %>%
+    as_epi_df() %>%
+    group_by(geo_value)
+  multi_columns_weekly <- dplyr::bind_rows(
+    dplyr::tibble(geo_value = "ak", time_value = test_date + 7 * (1:200), value = 1:200, value2 = -1:-200),
+    dplyr::tibble(geo_value = "al", time_value = test_date + 7 * (1:5), value = -(1:5), value2 = 1:5)
+  ) %>%
+    as_epi_df() %>%
+    group_by(geo_value)
+  yearmonthly <-
+    tibble::tibble(
+      geo_value = 1,
+      time_value = tsibble::make_yearmonth(2000, 1) + 1:30 - 1,
+      value = 1:30 %% 2 == 0
+    ) %>%
+    as_epi_df() %>%
+    group_by(geo_value)
+
+  # Auto-naming:
+  # * Changing .f and .window_size:
+  expect_equal(
+    multi_columns %>% epi_slide_opt(value2, frollmean, .window_size = 14) %>% names(),
+    c(names(multi_columns), "value2_14dav")
+  )
+  expect_equal(
+    multi_columns %>% epi_slide_opt(value2, slide_mean, .window_size = as.difftime(14, units = "days")) %>% names(),
+    c(names(multi_columns), "value2_14dav")
+  )
+  expect_equal(
+    multi_columns %>% epi_slide_opt(value2, slide_sum, .window_size = Inf) %>% names(),
+    c(names(multi_columns), "value2_running_sum")
+  )
+  # * Changing .f and .align:
+  expect_equal(
+    multi_columns %>% epi_slide_opt(value2, slide_min, .window_size = 14, .align = "center") %>% names(),
+    c(names(multi_columns), "value2_14dcmin")
+  )
+  expect_equal(
+    multi_columns %>% epi_slide_opt(value2, slide_max, .window_size = 14, .align = "left") %>% names(),
+    c(names(multi_columns), "value2_14dlmax")
+  )
+  # * Changing .f, time_type(, .window_size):
+  expect_equal(
+    multi_columns_weekly %>%
+      epi_slide_opt(value2, slide_prod, .window_size = as.difftime(2, units = "weeks")) %>%
+      names(),
+    c(names(multi_columns_weekly), "value2_2wprod")
+  )
+  expect_equal(
+    yearmonthly %>% epi_slide_opt(value, slide_any, .window_size = 3) %>% names(),
+    c(names(yearmonthly), "value_3many") # not the best name, but super unlikely anyway
+  )
+
+  # Manual naming:
+  expect_equal(
+    multi_columns %>%
+      epi_slide_opt(starts_with("value"), slide_sum, .window_size = 7, .suffix = "_s{.n}") %>%
+      names(),
+    c(names(multi_columns), "value_s7", "value2_s7")
+  )
+  expect_equal(
+    multi_columns %>%
+      epi_slide_opt(starts_with("value"), slide_sum, .window_size = 7, .prefix = "{.f_abbr}_", .suffix = "_{.n}") %>%
+      names(),
+    c(names(multi_columns), "sum_value_7", "sum_value2_7")
+  )
+  expect_equal(
+    multi_columns %>%
+      epi_slide_opt(starts_with("value"), slide_sum, .window_size = 7, .prefix = "slide_value_") %>%
+      names(),
+    c(names(multi_columns), "slide_value_value", "slide_value_value2")
+  )
+  expect_equal(
+    multi_columns %>%
+      epi_slide_opt(starts_with("value"), slide_sum, .window_size = 7, .new_col_names = c("slide_value", "sv2")) %>%
+      names(),
+    c(names(multi_columns), "slide_value", "sv2")
+  )
+
+  # Validation errors:
+  # * Wrong sizes:
+  expect_error(
+    multi_columns %>% epi_slide_opt(starts_with("value"), slide_sum,
+      .window_size = 7,
+      .suffix = c("a", "b")
+    )
+  )
+  expect_error(
+    multi_columns %>% epi_slide_opt(starts_with("value"), slide_sum,
+      .window_size = 7,
+      .new_col_names = "slide_value"
+    )
+  )
+  expect_error(
+    multi_columns %>% epi_slide_mean(starts_with("value"), .window_size = 7, .new_col_names = "output")
+  )
+  # * Incompatible args:
+  expect_error(
+    multi_columns %>% epi_slide_opt(value, slide_sum,
+      .window_size = 7,
+      .prefix = "a", .suffix = "b", .new_col_names = "slide_value"
+    ),
+    class = "epiprocess__epi_slide_opt_incompatible_naming_args"
+  )
+  # * Bad resulting output names:
+  expect_error(
+    multi_columns %>% epi_slide_mean(value, .window_size = 7, .new_col_names = "value"),
+    class = "epiprocess__epi_slide_opt_old_new_name_conflict"
+  )
+  expect_error(
+    multi_columns %>% epi_slide_mean(value:value2, .window_size = 7, .new_col_names = c("output", "output")),
+    class = "epiprocess__epi_slide_opt_new_name_duplicated"
+  )
+})

From 79ed2f399f82669ed17ab2a0f3a5a7047f6777dc Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Tue, 12 Nov 2024 11:38:41 -0800
Subject: [PATCH 08/39] Use different automatic names for slides on logical
 columns

---
 R/slide.R                       | 34 +++++++++++++++++----------------
 R/utils.R                       |  5 +++++
 man/epi_slide_opt.Rd            |  3 ++-
 tests/testthat/test-epi_slide.R | 25 ++++++++++++++++++++++++
 4 files changed, 50 insertions(+), 17 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index 9d383446..96beb828 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -587,7 +587,8 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'     `time_type` of `.x`
 #' - `{.align_abbr}` will be `""` if `.align` is the default of `"right"`;
 #'    otherwise, it will be the first letter of `.align`
-#' - `{.f_abbr}` will be a short string based on what `.f`
+#' - `{.f_abbr}` will be a character vector containing a short abbreviation
+#'    for `.f` factoring in the input column type(s) for `.col_names`
 #'
 #' @importFrom dplyr bind_rows mutate %>% arrange tibble select all_of
 #' @importFrom rlang enquo expr_label caller_arg quo_get_env
@@ -681,22 +682,23 @@ epi_slide_opt <- function(
   col_names_chr <- names(.x)[pos]
 
   # Check that slide function `.f` is one of those short-listed from
-  # `data.table` and `slider` (or a function that has the exact same
-  # definition, e.g. if the function has been reexported or defined
-  # locally).
+  # `data.table` and `slider` (or a function that has the exact same definition,
+  # e.g. if the function has been reexported or defined locally). Extract some
+  # metadata. `namer` will be mapped over columns (.x will be a column, not the
+  # entire edf).
   f_possibilities <-
     tibble::tribble(
-      ~f, ~package, ~abbr,
-      frollmean, "data.table", "av",
-      frollsum, "data.table", "sum",
-      frollapply, "data.table", "slide",
-      slide_sum, "slider", "sum",
-      slide_prod, "slider", "prod",
-      slide_mean, "slider", "av",
-      slide_min, "slider", "min",
-      slide_max, "slider", "max",
-      slide_all, "slider", "all",
-      slide_any, "slider", "any",
+      ~f, ~package, ~namer,
+      frollmean, "data.table", ~ if (is.logical(.x)) "prop" else "av",
+      frollsum, "data.table", ~ if (is.logical(.x)) "count" else "sum",
+      frollapply, "data.table", ~"slide",
+      slide_sum, "slider", ~ if (is.logical(.x)) "count" else "sum",
+      slide_prod, "slider", ~"prod",
+      slide_mean, "slider", ~ if (is.logical(.x)) "prop" else "av",
+      slide_min, "slider", ~"min",
+      slide_max, "slider", ~"max",
+      slide_all, "slider", ~"all",
+      slide_any, "slider", ~"any",
     )
   f_info <- f_possibilities %>%
     filter(map_lgl(.data$f, ~ identical(.f, .x)))
@@ -780,7 +782,7 @@ epi_slide_opt <- function(
       .n = n,
       .time_unit_abbr = time_unit_abbr,
       .align_abbr = align_abbr,
-      .f_abbr = f_info$abbr,
+      .f_abbr = purrr::map_chr(.x[col_names_chr], unwrap(f_info$namer)),
       quo_get_env(col_names_quo)
     )
     .new_col_names <- unclass(
diff --git a/R/utils.R b/R/utils.R
index 06876f08..6625e5c3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1174,3 +1174,8 @@ time_type_unit_abbr <- function(time_type) {
   }
   maybe_unit_abbr
 }
+
+unwrap <- function(x) {
+  checkmate::assert_list(x, len = 1L, names = "unnamed")
+  x[[1L]]
+}
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index 7f250cf4..c4526c0e 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -155,7 +155,8 @@ corresponding to the \code{.window_size}.
 \code{time_type} of \code{.x}
 \item \code{{.align_abbr}} will be \code{""} if \code{.align} is the default of \code{"right"};
 otherwise, it will be the first letter of \code{.align}
-\item \code{{.f_abbr}} will be a short string based on what \code{.f}
+\item \code{{.f_abbr}} will be a character vector containing a short abbreviation
+for \code{.f} factoring in the input column type(s) for \code{.col_names}
 }
 }
 
diff --git a/tests/testthat/test-epi_slide.R b/tests/testthat/test-epi_slide.R
index e8c318c7..2cb04eec 100644
--- a/tests/testthat/test-epi_slide.R
+++ b/tests/testthat/test-epi_slide.R
@@ -812,8 +812,24 @@ test_that("epi_slide_opt output naming features", {
     yearmonthly %>% epi_slide_opt(value, slide_any, .window_size = 3) %>% names(),
     c(names(yearmonthly), "value_3many") # not the best name, but super unlikely anyway
   )
+  # * Through forwarding functions:
+  expect_equal(
+    # XXX perhaps this should be an auto-naming feature?
+    yearmonthly %>%
+      epi_slide_mean(value, .window_size = Inf) %>%
+      names(),
+    c(names(yearmonthly), "value_running_prop")
+  )
+  expect_equal(
+    # XXX perhaps this should be an auto-naming feature?
+    yearmonthly %>%
+      epi_slide_sum(value, .window_size = Inf) %>%
+      names(),
+    c(names(yearmonthly), "value_running_count")
+  )
 
   # Manual naming:
+  # * Various combinations of args:
   expect_equal(
     multi_columns %>%
       epi_slide_opt(starts_with("value"), slide_sum, .window_size = 7, .suffix = "_s{.n}") %>%
@@ -838,6 +854,15 @@ test_that("epi_slide_opt output naming features", {
       names(),
     c(names(multi_columns), "slide_value", "sv2")
   )
+  # * Through forwarding functions:
+  expect_equal(
+    yearmonthly %>% epi_slide_mean(value, .window_size = Inf, .suffix = "_{.f_abbr}") %>% names(),
+    c(names(yearmonthly), "value_prop")
+  )
+  expect_equal(
+    yearmonthly %>% epi_slide_sum(value, .window_size = Inf, .suffix = "_{.f_abbr}") %>% names(),
+    c(names(yearmonthly), "value_count")
+  )
 
   # Validation errors:
   # * Wrong sizes:

From 97d17e8859588c81ae9ca662186e93dad5472ccd Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Wed, 13 Nov 2024 08:02:50 -0800
Subject: [PATCH 09/39] back to our custom workflow, no color handling

---
 .github/workflows/pkgdown.yaml | 17 ++++++++++++++++-
 _pkgdown.yml                   |  2 +-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3a1ff927..e9bfcc71 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -42,7 +42,22 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+# our versioning system+dev branch doesn't match the requirements for
+        # develop mode = auto
+        run: |
+           target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
+           override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
+             list(development = list(mode = "release"))
+           } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
+             list(development = list(mode = "devel"))
+           } else {
+             stop("Unexpected target_ref: ", target_ref)
+           }
+           pkg <- pkgdown::as_pkgdown(".", override = override)
+           cli::cli_rule("Cleaning files from old site...")
+           pkgdown::clean_site(pkg)
+           pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
+           pkgdown:::build_github_pages(pkg)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 743adc4b..a7d700e1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,5 +1,5 @@
 development:
-  mode: auto
+  mode: devel
 
 template:
   package: delphidocs

From f858ff9a5ced4b0db8e7740621b061baa71af6ab Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Wed, 13 Nov 2024 08:03:58 -0800
Subject: [PATCH 10/39] rm spaces

---
 .github/workflows/pkgdown.yaml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index e9bfcc71..19542ace 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -45,19 +45,19 @@ jobs:
 # our versioning system+dev branch doesn't match the requirements for
         # develop mode = auto
         run: |
-           target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
-           override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
-             list(development = list(mode = "release"))
-           } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
-             list(development = list(mode = "devel"))
-           } else {
-             stop("Unexpected target_ref: ", target_ref)
-           }
-           pkg <- pkgdown::as_pkgdown(".", override = override)
-           cli::cli_rule("Cleaning files from old site...")
-           pkgdown::clean_site(pkg)
-           pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
-           pkgdown:::build_github_pages(pkg)
+          target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
+          override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
+            list(development = list(mode = "release"))
+          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
+            list(development = list(mode = "devel"))
+          } else {
+            stop("Unexpected target_ref: ", target_ref)
+          }
+          pkg <- pkgdown::as_pkgdown(".", override = override)
+          cli::cli_rule("Cleaning files from old site...")
+          pkgdown::clean_site(pkg)
+          pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
+          pkgdown:::build_github_pages(pkg)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

From 2eaa5eb8b6dd2f7269e1187692010dad3fff3c08 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Wed, 13 Nov 2024 08:08:11 -0800
Subject: [PATCH 11/39] delphidocs in description

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index fd09aa57..8917f800 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -72,10 +72,12 @@ Suggests:
 VignetteBuilder:
     knitr
 Remotes:
+    cmu-delphi/delphidocs,
     cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     glmgen/genlasso,
     reconverse/outbreaks
+Config/Needs/website: cmu-delphi/delphidocs
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Copyright: file inst/COPYRIGHTS

From 4970ff4a7809ecc309e485e48677bbcc1d1f3f93 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Wed, 13 Nov 2024 16:28:03 -0800
Subject: [PATCH 12/39] style(.../workflows/pkgdown.yaml): indentation

---
 .github/workflows/pkgdown.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 19542ace..1381682d 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -42,7 +42,7 @@ jobs:
           needs: website
 
       - name: Build site
-# our versioning system+dev branch doesn't match the requirements for
+        # our versioning system+dev branch doesn't match the requirements for
         # develop mode = auto
         run: |
           target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"

From 05a0ca8900187068b13d744d66a55d0128f99691 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 11:40:12 -0800
Subject: [PATCH 13/39] Update epi_slide_{sum,mean} examples w/ naming options,
 cleanup

