From 9ede25a053c476591d92f70d9c4ea9cd94aa7354 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:38:27 -0800
Subject: [PATCH 01/27] add S3 method to quickly access the keys in an epi_df
 or epi_archive

---
 R/epi_keys.R | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 R/epi_keys.R

diff --git a/R/epi_keys.R b/R/epi_keys.R
new file mode 100644
index 00000000..324b4eff
--- /dev/null
+++ b/R/epi_keys.R
@@ -0,0 +1,42 @@
+#' Grab any keys associated to an epi_df
+#'
+#' @param x a data.frame, tibble, or epi_df
+#' @param ... additional arguments passed on to methods
+#'
+#' @return If an `epi_df`, this returns all "keys". Otherwise `NULL`
+#' @keywords internal
+#' @export
+epi_keys <- function(x, ...) {
+  UseMethod("epi_keys")
+}
+
+#' @export
+epi_keys.default <- function(x, ...) {
+  character(0L)
+}
+
+#' @export
+epi_keys.data.frame <- function(x, other_keys = character(0L), ...) {
+  arg_is_chr(other_keys, allow_empty = TRUE)
+  nm <- c("time_value", "geo_value", other_keys)
+  intersect(nm, names(x))
+}
+
+#' @export
+epi_keys.epi_df <- function(x, ...) {
+  c("time_value", "geo_value", attr(x, "metadata")$other_keys)
+}
+
+#' @export
+epi_keys.epi_archive <- function(x, ...) {
+  c("time_value", "geo_value", attr(x, "metadata")$other_keys)
+}
+
+kill_time_value <- function(v) {
+  arg_is_chr(v)
+  v[v != "time_value"]
+}
+
+epi_keys_only <- function(x, ...) {
+  kill_time_value(epi_keys(x, ...))
+}

From 96c7500901047fe0598e2e100d3867207bc0481f Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:39:04 -0800
Subject: [PATCH 02/27] grab autoplot method from ggplot2 and export

---
 DESCRIPTION   | 5 ++++-
 R/reexports.R | 7 +++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d9a8dea6..7895ee26 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,6 +33,7 @@ Imports:
     feasts,
     generics,
     genlasso,
+    ggplot2,
     lifecycle (>= 1.0.1),
     lubridate,
     magrittr,
@@ -49,7 +50,6 @@ Imports:
 Suggests:
     covidcast,
     epidatr,
-    ggplot2,
     knitr,
     outbreaks,
     rmarkdown,
@@ -72,9 +72,11 @@ Depends:
 URL: https://cmu-delphi.github.io/epiprocess/
 Collate: 
     'archive.R'
+    'autoplot.R'
     'correlation.R'
     'data.R'
     'epi_df.R'
+    'epi_keys.R'
     'epiprocess.R'
     'methods-epi_archive.R'
     'grouped_epi_archive.R'
@@ -83,5 +85,6 @@ Collate:
     'outliers.R'
     'reexports.R'
     'slide.R'
+    'utils-arg.R'
     'utils.R'
     'utils_pipe.R'
diff --git a/R/reexports.R b/R/reexports.R
index 4cc45e29..02f5af53 100644
--- a/R/reexports.R
+++ b/R/reexports.R
@@ -55,3 +55,10 @@ dplyr::slice
 #' @importFrom tidyr unnest
 #' @export
 tidyr::unnest
+
+
+# ggplot2 -----------------------------------------------------------------
+
+#' @importFrom ggplot2 autoplot
+#' @export
+ggplot2::autoplot

From 1638430040896f8366e952732c7a3f586393de5b Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:39:30 -0800
Subject: [PATCH 03/27] simplify enlist()

---
 R/utils.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 471fb053..c815161a 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -454,13 +454,13 @@ quiet = function(x) {
 
 # Create an auto-named list
 enlist = function(...) {
-  x = list(...)
-  n = as.character(sys.call())[-1]
-  if (!is.null(n0 <- names(x))) {
-    n[n0 != ""] = n0[n0 != ""]
-  }
-  names(x) = n
-  return(x) 
+  # converted to thin wrapper around
+  rlang::dots_list(
+    ...,
+    .homonyms = "error",
+    .named = TRUE,
+    .check_assign = TRUE
+  )
 }
 
 # Variable assignment from a list. NOT USED. Something is broken, this doesn't 

From a3cb78bb1e3ac68284fdd2028d0cf7bb137e28de Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:41:28 -0800
Subject: [PATCH 04/27] add a few argument checking functions, see also #380