- Show naming options, including with multi-column selections when we have
  accommodating example data sets
- Select away the pre-existing 7d aggregations in the example data set
- Ungroup output
---
 R/slide.R            | 51 ++++++++++++++++++++++++++++++++++++--------
 man/epi_slide.Rd     |  1 +
 man/epi_slide_opt.Rd | 50 +++++++++++++++++++++++++++++++++++--------
 3 files changed, 84 insertions(+), 18 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index 96beb828..5a6d8264 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -114,6 +114,7 @@
 #'     },
 #'     .window_size = 7
 #'   ) %>%
+#'   ungroup() %>%
 #'   dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
 #'
 #' # Use the geo_value or the ref_time_value in the slide computation
@@ -605,7 +606,8 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #' # Compute a 7-day trailing average on cases.
 #' cases_deaths_subset %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7)
+#'   epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) %>%
+#'   ungroup()
 #'
 #' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 #' # to allow partially-missing windows.
@@ -615,7 +617,8 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #'     cases,
 #'     .f = data.table::frollmean, .window_size = 7,
 #'     algo = "exact", hasNA = TRUE, na.rm = TRUE
-#'   )
+#'   ) %>%
+#'   ungroup()
 epi_slide_opt <- function(
     .x, .col_names, .f, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
@@ -919,20 +922,36 @@ epi_slide_opt <- function(
 #'
 #' @export
 #' @examples
-#' # Compute a 7-day trailing average on cases.
-#' cases_deaths_subset %>%
+#' # Compute a 7-day trailing average of case rates.
+#' covid_case_death_rates_extended %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_mean(cases, .window_size = 7)
+#'   epi_slide_mean(case_rate, .window_size = 7) %>%
+#'   ungroup()
 #'
 #' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 #' # to allow partially-missing windows.
-#' cases_deaths_subset %>%
+#' covid_case_death_rates_extended %>%
 #'   group_by(geo_value) %>%
 #'   epi_slide_mean(
-#'     cases,
+#'     case_rate,
 #'     .window_size = 7,
 #'     na.rm = TRUE, algo = "exact", hasNA = TRUE
-#'   )
+#'   ) %>%
+#'   ungroup()
+#'
+#' # Compute a 7-day trailing average of case rates and death rates, with custom
+#' # output column names:
+#' covid_case_death_rates_extended %>%
+#'   group_by(geo_value) %>%
+#'   epi_slide_mean(c(case_rate, death_rate),
+#'     .window_size = 7,
+#'     .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
+#'   ) %>%
+#'   ungroup()
+#' covid_case_death_rates_extended %>%
+#'   group_by(geo_value) %>%
+#'   epi_slide_mean(c(case_rate, death_rate), .window_size = 7, .suffix = "_{.n}{.time_unit_abbr}_avg") %>%
+#'   ungroup()
 epi_slide_mean <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
@@ -995,8 +1014,22 @@ epi_slide_mean <- function(
 #' @examples
 #' # Compute a 7-day trailing sum on cases.
 #' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
+#'   group_by(geo_value) %>%
+#'   epi_slide_sum(cases, .window_size = 7) %>%
+#'   ungroup()
+#'
+#' # Specify output column names and/or naming scheme:
+#' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
+#'   group_by(geo_value) %>%
+#'   epi_slide_sum(cases, .window_size = 7, .new_col_names = "case_sum") %>%
+#'   ungroup()
+#' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_sum(cases, .window_size = 7)
+#'   epi_slide_sum(cases, .window_size = 7, .prefix = "sum_") %>%
+#'   ungroup()
 epi_slide_sum <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index 1c399d35..511ba8a8 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -172,6 +172,7 @@ cases_deaths_subset \%>\%
     },
     .window_size = 7
   ) \%>\%
+  ungroup() \%>\%
   dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
 
 # Use the geo_value or the ref_time_value in the slide computation
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index c4526c0e..c014c2d1 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -164,7 +164,8 @@ for \code{.f} factoring in the input column type(s) for \code{.col_names}
 # Compute a 7-day trailing average on cases.
 cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7)
+  epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) \%>\%
+  ungroup()
 
 # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 # to allow partially-missing windows.
@@ -174,25 +175,56 @@ cases_deaths_subset \%>\%
     cases,
     .f = data.table::frollmean, .window_size = 7,
     algo = "exact", hasNA = TRUE, na.rm = TRUE
-  )
-# Compute a 7-day trailing average on cases.
-cases_deaths_subset \%>\%
+  ) \%>\%
+  ungroup()
+# Compute a 7-day trailing average of case rates.
+covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_mean(cases, .window_size = 7)
+  epi_slide_mean(case_rate, .window_size = 7) \%>\%
+  ungroup()
 
 # Same as above, but adjust `frollmean` settings for speed, accuracy, and
 # to allow partially-missing windows.
-cases_deaths_subset \%>\%
+covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
   epi_slide_mean(
-    cases,
+    case_rate,
     .window_size = 7,
     na.rm = TRUE, algo = "exact", hasNA = TRUE
-  )
+  ) \%>\%
+  ungroup()
+
+# Compute a 7-day trailing average of case rates and death rates, with custom
+# output column names:
+covid_case_death_rates_extended \%>\%
+  group_by(geo_value) \%>\%
+  epi_slide_mean(c(case_rate, death_rate),
+    .window_size = 7,
+    .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
+  ) \%>\%
+  ungroup()
+covid_case_death_rates_extended \%>\%
+  group_by(geo_value) \%>\%
+  epi_slide_mean(c(case_rate, death_rate), .window_size = 7, .suffix = "_{.n}{.time_unit_abbr}_avg") \%>\%
+  ungroup()
 # Compute a 7-day trailing sum on cases.
 cases_deaths_subset \%>\%
+  select(geo_value, time_value, cases) \%>\%
+  group_by(geo_value) \%>\%
+  epi_slide_sum(cases, .window_size = 7) \%>\%
+  ungroup()
+
+# Specify output column names and/or naming scheme:
+cases_deaths_subset \%>\%
+  select(geo_value, time_value, cases) \%>\%
+  group_by(geo_value) \%>\%
+  epi_slide_sum(cases, .window_size = 7, .new_col_names = "case_sum") \%>\%
+  ungroup()
+cases_deaths_subset \%>\%
+  select(geo_value, time_value, cases) \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_sum(cases, .window_size = 7)
+  epi_slide_sum(cases, .window_size = 7, .prefix = "sum_") \%>\%
+  ungroup()
 }
 \seealso{
 \code{\link{epi_slide}} for the more general slide function

From 5ffaf2f6b9285a4b8b570fe9b69243c5ebb623ac Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 12:51:00 -0800
Subject: [PATCH 14/39] Tweak&fix epi_slide docs regarding packing, nesting

---
 R/slide.R            | 55 +++++++++++++++++++++++++++++++++-----------
 man/epi_slide.Rd     | 55 +++++++++++++++++++++++++++++++++-----------
 man/epi_slide_opt.Rd |  6 ++---
 3 files changed, 86 insertions(+), 30 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index 5a6d8264..ba5f3f3a 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -70,6 +70,8 @@
 #' @export
 #' @seealso [`epi_slide_opt`] for optimized slide functions
 #' @examples
+#' library(dplyr)
+#'
 #' # Get the 7-day trailing standard deviation of cases and the 7-day trailing mean of cases
 #' cases_deaths_subset %>%
 #'   epi_slide(
@@ -77,45 +79,72 @@
 #'     cases_7dav = mean(cases, na.rm = TRUE),
 #'     .window_size = 7
 #'   ) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+#'   select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+#' # Note that epi_slide_mean could be used to more quickly calculate cases_7dav.
+#'
+#' # In addition to the [`dplyr::mutate`]-like syntax, you can feed in a function or
+#' # formula in a way similar to [`dplyr::group_modify`]:
+#' my_summarizer <- function(window_data) {
+#'   window_data %>%
+#'     summarize(
+#'       cases_7sd = sd(cases, na.rm = TRUE),
+#'       cases_7dav = mean(cases, na.rm = TRUE)
+#'     )
+#' }
+#' cases_deaths_subset %>%
+#'   epi_slide(
+#'     ~ my_summarizer(.x),
+#'     .window_size = 7
+#'   ) %>%
+#'   select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+#'
 #'
-#' # The same as above, but unpacking using an unnamed data.frame with a formula
+#'
+#'
+#'
+#' #### Advanced: ####
+#'
+#' # The tidyverse supports ["packing"][tidyr::pack] multiple columns into a
+#' # single tibble-type column contained within some larger tibble. Like dplyr,
+#' # we normally don't pack output columns together, but will if you provide a
+#' # name for a tibble-type output:
 #' cases_deaths_subset %>%
 #'   epi_slide(
-#'     ~ data.frame(
+#'     slide_packed = tibble(
 #'       cases_7sd = sd(.x$cases, na.rm = TRUE),
 #'       cases_7dav = mean(.x$cases, na.rm = TRUE)
 #'     ),
 #'     .window_size = 7
 #'   ) %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
-#'
-#' # The same as above, but packing using a named data.frame with a tidy evaluation
-#' # expression
+#'   select(geo_value, time_value, cases, slide_packed)
 #' cases_deaths_subset %>%
 #'   epi_slide(
-#'     slide_packed = data.frame(
+#'     ~ tibble(
 #'       cases_7sd = sd(.x$cases, na.rm = TRUE),
 #'       cases_7dav = mean(.x$cases, na.rm = TRUE)
 #'     ),
+#'     .new_col_name = "slide_packed",
 #'     .window_size = 7
 #'   ) %>%
-#'   dplyr::select(geo_value, time_value, cases, slide_packed)
+#'   select(geo_value, time_value, cases, slide_packed)
 #'
-#' # nested new columns
+#' # You can also get ["nested"][tidyr::nest] format by wrapping your results in
+#' # a list:
 #' cases_deaths_subset %>%
 #'   group_by(geo_value) %>%
 #'   epi_slide(
 #'     function(x, g, t) {
-#'       data.frame(
+#'       list(tibble(
 #'         cases_7sd = sd(x$cases, na.rm = TRUE),
 #'         cases_7dav = mean(x$cases, na.rm = TRUE)
-#'       )
+#'       ))
 #'     },
 #'     .window_size = 7
 #'   ) %>%
 #'   ungroup() %>%
-#'   dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+#'   select(geo_value, time_value, slide_value)
+#'
+#'
 #'
 #' # Use the geo_value or the ref_time_value in the slide computation
 #' cases_deaths_subset %>%
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index 511ba8a8..c497b5d3 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -128,6 +128,8 @@ determined the time window for the current computation.
 }
 }
 \examples{
+library(dplyr)
+
 # Get the 7-day trailing standard deviation of cases and the 7-day trailing mean of cases
 cases_deaths_subset \%>\%
   epi_slide(
@@ -135,45 +137,72 @@ cases_deaths_subset \%>\%
     cases_7dav = mean(cases, na.rm = TRUE),
     .window_size = 7
   ) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+  select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+# Note that epi_slide_mean could be used to more quickly calculate cases_7dav.
+
+# In addition to the [`dplyr::mutate`]-like syntax, you can feed in a function or
+# formula in a way similar to [`dplyr::group_modify`]:
+my_summarizer <- function(window_data) {
+  window_data \%>\%
+    summarize(
+      cases_7sd = sd(cases, na.rm = TRUE),
+      cases_7dav = mean(cases, na.rm = TRUE)
+    )
+}
+cases_deaths_subset \%>\%
+  epi_slide(
+    ~ my_summarizer(.x),
+    .window_size = 7
+  ) \%>\%
+  select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+
 
-# The same as above, but unpacking using an unnamed data.frame with a formula
+
+
+
+#### Advanced: ####
+
+# The tidyverse supports ["packing"][tidyr::pack] multiple columns into a
+# single tibble-type column contained within some larger tibble. Like dplyr,
+# we normally don't pack output columns together, but will if you provide a
+# name for a tibble-type output:
 cases_deaths_subset \%>\%
   epi_slide(
-    ~ data.frame(
+    slide_packed = tibble(
       cases_7sd = sd(.x$cases, na.rm = TRUE),
       cases_7dav = mean(.x$cases, na.rm = TRUE)
     ),
     .window_size = 7
   ) \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
-
-# The same as above, but packing using a named data.frame with a tidy evaluation
-# expression
+  select(geo_value, time_value, cases, slide_packed)
 cases_deaths_subset \%>\%
   epi_slide(
-    slide_packed = data.frame(
+    ~ tibble(
       cases_7sd = sd(.x$cases, na.rm = TRUE),
       cases_7dav = mean(.x$cases, na.rm = TRUE)
     ),
+    .new_col_name = "slide_packed",
     .window_size = 7
   ) \%>\%
-  dplyr::select(geo_value, time_value, cases, slide_packed)
+  select(geo_value, time_value, cases, slide_packed)
 
-# nested new columns
+# You can also get ["nested"][tidyr::nest] format by wrapping your results in
+# a list:
 cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
   epi_slide(
     function(x, g, t) {
-      data.frame(
+      list(tibble(
         cases_7sd = sd(x$cases, na.rm = TRUE),
         cases_7dav = mean(x$cases, na.rm = TRUE)
-      )
+      ))
     },
     .window_size = 7
   ) \%>\%
   ungroup() \%>\%
-  dplyr::select(geo_value, time_value, cases, cases_7sd, cases_7dav)
+  select(geo_value, time_value, slide_value)
+
+
 
 # Use the geo_value or the ref_time_value in the slide computation
 cases_deaths_subset \%>\%
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index c014c2d1..e61e94cd 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -198,10 +198,8 @@ covid_case_death_rates_extended \%>\%
 # output column names:
 covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_mean(c(case_rate, death_rate),
-    .window_size = 7,
-    .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
-  ) \%>\%
+  epi_slide_mean(c(case_rate, death_rate), .window_size = 7,
+                 .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")) \%>\%
   ungroup()
 covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%

From e099fd0cc39b276844717804ae67caa4b9593abe Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 13:28:28 -0800
Subject: [PATCH 15/39] Make epi_slide* all use autogrouping + make
 autogrouping temporary

---
 R/slide.R                        | 59 ++++++++++++++++----------------
 man-roxygen/basic-slide-params.R |  4 +--
 man/epi_slide.Rd                 |  4 +--
 man/epi_slide_opt.Rd             | 10 +++---
 tests/testthat/test-epi_slide.R  | 38 ++++++++++++++++++++
 5 files changed, 78 insertions(+), 37 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index ba5f3f3a..d94dd01a 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -186,15 +186,16 @@ epi_slide <- function(
 
   # Validate arguments
   assert_class(.x, "epi_df")
-  if (checkmate::test_class(.x, "grouped_df")) {
+  .x_orig_groups <- groups(.x)
+  if (inherits(.x, "grouped_df")) {
     expected_group_keys <- .x %>%
       key_colnames(exclude = "time_value") %>%
       sort()
     if (!identical(.x %>% group_vars() %>% sort(), expected_group_keys)) {
       cli_abort(
-        "epi_slide: `.x` must be either grouped by {expected_group_keys}. (Or you can just ungroup
-        `.x` and we'll do this grouping automatically.) You may need to aggregate your data first,
-        see aggregate_epi_df().",
+        "`.x` must be either grouped by {expected_group_keys} or ungrouped; if the latter,
+         we'll temporarily group by {expected_group_keys} for this operation. You may need
+        to aggregate your data first, see aggregate_epi_df().",
         class = "epiprocess__epi_slide__invalid_grouping"
       )
     }
@@ -300,7 +301,6 @@ epi_slide <- function(
   #   `epi_slide_one_group`.
   # - `...` from top of `epi_slide` are forwarded to `.f` here through
   #   group_modify and through the lambda.
-  .x_groups <- groups(.x)
   result <- group_map(
     .x,
     .f = function(.data_group, .group_key, ...) {
@@ -324,7 +324,7 @@ epi_slide <- function(
     filter(.real) %>%
     select(-.real) %>%
     arrange_col_canonical() %>%
-    group_by(!!!.x_groups)
+    group_by(!!!.x_orig_groups)
 
   # If every group in epi_slide_one_group takes the
   # length(available_ref_time_values) == 0 branch then we end up here.
@@ -691,12 +691,30 @@ epi_slide_opt <- function(
     )
   }
 
+  assert_class(.x, "epi_df")
+  .x_orig_groups <- groups(.x)
+  if (inherits(.x, "grouped_df")) {
+    expected_group_keys <- .x %>%
+      key_colnames(exclude = "time_value") %>%
+      sort()
+    if (!identical(.x %>% group_vars() %>% sort(), expected_group_keys)) {
+      cli_abort(
+        "`.x` must be either grouped by {expected_group_keys} or ungrouped; if the latter,
+         we'll temporarily group by {expected_group_keys} for this operation. You may need
+        to aggregate your data first, see aggregate_epi_df().",
+        class = "epiprocess__epi_slide__invalid_grouping"
+      )
+    }
+  } else {
+    .x <- group_epi_df(.x, exclude = "time_value")
+  }
   if (nrow(.x) == 0L) {
     cli_abort(
       c(
         "input data `.x` unexpectedly has 0 rows",
         "i" = "If this computation is occuring within an `epix_slide` call,
-          check that `epix_slide` `.versions` argument was set appropriately"
+          check that `epix_slide` `.versions` argument was set appropriately
+          so that you don't get any completely-empty snapshots"
       ),
       class = "epiprocess__epi_slide_opt__0_row_input",
       epiprocess__x = .x
@@ -857,27 +875,9 @@ epi_slide_opt <- function(
       arrange(.data$time_value)
 
     if (f_from_package == "data.table") {
-      # If a group contains duplicate time values, `frollmean` will still only
-      # use the last `k` obs. It isn't looking at dates, it just goes in row
-      # order. So if the computation is aggregating across multiple obs for the
-      # same date, `epi_slide_opt` and derivates will produce incorrect results;
-      # `epi_slide` should be used instead.
-      if (anyDuplicated(.data_group$time_value) != 0L) {
-        cli_abort(
-          c(
-            "group contains duplicate time values. Using `epi_slide_[opt/mean/sum]` on this
-              group will result in incorrect results",
-            "i" = "Please change the grouping structure of the input data so that
-              each group has non-duplicate time values (e.g. `x %>% group_by(geo_value)
-              %>% epi_slide_opt(.f = frollmean)`)",
-            "i" = "Use `epi_slide` to aggregate across groups"
-          ),
-          class = "epiprocess__epi_slide_opt__duplicate_time_values",
-          epiprocess__data_group = .data_group,
-          epiprocess__group_key = .group_key
-        )
-      }
-
+      # Grouping should ensure that we don't have duplicate time values.
+      # Completion above should ensure we have at least .window_size rows. Check
+      # that we don't have more than .window_size rows (or fewer somehow):
       if (nrow(.data_group) != length(c(all_dates, pad_early_dates, pad_late_dates))) {
         cli_abort(
           c(
@@ -928,7 +928,8 @@ epi_slide_opt <- function(
     group_modify(slide_one_grp, ..., .keep = FALSE) %>%
     filter(.data$.real) %>%
     select(-.real) %>%
-    arrange_col_canonical()
+    arrange_col_canonical() %>%
+    group_by(!!!.x_orig_groups)
 
   if (.all_rows) {
     result[!(result$time_value %in% ref_time_values), result_col_names] <- NA
diff --git a/man-roxygen/basic-slide-params.R b/man-roxygen/basic-slide-params.R
index 638307d6..8ccd35f9 100644
--- a/man-roxygen/basic-slide-params.R
+++ b/man-roxygen/basic-slide-params.R
@@ -1,5 +1,5 @@
-#' @param .x An `epi_df` object. If ungrouped, we group by `geo_value` and any
-#'   columns in `other_keys`. If grouped, we make sure the grouping is by
+#' @param .x An `epi_df` object. If ungrouped, we temporarily group by `geo_value`
+#'   and any columns in `other_keys`. If grouped, we make sure the grouping is by
 #'   `geo_value` and `other_keys`.
 #' @param .window_size The size of the sliding window. The accepted values
 #' depend on the type of the `time_value` column in `.x`:
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index c497b5d3..9f4abd36 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -16,8 +16,8 @@ epi_slide(
 )
 }
 \arguments{
-\item{.x}{An \code{epi_df} object. If ungrouped, we group by \code{geo_value} and any
-columns in \code{other_keys}. If grouped, we make sure the grouping is by
+\item{.x}{An \code{epi_df} object. If ungrouped, we temporarily group by \code{geo_value}
+and any columns in \code{other_keys}. If grouped, we make sure the grouping is by
 \code{geo_value} and \code{other_keys}.}
 
 \item{.f}{Function, formula, or missing; together with \code{...} specifies the
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index e61e94cd..13b03a1b 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -47,8 +47,8 @@ epi_slide_sum(
 )
 }
 \arguments{
-\item{.x}{An \code{epi_df} object. If ungrouped, we group by \code{geo_value} and any
-columns in \code{other_keys}. If grouped, we make sure the grouping is by
+\item{.x}{An \code{epi_df} object. If ungrouped, we temporarily group by \code{geo_value}
+and any columns in \code{other_keys}. If grouped, we make sure the grouping is by
 \code{geo_value} and \code{other_keys}.}
 
 \item{.col_names}{<\code{\link[=dplyr_tidy_select]{tidy-select}}> An unquoted column
@@ -198,8 +198,10 @@ covid_case_death_rates_extended \%>\%
 # output column names:
 covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_mean(c(case_rate, death_rate), .window_size = 7,
-                 .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")) \%>\%
+  epi_slide_mean(c(case_rate, death_rate),
+    .window_size = 7,
+    .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
+  ) \%>\%
   ungroup()
 covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
diff --git a/tests/testthat/test-epi_slide.R b/tests/testthat/test-epi_slide.R
index 2cb04eec..0aa4aca7 100644
--- a/tests/testthat/test-epi_slide.R
+++ b/tests/testthat/test-epi_slide.R
@@ -899,3 +899,41 @@ test_that("epi_slide_opt output naming features", {
     class = "epiprocess__epi_slide_opt_new_name_duplicated"
   )
 })
+
+test_that("epi_slide* output grouping matches input grouping", {
+  toy_edf <- as_epi_df(bind_rows(list(
+    tibble(geo_value = 1, age_group = 1, time_value = as.Date("2020-01-01") + 1:10 - 1, value = 1:10),
+    tibble(geo_value = 1, age_group = 2, time_value = as.Date("2020-01-01") + 1:10 - 1, value = 20:11),
+    tibble(geo_value = 2, age_group = 2, time_value = as.Date("2020-01-01") + 1:10 - 1, value = 31:40)
+  )), other_keys = "age_group", as_of = as.Date("2020-01-01") + 20)
+
+  # Preserving existing grouping:
+  expect_equal(
+    toy_edf %>%
+      group_by(age_group, geo_value) %>%
+      epi_slide(value_7dsum = sum(value), .window_size = 7) %>%
+      group_vars(),
+    c("age_group", "geo_value")
+  )
+  expect_equal(
+    toy_edf %>%
+      group_by(age_group, geo_value) %>%
+      epi_slide_sum(value, .window_size = 7) %>%
+      group_vars(),
+    c("age_group", "geo_value")
+  )
+
+  # Removing automatic grouping:
+  expect_equal(
+    toy_edf %>%
+      epi_slide(value_7dsum = sum(value), .window_size = 7) %>%
+      group_vars(),
+    character(0)
+  )
+  expect_equal(
+    toy_edf %>%
+      epi_slide_sum(value, .window_size = 7) %>%
+      group_vars(),
+    character(0)
+  )
+})

From 6d8bcf6c934f97564134217af6f2a417d4455ad8 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 13:41:47 -0800
Subject: [PATCH 16/39] Update NEWS.md with slide naming & autogrouping
 changes, bugfix

---
 NEWS.md | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 8ab77ee4..436b0c7d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -14,12 +14,10 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
   with `covid`. The data set previously named `jhu_confirmed_cumulative_num` has
   been removed from the package, but a renamed version is has been removed from
   the package, but a renamed version is still available in `epidatasets`.
-
-## Bug fixes
-
-- Removed `.window_size = 1` default from `epi_slide_{mean,sum,opt}`; this
-  argument is now mandatory, and should nearly always be greater than 1 except
-  for testing purposes.
+- `epi_slide_{sum,mean,opt}` have improved default output column names, and
+  additional arguments for specifying names: `.prefix`, `.suffix`,
+  `.new_col_names`. To obtain the old naming behavior, use `.prefix =
+  "slide_value_"`.
 
 ## Improvements
 
@@ -29,6 +27,18 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 - Improved validation of `.window_size` arguments.
 - Rewrote a lot of the package documentation to be more consistent and
   informative. Simplified and streamlined the vignettes.
+- `epi_slide_{sum,mean,opt}` on ungrouped `epi_df`s will now temporarily group
+  by `geo_value` and any `other_keys` for the slide operation rather than raise
+  an error about duplicated time values. `epi_slide`'s analogous automatic
+  grouping has been made temporary in order to match.
+
+## Bug fixes
+
+- Removed `.window_size = 1` default from `epi_slide_{mean,sum,opt}`; this
+  argument is now mandatory, and should nearly always be greater than 1 except
+  for testing purposes.
+- Fixed `epi_slide_{sum,mean,opt}` raising an error on certain tidyselect
+  expressions.
 
 ## Cleanup
 

From 03155dd73f4d4ea085506ba5603a0a46e5bcb7bd Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 14:00:50 -0800
Subject: [PATCH 17/39] docs(time_delta_to_n_steps): copyediting

---
 R/utils.R                    | 3 +--
 man/time_delta_to_n_steps.Rd | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 6625e5c3..c1804a90 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1125,8 +1125,7 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
 #'   to time values of time type `time_type`. If the given time type does not
 #'   support infinite values, then it should produce +Inf or -Inf for analogous
 #'   entries of `time_delta`, and match the addition result match the addition
-#'   result for non-infinite values, and product +Inf / -Inf when match the sign
-#'   and of `time_delta`.
+#'   result for non-infinite entries.
 #'
 #' @keywords internal
 time_delta_to_n_steps <- function(time_delta, time_type) {
diff --git a/man/time_delta_to_n_steps.Rd b/man/time_delta_to_n_steps.Rd
index 0f9325be..f5c6639b 100644
--- a/man/time_delta_to_n_steps.Rd
+++ b/man/time_delta_to_n_steps.Rd
@@ -22,8 +22,7 @@ infinite values) that produces the same result as \code{time_delta} when added
 to time values of time type \code{time_type}. If the given time type does not
 support infinite values, then it should produce +Inf or -Inf for analogous
 entries of \code{time_delta}, and match the addition result match the addition
-result for non-infinite values, and product +Inf / -Inf when match the sign
-and of \code{time_delta}.
+result for non-infinite entries.
 }
 \description{
 Convert a time delta to a compatible integerish number of steps between time values

From cac02c299ff034f6a56ddaf0a1ed421e32fb6bce Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 14:05:42 -0800
Subject: [PATCH 18/39] docs(time_delta_to_n_steps): fix inaccurate equivalency
 statement

---
 R/utils.R                    | 13 +++++++------
 man/time_delta_to_n_steps.Rd | 15 ++++++++-------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index c1804a90..348cf7fa 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1111,7 +1111,7 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
 }
 
 
-#' Convert a time delta to a compatible integerish number of steps between time values
+#' Convert a time delta to a integerish number of "unit" steps between time values
 #'
 #' @param time_delta a vector that can be added to time values of time type
 #'   `time_type` to arrive at other time values of that time type, or
@@ -1121,11 +1121,12 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
 #'   without sign and length restrictions.
 #' @param time_type as in [`validate_slide_window_arg`]
 #' @return [bare integerish][rlang::is_integerish] vector (with possible
-#'   infinite values) that produces the same result as `time_delta` when added
-#'   to time values of time type `time_type`. If the given time type does not
-#'   support infinite values, then it should produce +Inf or -Inf for analogous
-#'   entries of `time_delta`, and match the addition result match the addition
-#'   result for non-infinite entries.
+#'   infinite values) that produces the same result as `time_delta` when
+#'   multiplied by some "unit time step" for that time type and added to time
+#'   values of time type `time_type`. If the given time type does not support
+#'   infinite values, then it should produce +Inf or -Inf for analogous entries
+#'   of `time_delta`, and match the addition result match the addition result
+#'   for non-infinite entries.
 #'
 #' @keywords internal
 time_delta_to_n_steps <- function(time_delta, time_type) {
diff --git a/man/time_delta_to_n_steps.Rd b/man/time_delta_to_n_steps.Rd
index f5c6639b..4c0bdcd6 100644
--- a/man/time_delta_to_n_steps.Rd
+++ b/man/time_delta_to_n_steps.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/utils.R
 \name{time_delta_to_n_steps}
 \alias{time_delta_to_n_steps}
-\title{Convert a time delta to a compatible integerish number of steps between time values}
+\title{Convert a time delta to a integerish number of "unit" steps between time values}
 \usage{
 time_delta_to_n_steps(time_delta, time_type)
 }
@@ -18,13 +18,14 @@ without sign and length restrictions.}
 }
 \value{
 \link[rlang:is_integerish]{bare integerish} vector (with possible
-infinite values) that produces the same result as \code{time_delta} when added
-to time values of time type \code{time_type}. If the given time type does not
-support infinite values, then it should produce +Inf or -Inf for analogous
-entries of \code{time_delta}, and match the addition result match the addition
-result for non-infinite entries.
+infinite values) that produces the same result as \code{time_delta} when
+multiplied by some "unit time step" for that time type and added to time
+values of time type \code{time_type}. If the given time type does not support
+infinite values, then it should produce +Inf or -Inf for analogous entries
+of \code{time_delta}, and match the addition result match the addition result
+for non-infinite entries.
 }
 \description{
-Convert a time delta to a compatible integerish number of steps between time values
+Convert a time delta to a integerish number of "unit" steps between time values
 }
 \keyword{internal}

From 9cf52297e1591ef22c6c87e70856d4e650c25be5 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Thu, 14 Nov 2024 14:38:36 -0800
Subject: [PATCH 19/39] Remove invalid link to undocumented helper function

---
 R/utils.R                    | 12 ++++++------
 man/time_delta_to_n_steps.Rd | 12 ++++++------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 348cf7fa..cb99ceca 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1119,14 +1119,14 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
 #'   in, if supported by the class of `time_delta`, even if `time_type` doesn't
 #'   necessarily support Inf/-Inf entries. Basically a slide window arg but
 #'   without sign and length restrictions.
-#' @param time_type as in [`validate_slide_window_arg`]
+#' @param time_type as in `validate_slide_window_arg`
 #' @return [bare integerish][rlang::is_integerish] vector (with possible
 #'   infinite values) that produces the same result as `time_delta` when
-#'   multiplied by some "unit time step" for that time type and added to time
-#'   values of time type `time_type`. If the given time type does not support
-#'   infinite values, then it should produce +Inf or -Inf for analogous entries
-#'   of `time_delta`, and match the addition result match the addition result
-#'   for non-infinite entries.
+#'   multiplied by the "natural" "unit time delta" (not yet implemented) for
+#'   that time type and added to time values of time type `time_type`. If the
+#'   given time type does not support infinite values, then it should produce
+#'   +Inf or -Inf for analogous entries of `time_delta`, and match the addition
+#'   result match the addition result for non-infinite entries.
 #'
 #' @keywords internal
 time_delta_to_n_steps <- function(time_delta, time_type) {
diff --git a/man/time_delta_to_n_steps.Rd b/man/time_delta_to_n_steps.Rd
index 4c0bdcd6..db8cdaaa 100644
--- a/man/time_delta_to_n_steps.Rd
+++ b/man/time_delta_to_n_steps.Rd
@@ -14,16 +14,16 @@ in, if supported by the class of \code{time_delta}, even if \code{time_type} doe
 necessarily support Inf/-Inf entries. Basically a slide window arg but
 without sign and length restrictions.}
 