---
 R/utils-arg.R | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 R/utils-arg.R

diff --git a/R/utils-arg.R b/R/utils-arg.R
new file mode 100644
index 00000000..b5700b6d
--- /dev/null
+++ b/R/utils-arg.R
@@ -0,0 +1,63 @@
+handle_arg_list <- function(..., tests) {
+  values <- list(...)
+  names <- eval(substitute(alist(...)))
+  names <- purrr::map(names, deparse)
+  
+  purrr::walk2(names, values, tests)
+}
+
+arg_is_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
+  handle_arg_list(
+    ...,
+    tests = function(name, value) {
+      if (length(value) > 1 | (!allow_null & length(value) == 0)) {
+        cli::cli_abort("Argument {.val {name}} must be of length 1.")
+      }
+      if (!is.null(value)) {
+        if (is.na(value) & !allow_na) {
+          cli::cli_abort(
+            "Argument {.val {name}} must not be a missing value ({.val {NA}})."
+          )
+        }
+      }
+    }
+  )
+}
+
+arg_is_int <- function(..., allow_null = FALSE) {
+  arg_is_numeric(..., allow_null = allow_null)
+  handle_arg_list(
+    ...,
+    tests = function(name, value) {
+      if (!(all(value %% 1 == 0) | (is.null(value) & allow_null))) {
+        cli::cli_abort("All {.val {name}} must be whole positive number(s).")
+      }
+    }
+  )
+}
+
+arg_is_chr <- function(..., allow_null = FALSE, allow_na = FALSE, allow_empty = FALSE) {
+  handle_arg_list(
+    ...,
+    tests = function(name, value) {
+      if (is.null(value) & !allow_null) {
+        cli::cli_abort("Argument {.val {name}} may not be `NULL`.")
+      }
+      if (any(is.na(value)) & !allow_na) {
+        cli::cli_abort("Argument {.val {name}} must not contain any missing values ({.val {NA}}).")
+      }
+      if (!is.null(value) & (length(value) == 0L & !allow_empty)) {
+        cli::cli_abort("Argument {.val {name}} must have length > 0.")
+      }
+      if (!(is.character(value) | is.null(value) | all(is.na(value)))) {
+        cli::cli_abort("Argument {.val {name}} must be of character type.")
+      }
+    }
+  )
+}
+
+arg_is_chr_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
+  arg_is_chr(..., allow_null = allow_null, allow_na = allow_na)
+  arg_is_scalar(..., allow_null = allow_null, allow_na = allow_na)
+}
+

From f29936cf2df067de117f62fd4b2d36d80544f7be Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:41:56 -0800
Subject: [PATCH 05/27] add autoplot() for epi_df's

---
 R/autoplot.R | 154 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 R/autoplot.R