-\item{time_type}{as in \code{\link{validate_slide_window_arg}}}
+\item{time_type}{as in \code{validate_slide_window_arg}}
 }
 \value{
 \link[rlang:is_integerish]{bare integerish} vector (with possible
 infinite values) that produces the same result as \code{time_delta} when
-multiplied by some "unit time step" for that time type and added to time
-values of time type \code{time_type}. If the given time type does not support
-infinite values, then it should produce +Inf or -Inf for analogous entries
-of \code{time_delta}, and match the addition result match the addition result
-for non-infinite entries.
+multiplied by the "natural" "unit time delta" (not yet implemented) for
+that time type and added to time values of time type \code{time_type}. If the
+given time type does not support infinite values, then it should produce
++Inf or -Inf for analogous entries of \code{time_delta}, and match the addition
+result match the addition result for non-infinite entries.
 }
 \description{
 Convert a time delta to a integerish number of "unit" steps between time values

From 632c8d99e9f3fd06419d1dbc02f11594c7386656 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 15 Nov 2024 10:06:55 -0800
Subject: [PATCH 20/39] Address CHECK lints

---
 R/epiprocess-package.R | 2 +-
 R/slide.R              | 5 ++++-
 man/epi_slide_opt.Rd   | 5 ++++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/R/epiprocess-package.R b/R/epiprocess-package.R
index b640a0b5..68b7b9b5 100644
--- a/R/epiprocess-package.R
+++ b/R/epiprocess-package.R
@@ -27,5 +27,5 @@ utils::globalVariables(c(
   "fitted", ".response", "geo_value", "time_value",
   "value", ".real", "lag", "max_value", "min_value",
   "median_value", "spread", "rel_spread", "time_to",
-  "time_near_latest", "n_revisions"
+  "time_near_latest", "n_revisions", "min_lag", "max_lag"
 ))
diff --git a/R/slide.R b/R/slide.R
index d94dd01a..f212473e 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -980,7 +980,10 @@ epi_slide_opt <- function(
 #'   ungroup()
 #' covid_case_death_rates_extended %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_mean(c(case_rate, death_rate), .window_size = 7, .suffix = "_{.n}{.time_unit_abbr}_avg") %>%
+#'   epi_slide_mean(c(case_rate, death_rate),
+#'     .window_size = 7,
+#'     .suffix = "_{.n}{.time_unit_abbr}_avg"
+#'   ) %>%
 #'   ungroup()
 epi_slide_mean <- function(
     .x, .col_names, ...,
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index 13b03a1b..724a928e 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -205,7 +205,10 @@ covid_case_death_rates_extended \%>\%
   ungroup()
 covid_case_death_rates_extended \%>\%
   group_by(geo_value) \%>\%
-  epi_slide_mean(c(case_rate, death_rate), .window_size = 7, .suffix = "_{.n}{.time_unit_abbr}_avg") \%>\%
+  epi_slide_mean(c(case_rate, death_rate),
+    .window_size = 7,
+    .suffix = "_{.n}{.time_unit_abbr}_avg"
+  ) \%>\%
   ungroup()
 # Compute a 7-day trailing sum on cases.
 cases_deaths_subset \%>\%

From ad15b8f1c25f8f1abea355eed0dd9dd6ab5dd312 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 15 Nov 2024 10:14:13 -0800
Subject: [PATCH 21/39] Add unit_time_delta to make time_delta_to_n_steps make
 sense

---
 NAMESPACE                    |  1 +
 R/utils.R                    | 22 +++++++++++++-
 man/time_delta_to_n_steps.Rd |  2 +-
 man/unit_time_delta.Rd       | 21 ++++++++++++++
 tests/testthat/test-utils.R  | 56 ++++++++++++++++++++++++++++++++++++
 5 files changed, 100 insertions(+), 2 deletions(-)
 create mode 100644 man/unit_time_delta.Rd

diff --git a/NAMESPACE b/NAMESPACE
index e044739b..7b054fd6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -98,6 +98,7 @@ export(slice)
 export(sum_groups_epi_df)
 export(time_column_names)
 export(ungroup)
+export(unit_time_delta)
 export(unnest)
 export(validate_epi_archive)
 export(version_column_names)
diff --git a/R/utils.R b/R/utils.R
index cb99ceca..f3eb114d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1122,7 +1122,7 @@ validate_slide_window_arg <- function(arg, time_type, lower = 1, allow_inf = TRU
 #' @param time_type as in `validate_slide_window_arg`
 #' @return [bare integerish][rlang::is_integerish] vector (with possible
 #'   infinite values) that produces the same result as `time_delta` when
-#'   multiplied by the "natural" "unit time delta" (not yet implemented) for
+#'   multiplied by the natural [`unit_time_delta`] for
 #'   that time type and added to time values of time type `time_type`. If the
 #'   given time type does not support infinite values, then it should produce
 #'   +Inf or -Inf for analogous entries of `time_delta`, and match the addition
@@ -1157,6 +1157,26 @@ time_delta_to_n_steps <- function(time_delta, time_type) {
   }
 }
 
+#' Object that, added to time_values of time_type, advances by one time step/interval
+#'
+#' @param time_type string; `epi_df`'s or `epi_archive`'s `time_type`
+#' @return an object `u` such that `time_values + u` represents advancing by one
+#'   time step / moving to the subsequent time interval for any `time_values`
+#'   object of time type `time_type`, and such that `time_values + k * u` for
+#'   integerish vector `k` advances by `k` steps (with vectorization,
+#'   recycling).
+#'
+#' @export
+unit_time_delta <- function(time_type) {
+  switch(time_type,
+    day = as.difftime(1, units = "days"),
+    week = as.difftime(1, units = "weeks"),
+    yearmonth = 1,
+    integer = 1L,
+    cli_abort("Unsupported time_type: {time_type}")
+  )
+}
+
 # Using these unit abbreviations happens to make our automatic slide output
 # naming look like taking ISO-8601 duration designations, removing the P, and
 # lowercasing any characters. Fortnightly or sub-daily time types would need an
diff --git a/man/time_delta_to_n_steps.Rd b/man/time_delta_to_n_steps.Rd
index db8cdaaa..93715919 100644
--- a/man/time_delta_to_n_steps.Rd
+++ b/man/time_delta_to_n_steps.Rd
@@ -19,7 +19,7 @@ without sign and length restrictions.}
 \value{
 \link[rlang:is_integerish]{bare integerish} vector (with possible
 infinite values) that produces the same result as \code{time_delta} when
-multiplied by the "natural" "unit time delta" (not yet implemented) for
+multiplied by the natural \code{\link{unit_time_delta}} for
 that time type and added to time values of time type \code{time_type}. If the
 given time type does not support infinite values, then it should produce
 +Inf or -Inf for analogous entries of \code{time_delta}, and match the addition
diff --git a/man/unit_time_delta.Rd b/man/unit_time_delta.Rd
new file mode 100644
index 00000000..3b45840d
--- /dev/null
+++ b/man/unit_time_delta.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{unit_time_delta}
+\alias{unit_time_delta}
+\title{Object that, added to time_values of time_type, advances by one time step/interval}
+\usage{
+unit_time_delta(time_type)
+}
+\arguments{
+\item{time_type}{string; \code{epi_df}'s or \code{epi_archive}'s \code{time_type}}
+}
+\value{
+an object \code{u} such that \code{time_values + u} represents advancing by one
+time step / moving to the subsequent time interval for any \code{time_values}
+object of time type \code{time_type}, and such that \code{time_values + k * u} for
+integerish vector \code{k} advances by \code{k} steps (with vectorization,
+recycling).
+}
+\description{
+Object that, added to time_values of time_type, advances by one time step/interval
+}
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index c5e6c5aa..37125d53 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -362,3 +362,59 @@ test_that("validate_slide_window_arg works", {
     class = "epiprocess__validate_slide_window_arg"
   )
 })
+
+test_that("unit_time_delta works", {
+  expect_equal(
+    as.Date("2020-01-01") + 5 * unit_time_delta("day"),
+    as.Date("2020-01-06")
+  )
+  expect_equal(
+    as.Date("2020-01-01") + 2 * unit_time_delta("week"),
+    as.Date("2020-01-15")
+  )
+  expect_equal(
+    tsibble::make_yearmonth(2000, 1) + 5 * unit_time_delta("yearmonth"),
+    tsibble::make_yearmonth(2000, 6)
+  )
+  expect_equal(
+    1L + 5L * unit_time_delta("integer"),
+    6L
+  )
+  #
+  expect_equal(
+    as.Date("2020-01-01") +
+      time_delta_to_n_steps(as.Date("2020-01-06") - as.Date("2020-01-01"), "day") *
+        unit_time_delta("day"),
+    as.Date("2020-01-06")
+  )
+  expect_equal(
+    as.Date("2020-01-01") +
+      time_delta_to_n_steps(as.integer(as.Date("2020-01-06") - as.Date("2020-01-01")), "day") *
+        unit_time_delta("day"),
+    as.Date("2020-01-06")
+  )
+  expect_equal(
+    as.Date("2020-01-01") +
+      time_delta_to_n_steps(as.Date("2020-01-15") - as.Date("2020-01-01"), "week") *
+        unit_time_delta("week"),
+    as.Date("2020-01-15")
+  )
+  expect_equal(
+    as.Date("2020-01-01") +
+      time_delta_to_n_steps(as.difftime(2, units = "weeks"), "week") *
+        unit_time_delta("week"),
+    as.Date("2020-01-15")
+  )
+  expect_equal(
+    tsibble::make_yearmonth(2000, 1) +
+      time_delta_to_n_steps(5, "yearmonth") *
+        unit_time_delta("yearmonth"),
+    tsibble::make_yearmonth(2000, 6)
+  )
+  expect_equal(
+    1L +
+      time_delta_to_n_steps(5, "integer") *
+        unit_time_delta("integer"),
+    6L
+  )
+})

From 275290321aa648edfa2c3c8bb0c65144ea6eaea5 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 15 Nov 2024 10:17:56 -0800
Subject: [PATCH 22/39] Don't export unit_time_delta (yet)

We may later need it to make default args, in which case we should probably
export to be less "magical".
---
 NAMESPACE              | 1 -
 R/utils.R              | 2 +-
 man/unit_time_delta.Rd | 1 +
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 7b054fd6..e044739b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -98,7 +98,6 @@ export(slice)
 export(sum_groups_epi_df)
 export(time_column_names)
 export(ungroup)
-export(unit_time_delta)
 export(unnest)
 export(validate_epi_archive)
 export(version_column_names)
diff --git a/R/utils.R b/R/utils.R
index f3eb114d..55022677 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1166,7 +1166,7 @@ time_delta_to_n_steps <- function(time_delta, time_type) {
 #'   integerish vector `k` advances by `k` steps (with vectorization,
 #'   recycling).
 #'
-#' @export
+#' @keywords internal
 unit_time_delta <- function(time_type) {
   switch(time_type,
     day = as.difftime(1, units = "days"),
diff --git a/man/unit_time_delta.Rd b/man/unit_time_delta.Rd
index 3b45840d..46b3c48d 100644
--- a/man/unit_time_delta.Rd
+++ b/man/unit_time_delta.Rd
@@ -19,3 +19,4 @@ recycling).
 \description{
 Object that, added to time_values of time_type, advances by one time step/interval
 }
+\keyword{internal}

From ed9524ef8f73680db08af7e023eec165b487a5f1 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 10:30:42 -0800
Subject: [PATCH 23/39] Address CHECKS+workflow: don't document epidatasets
 re-exports

---
 R/reexports.R                          | 87 --------------------------
 man/archive_cases_dv_subset.Rd         | 84 -------------------------
 man/cases_deaths_subset.Rd             | 79 -----------------------
 man/covid_case_death_rates_extended.Rd | 74 ----------------------
 man/covid_incidence_county_subset.Rd   | 75 ----------------------
 man/covid_incidence_outliers.Rd        | 68 --------------------
 6 files changed, 467 deletions(-)
 delete mode 100644 man/archive_cases_dv_subset.Rd
 delete mode 100644 man/cases_deaths_subset.Rd
 delete mode 100644 man/covid_case_death_rates_extended.Rd
 delete mode 100644 man/covid_incidence_county_subset.Rd
 delete mode 100644 man/covid_incidence_outliers.Rd

diff --git a/R/reexports.R b/R/reexports.R
index e091ce12..72241175 100644
--- a/R/reexports.R
+++ b/R/reexports.R
@@ -79,104 +79,17 @@ ggplot2::autoplot
 
 # epidatasets -------------------------------------------------------------------
 
-#' @inherit epidatasets::cases_deaths_subset description source references title
-#' @inheritSection epidatasets::cases_deaths_subset Data dictionary
-#' @examples
-#' # Since this is a re-exported dataset, it cannot be loaded using
-#' # the `data()` function. `data()` looks for a file of the same name
-#' # in the `data/` directory, which doesn't exist in this package.
-#' # works
-#' epiprocess::cases_deaths_subset
-#'
-#' # works
-#' library(epiprocess)
-#' cases_deaths_subset
-#'
-#' # fails
-#' \dontrun{
-#' data(cases_deaths_subset, package = "epiprocess")
-#' }
 #' @export
 delayedAssign("cases_deaths_subset", epidatasets::cases_deaths_subset)
 
-#' @inherit epidatasets::covid_incidence_county_subset description source references title
-#' @inheritSection epidatasets::covid_incidence_county_subset Data dictionary
-#' @examples
-#' # Since this is a re-exported dataset, it cannot be loaded using
-#' # the `data()` function. `data()` looks for a file of the same name
-#' # in the `data/` directory, which doesn't exist in this package.
-#' # works
-#' epiprocess::covid_incidence_county_subset
-#'
-#' # works
-#' library(epiprocess)
-#' covid_incidence_county_subset
-#'
-#' # fails
-#' \dontrun{
-#' data(covid_incidence_county_subset, package = "epiprocess")
-#' }
 #' @export
 delayedAssign("covid_incidence_county_subset", epidatasets::covid_incidence_county_subset)
 
-#' @inherit epidatasets::covid_incidence_outliers description source references title
-#' @inheritSection epidatasets::covid_incidence_outliers Data dictionary
-#' @examples
-#' # Since this is a re-exported dataset, it cannot be loaded using
-#' # the `data()` function. `data()` looks for a file of the same name
-#' # in the `data/` directory, which doesn't exist in this package.
-#' # works
-#' epiprocess::covid_incidence_outliers
-#'
-#' # works
-#' library(epiprocess)
-#' covid_incidence_outliers
-#'
-#' # fails
-#' \dontrun{
-#' data(covid_incidence_outliers, package = "epiprocess")
-#' }
 #' @export
 delayedAssign("covid_incidence_outliers", epidatasets::covid_incidence_outliers)
 
-#' @inherit epidatasets::archive_cases_dv_subset description source references title
-#' @inheritSection epidatasets::archive_cases_dv_subset Data dictionary
-#' @examples
-#' # Since this is a re-exported dataset, it cannot be loaded using
-#' # the `data()` function. `data()` looks for a file of the same name
-#' # in the `data/` directory, which doesn't exist in this package.
-#' # works
-#' epiprocess::archive_cases_dv_subset
-#'
-#' # works
-#' library(epiprocess)
-#' archive_cases_dv_subset
-#'
-#' # fails
-#' \dontrun{
-#' data(archive_cases_dv_subset, package = "epiprocess")
-#' }
-#'
 #' @export
 delayedAssign("archive_cases_dv_subset", epidatasets::archive_cases_dv_subset)
 
-#' @inherit epidatasets::covid_case_death_rates_extended description source references title
-#' @inheritSection epidatasets::covid_case_death_rates_extended Data dictionary
-#' @examples
-#' # Since this is a re-exported dataset, it cannot be loaded using
-#' # the `data()` function. `data()` looks for a file of the same name
-#' # in the `data/` directory, which doesn't exist in this package.
-#' # works
-#' epiprocess::covid_case_death_rates_extended
-#'
-#' # works
-#' library(epiprocess)
-#' covid_case_death_rates_extended
-#'
-#' # fails
-#' \dontrun{
-#' data(covid_case_death_rates_extended, package = "epiprocess")
-#' }
-#'
 #' @export
 delayedAssign("covid_case_death_rates_extended", epidatasets::covid_case_death_rates_extended)
diff --git a/man/archive_cases_dv_subset.Rd b/man/archive_cases_dv_subset.Rd
deleted file mode 100644
index 207bb025..00000000
--- a/man/archive_cases_dv_subset.Rd
+++ /dev/null
@@ -1,84 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reexports.R
-\docType{data}
-\name{archive_cases_dv_subset}
-\alias{archive_cases_dv_subset}
-\title{Subset of daily COVID-19 doctor visits and cases from 6 states in archive format}
-\format{
-An object of class \code{epi_archive} of length 6.
-}
-\source{
-This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
-Copyright Johns Hopkins University 2020.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: \code{case_rate_7d_av} signal was computed by Delphi from the original JHU-CSSE data by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive.
-\item Furthermore, the data has been limited to a very small number of rows, the
-signal names slightly altered, and formatted into an \code{epi_archive}.
-}
-
-This object contains a modified part of the
-\href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html}{Delphi \code{doctor-visits} indicator}.
-This data source is computed by the Delphi
-Group from information about outpatient visits, provided to Delphi by
-health system partners, and published in the COVIDcast Epidata API. This
-data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by the Delphi group.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html}{From the COVIDcast Doctor Visits signal}: The signal \code{smoothed_adj_cli} is taken directly from the API without changes.
-\item Furthermore, the data has been limited to a very small number of rows, the
-signal names slightly altered, and formatted into an \code{epi_archive}.
-}
-}
-\usage{
-archive_cases_dv_subset
-}
-\description{
-This data source is based on information about outpatient visits, provided
-to us by health system partners, and also contains confirmed COVID-19
-cases based on reports made available by the Center for Systems Science
-and Engineering at Johns Hopkins University. This example data ranges from
-June 1, 2020 to December 1, 2021, issued on dates from June 1, 2020 to December 1,
-2021. It is limited to California, Florida, Texas, and New York.
-
-It is used in the {epiprocess} \code{compactify}, \code{epi_archive}, and
-advanced-use (\code{advanced}) vignettes.
-}
-\section{Data dictionary}{
-
-
-The data in the \code{epi_archive$DT} attribute has columns:
-\describe{
-\item{geo_value}{the geographic value associated with each row of measurements.}
-\item{time_value}{the time value associated with each row of measurements.}
-\item{version}{the time value specifying the version for each row of measurements. }
-\item{percent_cli}{percentage of doctor’s visits with CLI (COVID-like illness) computed from medical insurance claims}
-\item{case_rate_7d_av}{7-day average signal of number of new confirmed cases due to COVID-19 per 100,000 population, daily}
-}
-
-}
-
-\examples{
-# Since this is a re-exported dataset, it cannot be loaded using
-# the `data()` function. `data()` looks for a file of the same name
-# in the `data/` directory, which doesn't exist in this package.
-# works
-epiprocess::archive_cases_dv_subset
-
-# works
-library(epiprocess)
-archive_cases_dv_subset
-
-# fails
-\dontrun{
-data(archive_cases_dv_subset, package = "epiprocess")
-}
-
-}
-\keyword{datasets}
diff --git a/man/cases_deaths_subset.Rd b/man/cases_deaths_subset.Rd
deleted file mode 100644
index 45e8dd4c..00000000
--- a/man/cases_deaths_subset.Rd
+++ /dev/null
@@ -1,79 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reexports.R
-\docType{data}
-\name{cases_deaths_subset}
-\alias{cases_deaths_subset}
-\title{Subset of JHU daily state COVID-19 cases and deaths from 6 states}
-\format{
-An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 4026 rows and 6 columns.
-}
-\source{
-This object contains a modified part of the
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University}
-as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
-This data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by the Johns Hopkins University on behalf of its Center for Systems Science
-in Engineering. Copyright Johns Hopkins University 2020.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
-The case signal is taken directly from the JHU CSSE
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository}.
-The rate signals were computed by Delphi using Census population data.
-The 7-day average signals were computed by Delphi by calculating moving
-averages of the preceding 7 days, so the signal for June 7 is the
-average of the underlying data for June 1 through 7, inclusive.
-\item Furthermore, the data has been limited to a very small number of rows, the
-signal names slightly altered, and formatted into an \code{epi_df}.
-}
-}
-\usage{
-cases_deaths_subset
-}
-\description{
-This data source of confirmed COVID-19 cases and deaths is based on reports
-made available by the Center for Systems Science and Engineering at Johns
-Hopkins University. This example data is a snapshot as of March 20, 2024, and
-ranges from March 1, 2020 to December 31, 2021. It is limited to California,
-Florida, Texas, New York, Georgia, and Pennsylvania.
-
-It is used in the {epiprocess} growth rate and \code{epi_slide} vignettes.
-}
-\section{Data dictionary}{
-
-
-The data has columns:
-\describe{
-\item{geo_value}{the geographic value associated with each row
-of measurements.}
-\item{time_value}{the time value associated with each row of measurements.}
-\item{case_rate_7d_av}{7-day average signal of number of new
-confirmed COVID-19 cases per 100,000 population, daily}
-\item{death_rate_7d_av}{7-day average signal of number of new confirmed
-deaths due to COVID-19 per 100,000 population, daily}
-\item{cases}{Number of new confirmed COVID-19 cases, daily}
-\item{cases_7d_av}{7-day average signal of number of new confirmed
-COVID-19 cases, daily}
-}
-
-}
-
-\examples{
-# Since this is a re-exported dataset, it cannot be loaded using
-# the `data()` function. `data()` looks for a file of the same name
-# in the `data/` directory, which doesn't exist in this package.
-# works
-epiprocess::cases_deaths_subset
-
-# works
-library(epiprocess)
-cases_deaths_subset
-
-# fails
-\dontrun{
-data(cases_deaths_subset, package = "epiprocess")
-}
-}
-\keyword{datasets}
diff --git a/man/covid_case_death_rates_extended.Rd b/man/covid_case_death_rates_extended.Rd
deleted file mode 100644
index 72482edd..00000000
--- a/man/covid_case_death_rates_extended.Rd
+++ /dev/null
@@ -1,74 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reexports.R
-\docType{data}
-\name{covid_case_death_rates_extended}
-\alias{covid_case_death_rates_extended}
-\title{JHU daily COVID-19 cases and deaths rates from all states}
-\format{
-An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 37576 rows and 4 columns.
-}
-\source{
-This object contains a modified part of the
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University}
-as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
-This data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by the Johns Hopkins University on behalf of its Center for Systems Science
-in Engineering. Copyright Johns Hopkins University 2020.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
-These signals are taken directly from the JHU CSSE
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository}
-without changes. The 7-day average signals are computed by Delphi by
-calculating moving averages of the preceding 7 days, so the signal for
-June 7 is the average of the underlying data for June 1 through 7,
-inclusive.
-}
-}
-\usage{
-covid_case_death_rates_extended
-}
-\description{
-This data source of confirmed COVID-19 cases and deaths is based on reports
-made available by the Center for Systems Science and Engineering at Johns
-Hopkins University, as downloaded from the CMU Delphi COVIDcast Epidata
-API. This example data is a snapshot as of May 31, 2022, and
-ranges from March 1, 2020 to December 31, 2021. It
-includes all states.
-}
-\section{Data dictionary}{
-
-
-The data has columns:
-\describe{
-\item{geo_value}{the geographic value associated with each row
-of measurements.}
-\item{time_value}{the time value associated with each row of measurements.}
-\item{case_rate}{7-day average signal of number of new
-confirmed COVID-19 cases per 100,000 population, daily}
-\item{death_rate}{7-day average signal of number of new confirmed
-deaths due to COVID-19 per 100,000 population, daily}
-}
-
-}
-
-\examples{
-# Since this is a re-exported dataset, it cannot be loaded using
-# the `data()` function. `data()` looks for a file of the same name
-# in the `data/` directory, which doesn't exist in this package.
-# works
-epiprocess::covid_case_death_rates_extended
-
-# works
-library(epiprocess)
-covid_case_death_rates_extended
-
-# fails
-\dontrun{
-data(covid_case_death_rates_extended, package = "epiprocess")
-}
-
-}
-\keyword{datasets}
diff --git a/man/covid_incidence_county_subset.Rd b/man/covid_incidence_county_subset.Rd
deleted file mode 100644
index edc881d9..00000000
--- a/man/covid_incidence_county_subset.Rd
+++ /dev/null
@@ -1,75 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reexports.R
-\docType{data}
-\name{covid_incidence_county_subset}
-\alias{covid_incidence_county_subset}
-\title{Subset of JHU daily COVID-19 cases from counties in Massachusetts and Vermont}
-\format{
-An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 16212 rows and 5 columns.
-}
-\source{
-This object contains a modified part of the
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as
-\href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
-This data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by the Johns Hopkins University on behalf of its Center for Systems
-Science in Engineering. Copyright Johns Hopkins University 2020.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
-These signals are taken directly from the JHU CSSE
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository}
-without changes. The 7-day average signals are computed by Delphi by
-as moving averages of the preceding 7 days, so the signal for
-June 7 is the average of the underlying data for June 1 through 7,
-inclusive.
-\item Furthermore, the data has been limited to a very small number of rows,
-formatted into an \code{epi_df}, and the signal names slightly altered.
-}
-}
-\usage{
-covid_incidence_county_subset
-}
-\description{
-This data source of confirmed COVID-19 cases and deaths
-is based on reports made available by the Center for
-Systems Science and Engineering at Johns Hopkins University.
-This example data is a snapshot as of March 20, 2024, and
-ranges from March 1, 2020 to December 31, 2021.
-It is limited to counties from Massachusetts and Vermont.
-
-It is used in the {epiprocess} aggregation vignette.
-}
-\section{Data dictionary}{
-
-
-The data has columns:
-\describe{
-\item{geo_value}{the geographic value associated with each row of measurements.}
-\item{time_value}{the time value associated with each row of measurements.}
-\item{cases}{Number of new confirmed COVID-19 cases, daily}
-\item{county_name}{the name of the county}
-\item{state_name}{the full name of the state}
-}
-
-}
-
-\examples{
-# Since this is a re-exported dataset, it cannot be loaded using
-# the `data()` function. `data()` looks for a file of the same name
-# in the `data/` directory, which doesn't exist in this package.
-# works
-epiprocess::covid_incidence_county_subset
-
-# works
-library(epiprocess)
-covid_incidence_county_subset
-
-# fails
-\dontrun{
-data(covid_incidence_county_subset, package = "epiprocess")
-}
-}
-\keyword{datasets}
diff --git a/man/covid_incidence_outliers.Rd b/man/covid_incidence_outliers.Rd
deleted file mode 100644
index 52b49fd3..00000000
--- a/man/covid_incidence_outliers.Rd
+++ /dev/null
@@ -1,68 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reexports.R
-\docType{data}
-\name{covid_incidence_outliers}
-\alias{covid_incidence_outliers}
-\title{Subset of JHU daily COVID-19 cases from New Jersey and Florida}
-\format{
-An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 730 rows and 3 columns.
-}
-\source{
-This object contains a modified part of the
-\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University}
-as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
-This data set is licensed under the terms of the
-\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
-by the Johns Hopkins University on behalf of its Center for Systems
-Science in Engineering. Copyright Johns Hopkins University 2020.
-
-Modifications:
-\itemize{
-\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
-These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes.
-\item Furthermore, the data has been limited to a very small number of rows,
-formatted into an \code{epi_df}, and the signal names slightly altered.
-}
-}
-\usage{
-covid_incidence_outliers
-}
-\description{
-This data source of confirmed COVID-19 cases is based on reports made
-available by the Center for Systems Science and Engineering at Johns
-Hopkins University. This example data is downloaded from the CMU Delphi
-COVIDcast Epidata API. It is a snapshot as of October 28, 2021, and captures the
-cases from June 1, 2020 to May 31, 2021. It is limited to New Jersey and
-Florida.
-
-This data set is used in the {epiprocess} vignette on outliers.
-}
-\section{Data dictionary}{
-
-
-The data has columns:
-\describe{
-\item{geo_value}{the geographic value associated with each row of measurements.}
-\item{time_value}{the time value associated with each row of measurements.}
-\item{cases}{Number of new confirmed COVID-19 cases, daily}
-}
-
-}
-
-\examples{
-# Since this is a re-exported dataset, it cannot be loaded using
-# the `data()` function. `data()` looks for a file of the same name
-# in the `data/` directory, which doesn't exist in this package.
-# works
-epiprocess::covid_incidence_outliers
-
-# works
-library(epiprocess)
-covid_incidence_outliers
-
-# fails
-\dontrun{
-data(covid_incidence_outliers, package = "epiprocess")
-}
-}
-\keyword{datasets}

From 5cc0d159d0a20dc0ff2f0388c426625354253713 Mon Sep 17 00:00:00 2001
From: brookslogan <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 11:02:25 -0800
Subject: [PATCH 24/39] Fix error class name that referred to different
 function

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>
---
 R/slide.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/slide.R b/R/slide.R
index f212473e..e8e66966 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -702,7 +702,7 @@ epi_slide_opt <- function(
         "`.x` must be either grouped by {expected_group_keys} or ungrouped; if the latter,
          we'll temporarily group by {expected_group_keys} for this operation. You may need
         to aggregate your data first, see aggregate_epi_df().",
-        class = "epiprocess__epi_slide__invalid_grouping"
+        class = "epiprocess__epi_slide_opt__invalid_grouping"
       )
     }
   } else {

From 9d64bdabea1f563aef19b0117d1648be957653cc Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 10:50:22 -0800
Subject: [PATCH 25/39] Fix partial rename: aggregate_epi_df ->
 sum_groups_epi_df in messages

---
 R/slide.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index e8e66966..d56623cc 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -195,7 +195,7 @@ epi_slide <- function(
       cli_abort(
         "`.x` must be either grouped by {expected_group_keys} or ungrouped; if the latter,
          we'll temporarily group by {expected_group_keys} for this operation. You may need
-        to aggregate your data first, see aggregate_epi_df().",
+        to aggregate your data first; see sum_groups_epi_df().",
         class = "epiprocess__epi_slide__invalid_grouping"
       )
     }
@@ -701,7 +701,7 @@ epi_slide_opt <- function(
       cli_abort(
         "`.x` must be either grouped by {expected_group_keys} or ungrouped; if the latter,
          we'll temporarily group by {expected_group_keys} for this operation. You may need
-        to aggregate your data first, see aggregate_epi_df().",
+        to aggregate your data first; see sum_groups_epi_df().",
         class = "epiprocess__epi_slide_opt__invalid_grouping"
       )
     }

From 5c68195843b608e4a27025ca7b5dc3eaccdb1d69 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 12:01:17 -0800
Subject: [PATCH 26/39] Describe output grouping in basic-slide-params.R

---
 man-roxygen/basic-slide-params.R | 3 ++-
 man/epi_slide.Rd                 | 3 ++-
 man/epi_slide_opt.Rd             | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/man-roxygen/basic-slide-params.R b/man-roxygen/basic-slide-params.R
index 8ccd35f9..0e5f28ae 100644
--- a/man-roxygen/basic-slide-params.R
+++ b/man-roxygen/basic-slide-params.R
@@ -32,4 +32,5 @@
 #'   a missing value marker (typically NA, but more technically the result of
 #'   `vctrs::vec_cast`-ing `NA` to the type of the slide computation output).
 #' @return An `epi_df` object with one or more new slide computation columns
-#'   added.
+#'   added. It will be ungrouped if `.x` was ungrouped, and have the same groups
+#'   as `.x` if `.x` was grouped.
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index 9f4abd36..ce94c67b 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -91,7 +91,8 @@ a missing value marker (typically NA, but more technically the result of
 }
 \value{
 An \code{epi_df} object with one or more new slide computation columns
-added.
+added. It will be ungrouped if \code{.x} was ungrouped, and have the same groups
+as \code{.x} if \code{.x} was grouped.
 }
 \description{
 Slides a given function over variables in an \code{epi_df} object.
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index 724a928e..da65cb00 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -130,7 +130,8 @@ a missing value marker (typically NA, but more technically the result of
 }
 \value{
 An \code{epi_df} object with one or more new slide computation columns
-added.
+added. It will be ungrouped if \code{.x} was ungrouped, and have the same groups
+as \code{.x} if \code{.x} was grouped.
 }
 \description{
 \code{epi_slide_opt} allows sliding an n-timestep \link[data.table:froll]{data.table::froll}

From d3695270d7105b69c48b3b4e820c57911637b0ff Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 12:06:27 -0800
Subject: [PATCH 27/39] docs: roughly describe grouping of epix_slide output

---
 R/methods-epi_archive.R | 8 ++++----
 man/epix_slide.Rd       | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/methods-epi_archive.R b/R/methods-epi_archive.R
index 04bb841f..9ad45673 100644
--- a/R/methods-epi_archive.R
+++ b/R/methods-epi_archive.R
@@ -688,10 +688,10 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'   requested `.versions`) for rows having a `time_value` of at least `.version
 #'   - before`. Otherwise, the slide computation will be passed only the most
 #'   recent `version` for every unique `time_value`. Default is `FALSE`.
-#' @return A tibble whose columns are: the grouping variables, `time_value`,
-#'   containing the reference time values for the slide computation, and a
-#'   column named according to the `.new_col_name` argument, containing the slide
-#'   values.
+#' @return A tibble whose columns are: the grouping variables (if any),
+#'   `time_value`, containing the reference time values for the slide
+#'   computation, and a column named according to the `.new_col_name` argument,
+#'   containing the slide values. It will be grouped by the grouping variables.
 #'
 #' @details A few key distinctions between the current function and `epi_slide()`:
 #'   1. In `.f` functions for `epix_slide`, one should not assume that the input
diff --git a/man/epix_slide.Rd b/man/epix_slide.Rd
index 6fe2cfa5..cadb1983 100644
--- a/man/epix_slide.Rd
+++ b/man/epix_slide.Rd
@@ -104,10 +104,10 @@ requested \code{.versions}) for rows having a \code{time_value} of at least `.ve
 }}
 }
 \value{
-A tibble whose columns are: the grouping variables, \code{time_value},
-containing the reference time values for the slide computation, and a
-column named according to the \code{.new_col_name} argument, containing the slide
-values.
+A tibble whose columns are: the grouping variables (if any),
+\code{time_value}, containing the reference time values for the slide
+computation, and a column named according to the \code{.new_col_name} argument,
+containing the slide values. It will be grouped by the grouping variables.
 }
 \description{
 Slides a given function over variables in an \code{epi_archive} object. This

From 6191b61d5e06bc1609aa5efbdb1c00828ca30c8c Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 16:02:56 -0800
Subject: [PATCH 28/39] Rework `epi_slide_{opt,mean,sum}` examples as they are
 1 help topic

---
 R/slide.R            | 104 +++++++++++++++++--------------------------
 man/epi_slide_opt.Rd |  82 +++++++++++++---------------------
 2 files changed, 72 insertions(+), 114 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index d56623cc..cf19075c 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -632,22 +632,53 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #' @export
 #' @seealso [`epi_slide`] for the more general slide function
 #' @examples
-#' # Compute a 7-day trailing average on cases.
+#' # Add a column (`cases_7dsum`) containing a 7-day trailing sum on `cases`:
 #' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
+#'   epi_slide_sum(cases, .window_size = 7)
+#'
+#' # Add a column (`cases_rate_7dav`) containing a 7-day trailing average on `case_rate`:
+#' covid_case_death_rates_extended %>%
+#'   epi_slide_mean(case_rate, .window_size = 7)
+#'
+#' # Use a less common specialized slide function:
+#' cases_deaths_subset %>%
+#'   epi_slide_opt(cases, slider::slide_min, .window_size = 7)
+#'
+#' # Specify output column names and/or a naming scheme:
+#' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) %>%
+#'   epi_slide_sum(cases, .window_size = 7, .new_col_names = "case_sum") %>%
 #'   ungroup()
-#'
-#' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
-#' # to allow partially-missing windows.
 #' cases_deaths_subset %>%
+#'   select(geo_value, time_value, cases) %>%
 #'   group_by(geo_value) %>%
-#'   epi_slide_opt(
-#'     cases,
-#'     .f = data.table::frollmean, .window_size = 7,
-#'     algo = "exact", hasNA = TRUE, na.rm = TRUE
-#'   ) %>%
+#'   epi_slide_sum(cases, .window_size = 7, .prefix = "sum_") %>%
 #'   ungroup()
+#'
+#' # Additional settings can be sent to the {data.table} and {slider} functions
+#' # via `...`. This example passes some arguments to `frollmean` settings for
+#' # speed, accuracy, and to allow partially-missing windows:
+#' covid_case_death_rates_extended %>%
+#'   epi_slide_mean(
+#'     case_rate,
+#'     .window_size = 7,
+#'     na.rm = TRUE, algo = "exact", hasNA = TRUE
+#'   )
+#'
+#' # If the more specialized possibilities for `.f` don't cover your needs, you
+#' # can use `epi_slide_opt` with `.f = data.table::frollapply` to apply a
+#' # custom function at the cost of more computation time. See also `epi_slide`
+#' # if you need something even more general.
+#' cases_deaths_subset %>%
+#'   select(geo_value, time_value, case_rate_7d_av, death_rate_7d_av) %>%
+#'   epi_slide_opt(c(case_rate_7d_av, death_rate_7d_av),
+#'     data.table::frollapply,
+#'     FUN = median, .window_size = 28,
+#'     .suffix = "_{.n}{.time_unit_abbr}_median"
+#'   ) %>%
+#'   print(n = 40)
 epi_slide_opt <- function(
     .x, .col_names, .f, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
@@ -951,40 +982,6 @@ epi_slide_opt <- function(
 #' datatable::frollmean`.
 #'
 #' @export
-#' @examples
-#' # Compute a 7-day trailing average of case rates.
-#' covid_case_death_rates_extended %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_mean(case_rate, .window_size = 7) %>%
-#'   ungroup()
-#'
-#' # Same as above, but adjust `frollmean` settings for speed, accuracy, and
-#' # to allow partially-missing windows.
-#' covid_case_death_rates_extended %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_mean(
-#'     case_rate,
-#'     .window_size = 7,
-#'     na.rm = TRUE, algo = "exact", hasNA = TRUE
-#'   ) %>%
-#'   ungroup()
-#'
-#' # Compute a 7-day trailing average of case rates and death rates, with custom
-#' # output column names:
-#' covid_case_death_rates_extended %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_mean(c(case_rate, death_rate),
-#'     .window_size = 7,
-#'     .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
-#'   ) %>%
-#'   ungroup()
-#' covid_case_death_rates_extended %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_mean(c(case_rate, death_rate),
-#'     .window_size = 7,
-#'     .suffix = "_{.n}{.time_unit_abbr}_avg"
-#'   ) %>%
-#'   ungroup()
 epi_slide_mean <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
@@ -1044,25 +1041,6 @@ epi_slide_mean <- function(
 #' datatable::frollsum`.
 #'
 #' @export
-#' @examples
-#' # Compute a 7-day trailing sum on cases.
-#' cases_deaths_subset %>%
-#'   select(geo_value, time_value, cases) %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_sum(cases, .window_size = 7) %>%
-#'   ungroup()
-#'
-#' # Specify output column names and/or naming scheme:
-#' cases_deaths_subset %>%
-#'   select(geo_value, time_value, cases) %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_sum(cases, .window_size = 7, .new_col_names = "case_sum") %>%
-#'   ungroup()
-#' cases_deaths_subset %>%
-#'   select(geo_value, time_value, cases) %>%
-#'   group_by(geo_value) %>%
-#'   epi_slide_sum(cases, .window_size = 7, .prefix = "sum_") %>%
-#'   ungroup()
 epi_slide_sum <- function(
     .x, .col_names, ...,
     .window_size = NULL, .align = c("right", "center", "left"),
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index da65cb00..7dc47a16 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -162,63 +162,20 @@ for \code{.f} factoring in the input column type(s) for \code{.col_names}
 }
 
 \examples{
-# Compute a 7-day trailing average on cases.
+# Add a column (`cases_7dsum`) containing a 7-day trailing sum on `cases`:
 cases_deaths_subset \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_opt(cases, .f = data.table::frollmean, .window_size = 7) \%>\%
-  ungroup()
-
-# Same as above, but adjust `frollmean` settings for speed, accuracy, and
-# to allow partially-missing windows.
-cases_deaths_subset \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_opt(
-    cases,
-    .f = data.table::frollmean, .window_size = 7,
-    algo = "exact", hasNA = TRUE, na.rm = TRUE
-  ) \%>\%
-  ungroup()
-# Compute a 7-day trailing average of case rates.
-covid_case_death_rates_extended \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_mean(case_rate, .window_size = 7) \%>\%
-  ungroup()
+  select(geo_value, time_value, cases) \%>\%
+  epi_slide_sum(cases, .window_size = 7)
 
-# Same as above, but adjust `frollmean` settings for speed, accuracy, and
-# to allow partially-missing windows.
+# Add a column (`cases_rate_7dav`) containing a 7-day trailing average on `case_rate`:
 covid_case_death_rates_extended \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_mean(
-    case_rate,
-    .window_size = 7,
-    na.rm = TRUE, algo = "exact", hasNA = TRUE
-  ) \%>\%
-  ungroup()
+  epi_slide_mean(case_rate, .window_size = 7)
 
-# Compute a 7-day trailing average of case rates and death rates, with custom
-# output column names:
-covid_case_death_rates_extended \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_mean(c(case_rate, death_rate),
-    .window_size = 7,
-    .new_col_names = c("smoothed_case_rate", "smoothed_death_rate")
-  ) \%>\%
-  ungroup()
-covid_case_death_rates_extended \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_mean(c(case_rate, death_rate),
-    .window_size = 7,
-    .suffix = "_{.n}{.time_unit_abbr}_avg"
-  ) \%>\%
-  ungroup()
-# Compute a 7-day trailing sum on cases.
+# Use a less common specialized slide function:
 cases_deaths_subset \%>\%
-  select(geo_value, time_value, cases) \%>\%
-  group_by(geo_value) \%>\%
-  epi_slide_sum(cases, .window_size = 7) \%>\%
-  ungroup()
+  epi_slide_opt(cases, slider::slide_min, .window_size = 7)
 
-# Specify output column names and/or naming scheme:
+# Specify output column names and/or a naming scheme:
 cases_deaths_subset \%>\%
   select(geo_value, time_value, cases) \%>\%
   group_by(geo_value) \%>\%
@@ -229,6 +186,29 @@ cases_deaths_subset \%>\%
   group_by(geo_value) \%>\%
   epi_slide_sum(cases, .window_size = 7, .prefix = "sum_") \%>\%
   ungroup()
+
+# Additional settings can be sent to the {data.table} and {slider} functions
+# via `...`. This example passes some arguments to `frollmean` settings for
+# speed, accuracy, and to allow partially-missing windows:
+covid_case_death_rates_extended \%>\%
+  epi_slide_mean(
+    case_rate,
+    .window_size = 7,
+    na.rm = TRUE, algo = "exact", hasNA = TRUE
+  )
+
+# If the more specialized possibilities for `.f` don't cover your needs, you
+# can use `epi_slide_opt` with `.f = data.table::frollapply` to apply a
+# custom function at the cost of more computation time. See also `epi_slide`
+# if you need something even more general.
+cases_deaths_subset \%>\%
+  select(geo_value, time_value, case_rate_7d_av, death_rate_7d_av) \%>\%
+  epi_slide_opt(c(case_rate_7d_av, death_rate_7d_av),
+    data.table::frollapply,
+    FUN = median, .window_size = 28,
+    .suffix = "_{.n}{.time_unit_abbr}_median"
+  ) \%>\%
+  print(n = 40)
 }
 \seealso{
 \code{\link{epi_slide}} for the more general slide function

From 6ab73d541fe5c2368d109ad0ca3fbb17664c7287 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 16:11:35 -0800
Subject: [PATCH 29/39] feat(epi_slide_opt): guard against multiple .f matches

---
 R/slide.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/slide.R b/R/slide.R
index cf19075c..3da3c473 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -797,6 +797,12 @@ epi_slide_opt <- function(
       epiprocess__f = .f
     )
   }
+  if (nrow(f_info) > 1L) {
+    cli_abort('epiprocess internal error: looking up `.f` in table of possible
+               functions yielded multiple matches. Please report it using "New
+               issue" at https://github.com/cmu-delphi/epiprocess/issues, using
+               reprex::reprex to provide a minimal reproducible example.')
+  }
   f_from_package <- f_info$package
 
   user_provided_rtvs <- !is.null(.ref_time_values)

From c78bcca16d59c9d88efada6a561d43d18fdabc3e Mon Sep 17 00:00:00 2001
From: brookslogan <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 22 Nov 2024 16:15:39 -0800
Subject: [PATCH 30/39] Improve slide output packing example comments

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>
---
 R/slide.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index 3da3c473..0c747d17 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -106,8 +106,8 @@
 #'
 #' # The tidyverse supports ["packing"][tidyr::pack] multiple columns into a
 #' # single tibble-type column contained within some larger tibble. Like dplyr,
-#' # we normally don't pack output columns together, but will if you provide a
-#' # name for a tibble-type output:
+#' # we normally don't pack output columns together. However, packing behavior can be turned on
+#' # by providing a name for a tibble-type output:
 #' cases_deaths_subset %>%
 #'   epi_slide(
 #'     slide_packed = tibble(

From 53505d3f842328e944739857982a5efa4ca1e05a Mon Sep 17 00:00:00 2001
From: brookslogan <brookslogan@users.noreply.github.com>
Date: Sat, 23 Nov 2024 00:18:20 +0000
Subject: [PATCH 31/39] docs: document (GHA)

---
 man/epi_slide.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index ce94c67b..f053909d 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -165,8 +165,8 @@ cases_deaths_subset \%>\%
 
 # The tidyverse supports ["packing"][tidyr::pack] multiple columns into a
 # single tibble-type column contained within some larger tibble. Like dplyr,
-# we normally don't pack output columns together, but will if you provide a
-# name for a tibble-type output:
+# we normally don't pack output columns together. However, packing behavior can be turned on
+# by providing a name for a tibble-type output:
 cases_deaths_subset \%>\%
   epi_slide(
     slide_packed = tibble(

From 0352d7b31e99045ce63f5cabadb1e836a5fefcc0 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Tue, 26 Nov 2024 03:47:21 -0800
Subject: [PATCH 32/39] Make `as_epi_df` remove grouping

---
 NAMESPACE                    |  1 +
 R/epi_df.R                   | 17 +++++++++++++++--
 man/epi_df.Rd                | 24 ++++++++++++++++++------
 tests/testthat/test-epi_df.R | 16 ++++++++++++++++
 4 files changed, 50 insertions(+), 8 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e044739b..e214d8f3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ S3method(arrange_row_canonical,default)
 S3method(arrange_row_canonical,epi_df)
 S3method(as_epi_df,data.frame)
 S3method(as_epi_df,epi_df)
+S3method(as_epi_df,grouped_df)
 S3method(as_epi_df,tbl_df)
 S3method(as_epi_df,tbl_ts)
 S3method(as_tibble,epi_df)
diff --git a/R/epi_df.R b/R/epi_df.R
index 5cf379e2..83cca073 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -174,7 +174,7 @@ NULL
 #' @param other_keys If your tibble has additional keys, be sure to specify them
 #'   as a character vector here (typical examples are "age" or sub-geographies).
 #' @param ... Additional arguments passed to methods.
-#' @return An `epi_df` object.
+#' @return * Of `new_epi_df()`: an `epi_df`
 #'
 #' @export
 new_epi_df <- function(x = tibble::tibble(geo_value = character(), time_value = as.Date(integer())),
@@ -205,6 +205,8 @@ new_epi_df <- function(x = tibble::tibble(geo_value = character(), time_value =
 #'   to be converted
 #' @param ... used for specifying column names, as in [`dplyr::rename`]. For
 #'   example, `geo_value = STATEFP, time_value = end_date`.
+#' @return * Of `as_epi_df()`: an (ungrouped) `epi_df`
+#'
 #' @export
 as_epi_df <- function(x, ...) {
   UseMethod("as_epi_df")
@@ -215,6 +217,7 @@ as_epi_df <- function(x, ...) {
 #' @method as_epi_df epi_df
 #' @export
 as_epi_df.epi_df <- function(x, ...) {
+  x <- ungroup(x)
   return(x)
 }
 
@@ -296,6 +299,14 @@ as_epi_df.tbl_df <- function(
   new_epi_df(x, geo_type, time_type, as_of, other_keys)
 }
 
+#' @rdname epi_df
+#' @order 1
+#' @method as_epi_df grouped_df
+#' @export
+as_epi_df.grouped_df <- function(x, ...) {
+  as_epi_df(ungroup(x), ...)
+}
+
 #' @rdname epi_df
 #' @order 1
 #' @method as_epi_df data.frame
@@ -319,9 +330,11 @@ as_epi_df.tbl_ts <- function(x, as_of, other_keys = character(), ...) {
 #' Test for `epi_df` format
 #'
 #' @param x An object.
-#' @return `TRUE` if the object inherits from `epi_df`.
+#' @return * Of `is_epi_df`: `TRUE` if the object inherits from `epi_df`,
+#'           otherwise `FALSE`.
 #'
 #' @rdname epi_df
+#' @order 1
 #' @export
 is_epi_df <- function(x) {
   inherits(x, "epi_df")
diff --git a/man/epi_df.Rd b/man/epi_df.Rd
index 4c592ab7..a6782718 100644
--- a/man/epi_df.Rd
+++ b/man/epi_df.Rd
@@ -4,12 +4,13 @@
 \alias{as_epi_df}
 \alias{as_epi_df.epi_df}
 \alias{as_epi_df.tbl_df}
+\alias{as_epi_df.grouped_df}
 \alias{as_epi_df.data.frame}
 \alias{as_epi_df.tbl_ts}
+\alias{is_epi_df}
 \alias{new_epi_df}
 \alias{epi_df}
-\alias{is_epi_df}
-\title{\code{epi_df} object}
+\title{Test for \code{epi_df} format}
 \usage{
 as_epi_df(x, ...)
 
@@ -24,10 +25,14 @@ as_epi_df(x, ...)
   ...
 )
 
+\method{as_epi_df}{grouped_df}(x, ...)
+
 \method{as_epi_df}{data.frame}(x, as_of, other_keys = character(), ...)
 
 \method{as_epi_df}{tbl_ts}(x, as_of, other_keys = character(), ...)
 
+is_epi_df(x)
+
 new_epi_df(
   x = tibble::tibble(geo_value = character(), time_value = as.Date(integer())),
   geo_type,
@@ -36,8 +41,6 @@ new_epi_df(
   other_keys = character(),
   ...
 )
-
-is_epi_df(x)
 }
 \arguments{
 \item{x}{An object.}
@@ -65,9 +68,18 @@ then the current day-time will be used.}
 as a character vector here (typical examples are "age" or sub-geographies).}
 }
 \value{
-An \code{epi_df} object.
+\itemize{
+\item Of \code{as_epi_df()}: an (ungrouped) \code{epi_df}
+}
 
-\code{TRUE} if the object inherits from \code{epi_df}.
+\itemize{
+\item Of \code{is_epi_df}: \code{TRUE} if the object inherits from \code{epi_df},
+otherwise \code{FALSE}.
+}
+
+\itemize{
+\item Of \code{new_epi_df()}: an \code{epi_df}
+}
 }
 \description{
 One of the two main data structures for storing time series in \code{epiprocess}.
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 297d68df..44bb62e2 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -75,6 +75,22 @@ test_that("as_epi_df works for nonstandard input", {
   )
 })
 
+test_that("as_epi_df ungroups", {
+  expect_false(
+    tibble::tibble(geo_value = 1, time_value = 1) %>%
+      dplyr::group_by(geo_value) %>%
+      as_epi_df(as_of = 2) %>%
+      dplyr::is_grouped_df()
+  )
+  expect_false(
+    tibble::tibble(geo_value = 1, time_value = 1) %>%
+      as_epi_df(as_of = 2) %>%
+      dplyr::group_by(geo_value) %>%
+      as_epi_df(as_of = 2) %>%
+      dplyr::is_grouped_df()
+  )
+})
+
 # select fixes
 tib <- tibble::tibble(
   x = 1:10, y = 1:10,

From 081bd22f69c5924c9c173050a5e6a9a71cd886da Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Tue, 26 Nov 2024 04:54:03 -0800
Subject: [PATCH 33/39] Bring back slide unique-key checks, make as_epi_df ukey
 checks faster

---
 DESCRIPTION                     |  2 +-
 NAMESPACE                       |  5 +++
 NEWS.md                         |  2 ++
 R/epi_df.R                      | 20 ++++++------
 R/epiprocess-package.R          |  6 ++++
 R/slide.R                       | 16 +++-------
 R/utils.R                       | 54 +++++++++++++++++++++++++++++++++
 man/check_ukey_unique.Rd        | 27 +++++++++++++++++
 man/unwrap.Rd                   | 18 +++++++++++
 tests/testthat/_snaps/epi_df.md | 15 +++++++++
 tests/testthat/test-epi_df.R    | 14 +++++++++
 11 files changed, 155 insertions(+), 24 deletions(-)
 create mode 100644 man/check_ukey_unique.Rd
 create mode 100644 man/unwrap.Rd
 create mode 100644 tests/testthat/_snaps/epi_df.md

diff --git a/DESCRIPTION b/DESCRIPTION
index fd09aa57..c3f67c08 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: epiprocess
 Type: Package
 Title: Tools for basic signal processing in epidemiology
-Version: 0.9.6
+Version: 0.9.7
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = c("aut", "cre")),
diff --git a/NAMESPACE b/NAMESPACE
index e214d8f3..1f5180fb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -109,6 +109,7 @@ importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_class)
 importFrom(checkmate,assert_data_frame)
+importFrom(checkmate,assert_false)
 importFrom(checkmate,assert_function)
 importFrom(checkmate,assert_int)
 importFrom(checkmate,assert_list)
@@ -116,6 +117,8 @@ importFrom(checkmate,assert_logical)
 importFrom(checkmate,assert_numeric)
 importFrom(checkmate,assert_scalar)
 importFrom(checkmate,assert_string)
+importFrom(checkmate,assert_subset)
+importFrom(checkmate,assert_tibble)
 importFrom(checkmate,checkInt)
 importFrom(checkmate,check_atomic)
 importFrom(checkmate,check_data_frame)
@@ -165,6 +168,7 @@ importFrom(dplyr,groups)
 importFrom(dplyr,if_all)
 importFrom(dplyr,if_any)
 importFrom(dplyr,if_else)
+importFrom(dplyr,is_grouped_df)
 importFrom(dplyr,lag)
 importFrom(dplyr,mutate)
 importFrom(dplyr,near)
@@ -236,3 +240,4 @@ importFrom(tsibble,as_tsibble)
 importFrom(utils,capture.output)
 importFrom(utils,tail)
 importFrom(vctrs,vec_data)
+importFrom(vctrs,vec_equal)
diff --git a/NEWS.md b/NEWS.md
index 436b0c7d..ba6826da 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -18,6 +18,7 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
   additional arguments for specifying names: `.prefix`, `.suffix`,
   `.new_col_names`. To obtain the old naming behavior, use `.prefix =
   "slide_value_"`.
+- `as_epi_df` now removes any grouping that `x` had applied.
 
 ## Improvements
 
@@ -31,6 +32,7 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
   by `geo_value` and any `other_keys` for the slide operation rather than raise
   an error about duplicated time values. `epi_slide`'s analogous automatic
   grouping has been made temporary in order to match.
+- Improved speed of key-uniqueness checks.
 
 ## Bug fixes
 
diff --git a/R/epi_df.R b/R/epi_df.R
index 83cca073..6cae22dd 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -279,22 +279,20 @@ as_epi_df.tbl_df <- function(
   }
 
   assert_character(other_keys)
+  assert_subset(other_keys, names(x))
+  # Fix up if given more than just other keys, at least until epipredict#428
+  # merged:
+  other_keys <- other_keys[!other_keys %in% c("geo_value", "time_value")]
 
   if (".time_value_counts" %in% other_keys) {
     cli_abort("as_epi_df: `other_keys` can't include \".time_value_counts\"")
   }
 
-  if (anyDuplicated(x[c("geo_value", "time_value", other_keys)])) {
-    duplicated_time_values <- x %>%
-      group_by(across(all_of(c("geo_value", "time_value", other_keys)))) %>%
-      filter(dplyr::n() > 1) %>%
-      ungroup()
-    bad_data <- capture.output(duplicated_time_values)
-    cli_abort(
-      "as_epi_df: some groups in the data have duplicated time values. epi_df requires a unique time_value per group.",
-      body = c("Sample groups:", bad_data)
-    )
-  }
+  assert(check_ukey_unique(x, c("geo_value", other_keys, "time_value"), c(
+    ">" = "If this is line list data, convert it to counts/rates first.",
+    ">" = "If this contains a demographic breakdown, check that you have
+           specified appropriate `other_keys`" # . from checkmate
+  )))
 
   new_epi_df(x, geo_type, time_type, as_of, other_keys)
 }
diff --git a/R/epiprocess-package.R b/R/epiprocess-package.R
index 68b7b9b5..675d000d 100644
--- a/R/epiprocess-package.R
+++ b/R/epiprocess-package.R
@@ -5,8 +5,11 @@
 #' @import epidatasets
 #' @importFrom checkmate anyInfinite anyMissing assert assert_character
 #' @importFrom checkmate assert_class assert_data_frame assert_int assert_list
+#' @importFrom checkmate assert_false
 #' @importFrom checkmate assert_logical assert_numeric assert_scalar checkInt
 #' @importFrom checkmate assert_string
+#' @importFrom checkmate assert_subset
+#' @importFrom checkmate assert_tibble
 #' @importFrom checkmate check_atomic check_data_frame expect_class test_int
 #' @importFrom checkmate check_names
 #' @importFrom checkmate test_subset test_set_equal vname
@@ -14,11 +17,14 @@
 #' @importFrom data.table as.data.table
 #' @importFrom data.table key
 #' @importFrom data.table setkeyv
+#' @importFrom dplyr arrange
+#' @importFrom dplyr is_grouped_df
 #' @importFrom dplyr select
 #' @importFrom lifecycle deprecated
 #' @importFrom rlang %||%
 #' @importFrom rlang is_bare_integerish
 #' @importFrom vctrs vec_data
+#' @importFrom vctrs vec_equal
 ## usethis namespace: end
 NULL
 
diff --git a/R/slide.R b/R/slide.R
index 0c747d17..7342e0fd 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -259,18 +259,7 @@ epi_slide <- function(
   assert_logical(.all_rows, len = 1)
 
   # Check for duplicated time values within groups
-  duplicated_time_values <- .x %>%
-    group_epi_df() %>%
-    filter(dplyr::n() > 1) %>%
-    ungroup()
-  if (nrow(duplicated_time_values) > 0) {
-    bad_data <- capture.output(duplicated_time_values)
-    cli_abort(
-      "as_epi_df: some groups in a resulting dplyr computation have duplicated time values.
-      epi_df requires a unique time_value per group.",
-      body = c("Sample groups:", bad_data)
-    )
-  }
+  assert(check_ukey_unique(ungroup(.x), c(group_vars(.x), "time_value")))
 
   # Begin handling completion. This will create a complete time index between
   # the smallest and largest time values in the data. This is used to ensure
@@ -752,6 +741,9 @@ epi_slide_opt <- function(
     )
   }
 
+  # Check for duplicated time values within groups
+  assert(check_ukey_unique(ungroup(.x), c(group_vars(.x), "time_value")))
+
   # The position of a given column can be differ between input `.x` and
   # `.data_group` since the grouping step by default drops grouping columns.
   # To avoid rerunning `eval_select` for every `.data_group`, convert
diff --git a/R/utils.R b/R/utils.R
index 55022677..e350ade2 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1195,7 +1195,61 @@ time_type_unit_abbr <- function(time_type) {
   maybe_unit_abbr
 }
 
+#' Extract singular element of a length-1 unnamed list (validated)
+#'
+#' Inverse of `list(elt)`.
+#'
+#' @param x a length-1 list
+#' @return x[[1L]], if x actually was a length-1 list; error otherwise
+#'
+#' @keywords internal
 unwrap <- function(x) {
   checkmate::assert_list(x, len = 1L, names = "unnamed")
   x[[1L]]
 }
+
+#' Check that a unique key is indeed unique in a tibble (TRUE/str)
+#'
+#' A `checkmate`-style check function.
+#'
+#' @param x a tibble, with no particular row or column order (if you have a
+#'   guaranteed row order based on the ukey you can probably do something more
+#'   efficient)
+#' @param ukey_names character vector; subset of column names of `x` denoting a
+#'   unique key.
+#' @param end_cli_message optional character vector, a cli message format
+#'   string/vector; information/advice to tack onto any error messages.
+#' @return `TRUE` if no ukey is duplicated (i.e., `x[ukey_names]` has no
+#'   duplicated rows); string with an error message if there are errors.
+#'
+#' @keywords internal
+check_ukey_unique <- function(x, ukey_names, end_cli_message = character()) {
+  assert_tibble(x) # to not have to think about `data.table` perf, xface
+  assert_false(is_grouped_df(x)) # to not have to think about `grouped_df` perf, xface
+  assert_character(ukey_names)
+  assert_subset(ukey_names, names(x))
+  #
+  if (nrow(x) <= 1L) {
+    TRUE
+  } else {
+    # Fast check, slow error message.
+    arranged_ukeys <- arrange(x[ukey_names], across(all_of(ukey_names)))
+    if (!any(vec_equal(arranged_ukeys[-1L, ], arranged_ukeys[-nrow(arranged_ukeys), ]))) {
+      TRUE
+    } else {
+      bad_data <- x %>%
+        group_by(across(all_of(ukey_names))) %>%
+        filter(dplyr::n() > 1) %>%
+        ungroup()
+      lines <- c(
+        cli::format_error("
+          There cannot be more than one row with the same combination of
+          {format_varnames(ukey_names)}.  Problematic rows:
+        "),
+        capture.output(bad_data),
+        cli::format_message(end_cli_message)
+      )
+      paste(collapse = "\n", lines)
+    }
+  }
+}
diff --git a/man/check_ukey_unique.Rd b/man/check_ukey_unique.Rd
new file mode 100644
index 00000000..c6306f07
--- /dev/null
+++ b/man/check_ukey_unique.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{check_ukey_unique}
+\alias{check_ukey_unique}
+\title{Check that a unique key is indeed unique in a tibble (TRUE/str)}
+\usage{
+check_ukey_unique(x, ukey_names, end_cli_message = character())
+}
+\arguments{
+\item{x}{a tibble, with no particular row or column order (if you have a
+guaranteed row order based on the ukey you can probably do something more
+efficient)}
+
+\item{ukey_names}{character vector; subset of column names of \code{x} denoting a
+unique key.}
+
+\item{end_cli_message}{optional character vector, a cli message format
+string/vector; information/advice to tack onto any error messages.}
+}
+\value{
+\code{TRUE} if no ukey is duplicated (i.e., \code{x[ukey_names]} has no
+duplicated rows); string with an error message if there are errors.
+}
+\description{
+A \code{checkmate}-style check function.
+}
+\keyword{internal}
diff --git a/man/unwrap.Rd b/man/unwrap.Rd
new file mode 100644
index 00000000..dad0b441
--- /dev/null
+++ b/man/unwrap.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{unwrap}
+\alias{unwrap}
+\title{Extract singular element of a length-1 unnamed list (validated)}
+\usage{
+unwrap(x)
+}
+\arguments{
+\item{x}{a length-1 list}
+}
+\value{
+x[\link{1L}], if x actually was a length-1 list; error otherwise
+}
+\description{
+Inverse of \code{list(elt)}.
+}
+\keyword{internal}
diff --git a/tests/testthat/_snaps/epi_df.md b/tests/testthat/_snaps/epi_df.md
new file mode 100644
index 00000000..29280bf8
--- /dev/null
+++ b/tests/testthat/_snaps/epi_df.md
@@ -0,0 +1,15 @@
+# as_epi_df errors on nonunique epikeytime
+
+    Code
+      as_epi_df(tibble::tibble(geo_value = 1, time_value = 1, value = 1:2), as_of = 5)
+    Condition
+      Error:
+      ! Assertion on 'x' failed: There cannot be more than one row with the same combination of geo_value and time_value.  Problematic rows:
+      # A tibble: 2 x 3
+        geo_value time_value value
+            <dbl>      <dbl> <int>
+      1         1          1     1
+      2         1          1     2
+      > If this is line list data, convert it to counts/rates first.
+      > If this contains a demographic breakdown, check that you have specified appropriate `other_keys`.
+
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 44bb62e2..c3e51aa2 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -40,6 +40,20 @@ test_that("as_epi_df errors for non-character other_keys", {
   expect_silent(as_epi_df(ex_input, other_keys = c("state", "pol")))
 })
 
+test_that("as_epi_df errors on nonunique epikeytime", {
+  expect_snapshot(
+    as_epi_df(tibble::tibble(
+      geo_value = 1, time_value = 1, value = 1:2
+    ), as_of = 5),
+    error = TRUE
+  )
+  expect_no_error(
+    as_epi_df(tibble::tibble(
+      geo_value = 1, age_group = 1:2, time_value = 1, value = 1:2
+    ), other_keys = "age_group", as_of = 5)
+  )
+})
+
 test_that("as_epi_df works for nonstandard input", {
   tib <- tibble::tibble(
     x = 1:10, y = 1:10,

From 79093a8b97231301881b6fb6d1bc291180784379 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Tue, 26 Nov 2024 05:32:53 -0800
Subject: [PATCH 34/39] Fix _pkgdown.yml (data set topics removed; link
 epidatasets topics)

---
 _pkgdown.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2214df7c..1344705c 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -103,11 +103,11 @@ reference:
 
   - title: Example data
   - contents:
-      - cases_deaths_subset
-      - archive_cases_dv_subset
-      - covid_incidence_county_subset
-      - covid_incidence_outliers
-      - covid_case_death_rates_extended
+      - epidatasets::cases_deaths_subset
+      - epidatasets::archive_cases_dv_subset
+      - epidatasets::covid_incidence_county_subset
+      - epidatasets::covid_incidence_outliers
+      - epidatasets::covid_case_death_rates_extended
 
   - title: internal
   - contents:

From b4bacf865259af914c1b171df89c19bad06a0366 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Tue, 26 Nov 2024 06:06:41 -0800
Subject: [PATCH 35/39] Mollify CHECK regarding epidatasets re-exports

---
 R/reexports.R                | 19 +++++++++++++++++
 man/epidatasets_reexports.Rd | 40 ++++++++++++++++++++++++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 man/epidatasets_reexports.Rd

diff --git a/R/reexports.R b/R/reexports.R
index 72241175..9a33e94b 100644
--- a/R/reexports.R
+++ b/R/reexports.R
@@ -79,17 +79,36 @@ ggplot2::autoplot
 
 # epidatasets -------------------------------------------------------------------
 
+#' @rdname epidatasets_reexports
+#'
+#' @title Selected example data sets from `epidatasets`
+#'
+#' @description Data sets re-exported from `epidatasets`; please see
+#'   documentation for each of these objects in `epidatasets`.
+#'
+#' A brief description of the format of each of the objects above are described
+#' in matching order below.
+#'
+#' @keywords internal
 #' @export
 delayedAssign("cases_deaths_subset", epidatasets::cases_deaths_subset)
 
+#' @rdname epidatasets_reexports
+#' @keywords internal
 #' @export
 delayedAssign("covid_incidence_county_subset", epidatasets::covid_incidence_county_subset)
 
+#' @rdname epidatasets_reexports
+#' @keywords internal
 #' @export
 delayedAssign("covid_incidence_outliers", epidatasets::covid_incidence_outliers)
 
+#' @rdname epidatasets_reexports
+#' @keywords internal
 #' @export
 delayedAssign("archive_cases_dv_subset", epidatasets::archive_cases_dv_subset)
 
+#' @rdname epidatasets_reexports
+#' @keywords internal
 #' @export
 delayedAssign("covid_case_death_rates_extended", epidatasets::covid_case_death_rates_extended)
diff --git a/man/epidatasets_reexports.Rd b/man/epidatasets_reexports.Rd
new file mode 100644
index 00000000..3dc809e4
--- /dev/null
+++ b/man/epidatasets_reexports.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reexports.R
+\docType{data}
+\name{cases_deaths_subset}
+\alias{cases_deaths_subset}
+\alias{covid_incidence_county_subset}
+\alias{covid_incidence_outliers}
+\alias{archive_cases_dv_subset}
+\alias{covid_case_death_rates_extended}
+\title{Selected example data sets from \code{epidatasets}}
+\format{
+An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 4026 rows and 6 columns.
+
+An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 16212 rows and 5 columns.
+
+An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 730 rows and 3 columns.
+
+An object of class \code{epi_archive} of length 6.
+
+An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 37576 rows and 4 columns.
+}
+\usage{
+cases_deaths_subset
+
+covid_incidence_county_subset
+
+covid_incidence_outliers
+
+archive_cases_dv_subset
+
+covid_case_death_rates_extended
+}
+\description{
+Data sets re-exported from \code{epidatasets}; please see
+documentation for each of these objects in \code{epidatasets}.
+
+A brief description of the format of each of the objects above are described
+in matching order below.
+}
+\keyword{internal}

From 7bf4c6a34ab7c6f7dce70a0065136cfdadde96bc Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Mon, 9 Dec 2024 15:29:31 -0800
Subject: [PATCH 36/39] Add missing dplyr import in slide example

---
 R/slide.R            | 2 ++
 man/epi_slide_opt.Rd | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/R/slide.R b/R/slide.R
index 7342e0fd..e8fafa7a 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -621,6 +621,8 @@ get_before_after_from_window <- function(window_size, align, time_type) {
 #' @export
 #' @seealso [`epi_slide`] for the more general slide function
 #' @examples
+#' library(dplyr)
+#'
 #' # Add a column (`cases_7dsum`) containing a 7-day trailing sum on `cases`:
 #' cases_deaths_subset %>%
 #'   select(geo_value, time_value, cases) %>%
diff --git a/man/epi_slide_opt.Rd b/man/epi_slide_opt.Rd
index 7dc47a16..68244410 100644
--- a/man/epi_slide_opt.Rd
+++ b/man/epi_slide_opt.Rd
@@ -162,6 +162,8 @@ for \code{.f} factoring in the input column type(s) for \code{.col_names}
 }
 
 \examples{
+library(dplyr)
+
 # Add a column (`cases_7dsum`) containing a 7-day trailing sum on `cases`:
 cases_deaths_subset \%>\%
   select(geo_value, time_value, cases) \%>\%

From 101aad80633c080583af15bf4d5d71f231d98df5 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Mon, 9 Dec 2024 15:43:40 -0800
Subject: [PATCH 37/39] Bump to 0.10.0, update Author info

---
 DESCRIPTION | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e1568a9e..e894f099 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: epiprocess
 Type: Package
 Title: Tools for basic signal processing in epidemiology
-Version: 0.9.7
+Version: 0.10.0
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
-    person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = c("aut", "cre")),
+    person("Logan", "Brooks", , "lcbrooks+github@andrew.cmu.edu", role = c("aut", "cre")),
     person("Rafael", "Catoia", role = "ctb"),
     person("Nat", "DeFries", role = "ctb"),
     person("Daniel", "McDonald", role = "aut"),
@@ -13,8 +13,9 @@ Authors@R: c(
     person("Chloe", "You", role = "ctb"),
     person("Quang", "Nguyen", role = "ctb"),
     person("Evan", "Ray", role = "aut"),
-    person("Dmitry", "Shemetov", role = "ctb"),
+    person("Dmitry", "Shemetov", role = "aut"),
     person("Ryan", "Tibshirani", role = "aut"),
+    person("David", "Weber", , "davidweb@andrew.cmu.edu", role = "ctb"),
     person("Lionel", "Henry", role = "ctb",
            comment = "Author of included rlang fragments"),
     person("Hadley", "Wickham", role = "ctb",

From 271aaaa8974451db20896d104fa21e686ddcebb8 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Mon, 9 Dec 2024 22:39:54 -0800
Subject: [PATCH 38/39] Improve unsupported arg check messages in
 epi_slide_{sum,mean}

---
 R/slide.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/slide.R b/R/slide.R
index e8fafa7a..761639d4 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -1010,8 +1010,9 @@ epi_slide_mean <- function(
   }
   if ("new_col_name" %in% provided_args || ".new_col_name" %in% provided_args) {
     cli::cli_abort(
-      "epi_slide_mean: the argument `new_col_name` is not supported. If you want to customize
-      the output column names, use `dplyr::rename` after the slide."
+      "epi_slide_opt: the argument `new_col_name` is not supported for `epi_slide_opt`. If you want to customize
+      the output column names, use `.prefix =`, `.suffix =`, or `.new_col_**names** =`.",
+      class = "epiprocess__epi_slide_opt__new_name_not_supported"
     )
   }
   if ("names_sep" %in% provided_args || ".names_sep" %in% provided_args) {
@@ -1069,8 +1070,9 @@ epi_slide_sum <- function(
   }
   if ("new_col_name" %in% provided_args || ".new_col_name" %in% provided_args) {
     cli::cli_abort(
-      "epi_slide_sum: the argument `new_col_name` is not supported. If you want to customize
-      the output column names, use `dplyr::rename` after the slide."
+      "epi_slide_opt: the argument `new_col_name` is not supported for `epi_slide_opt`. If you want to customize
+      the output column names, use `.prefix =`, `.suffix =`, or `.new_col_**names** =`.",
+      class = "epiprocess__epi_slide_opt__new_name_not_supported"
     )
   }
   if ("names_sep" %in% provided_args || ".names_sep" %in% provided_args) {

From 5da97c7bfd15b27195eb0637a6ce44aefb8ada43 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Mon, 9 Dec 2024 22:40:28 -0800
Subject: [PATCH 39/39] Re-document

---
 man/epiprocess-package.Rd | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/man/epiprocess-package.Rd b/man/epiprocess-package.Rd
index b4f3e174..774d5f8a 100644
--- a/man/epiprocess-package.Rd
+++ b/man/epiprocess-package.Rd
@@ -16,12 +16,13 @@ Useful links:
 
 }
 \author{
-\strong{Maintainer}: Logan Brooks \email{lcbrooks@andrew.cmu.edu}
+\strong{Maintainer}: Logan Brooks \email{lcbrooks+github@andrew.cmu.edu}
 
 Authors:
 \itemize{
   \item Daniel McDonald
   \item Evan Ray
+  \item Dmitry Shemetov
   \item Ryan Tibshirani
 }
 
@@ -34,7 +35,7 @@ Other contributors:
   \item Ken Mawer [contributor]
   \item Chloe You [contributor]
   \item Quang Nguyen [contributor]
-  \item Dmitry Shemetov [contributor]
+  \item David Weber \email{davidweb@andrew.cmu.edu} [contributor]
   \item Lionel Henry (Author of included rlang fragments) [contributor]
   \item Hadley Wickham (Author of included rlang fragments) [contributor]
   \item Posit (Copyright holder of included rlang fragments) [copyright holder]