diff --git a/R/autoplot.R b/R/autoplot.R
new file mode 100644
index 00000000..8263818d
--- /dev/null
+++ b/R/autoplot.R
@@ -0,0 +1,154 @@
+#' Automatically plot an epi_df
+#'
+#' @param object An `epi_df`
+#' @param ... <[`tidy-select`][dplyr_tidy_select]> One or more unquoted
+#'   expressions separated by commas. Variable names can be used as if they
+#'   were positions in the data frame, so expressions like `x:y` can
+#'   be used to select a range of variables.
+#' @param .color_by Which variables should determine the color(s) used to plot
+#'   lines. Options include:
+#'   * `all_keys` - the default uses the interaction of any key variables
+#'     including the `geo_value`
+#'   * `geo_value` - `geo_value` only
+#'   * `other_keys` - any available keys that are not `geo_value`
+#'   * `.response` - the numeric variables (same as the y-axis)
+#'   * `all` - uses the interaction of all keys and numeric variables
+#'   * `none` - no coloring aesthetic is applied
+#' @param .facet_by Similar to `.color_by` except that the default is to display
+#'   each numeric variable on a separate facet
+#' @param .base_color Lines will be shown with this color. For example, with a
+#'   single numeric variable and faceting by `geo_value`, all locations would
+#'   share the same color line.
+#' @param .max_facets Cut down of the number of facets displayed. Especially
+#'   useful for testing when there are many `geo_value`'s or keys.
+#'
+#' @return
+#' @export
+#'
+#' @examples
+#' autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+#'   .facet_by = "geo_value")
+autoplot.epi_df <- function(
+    object, ...,
+    .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
+    .facet_by = c(".response", "other_keys", "all_keys", "geo_value", "all", "none"),
+    .base_color = "#3A448F",
+    .max_facets = Inf) {
+  .color_by <- match.arg(.color_by)
+  .facet_by <- match.arg(.facet_by)
+  
+  arg_is_scalar(.max_facets)
+  if (is.finite(.max_facets)) arg_is_int(.max_facets)
+  arg_is_chr_scalar(.base_color)
+  
+  ek <- epi_keys(object)
+  mv <- setdiff(names(object), ek)
+  ek <- kill_time_value(ek)
+  
+  # --- check for numeric variables
+  allowed <- purrr::map_lgl(object[mv], is.numeric)
+  if (length(allowed) == 0) {
+    cli::cli_abort("No numeric variables were available to plot automatically.")
+  }
+  vars <- tidyselect::eval_select(rlang::expr(c(...)), object)
+  if (rlang::is_empty(vars)) { # find them automatically if unspecified
+    vars <- tidyselect::eval_select(names(allowed)[1], object)
+    cli::cli_warn(
+      "Plot variable was unspecified. Automatically selecting {.var {names(allowed)[1]}}."
+    )
+  } else { # if variables were specified, ensure that they are numeric
+    ok <- names(vars) %in% names(allowed)
+    if (!any(ok)) {
+      cli::cli_abort(
+        "None of the requested variables {.var {names(vars)}} are numeric."
+      )
+    } else if (!all(ok)) {
+      cli::cli_warn(c(
+        "Only the requested variables {.var {names(vars)[ok]}} are numeric.",
+        i = "`autoplot()` cannot display {.var {names(vars)[!ok]}}."
+      ))
+      vars <- vars[ok]
+    }
+  }
+  
+  # --- create a viable df to plot
+  pos <- tidyselect::eval_select(
+    rlang::expr(c("time_value", ek, names(vars))), object
+  )
+  if (length(vars) > 1) {
+    object <- tidyr::pivot_longer(
+      object[pos], tidyselect::all_of(names(vars)),
+      values_to = ".response",
+      names_to = ".response_name"
+    )
+  } else {
+    object <- dplyr::rename(object[pos], .response := !!names(vars))
+  }
+  all_keys <- rlang::syms(as.list(ek))
+  other_keys <- rlang::syms(as.list(setdiff(ek, "geo_value")))
+  all_avail <- rlang::syms(as.list(c(ek, ".response_name")))
+  
+  object <- object %>%
+    dplyr::mutate(
+      .colours = switch(.color_by,
+                        all_keys = interaction(!!!all_keys, sep = "/"),
+                        geo_value = geo_value,
+                        other_keys = interaction(!!!other_keys, sep = "/"),
+                        all = interaction(!!!all_avail, sep = "/"),
+                        NULL
+      ),
+      .facets = switch(.facet_by,
+                       all_keys = interaction(!!!all_keys, sep = "/"),
+                       geo_value = as.factor(geo_value),
+                       other_keys = interaction(!!!other_keys, sep = "/"),
+                       all = interaction(!!!all_avail, sep = "/"),
+                       NULL
+      )
+    )
+  
+  if (.max_facets < Inf && ".facets" %in% names(object)) {
+    n_facets <- nlevels(object$.facets)
+    if (n_facets > .max_facets) {
+      top_n <- levels(as.factor(object$.facets))[seq_len(.max_facets)]
+      object <- dplyr::filter(object, .facets %in% top_n) %>%
+        dplyr::mutate(.facets = droplevels(.facets))
+      if (".colours" %in% names(object)) {
+        object <- dplyr::mutate(object, .colours = droplevels(.colours))
+      }
+    }
+  }
+  
+  p <- ggplot2::ggplot(object, ggplot2::aes(x = .data$time_value)) +
+    ggplot2::theme_bw()
+  
+  if (".colours" %in% names(object)) {
+    p <- p + ggplot2::geom_line(
+      ggplot2::aes(y = .data$.response, colour = .data$.colours),
+      key_glyph = "timeseries"
+    ) +
+      ggplot2::scale_colour_viridis_d(name = "")
+  } else if (length(vars) > 1 && .color_by == ".response") {
+    p <- p +
+      ggplot2::geom_line(ggplot2::aes(
+        y = .data$.response, colour = .data$.response_name
+      )) +
+      ggplot2::scale_colour_viridis_d(name = "")
+  } else { # none
+    p <- p +
+      ggplot2::geom_line(ggplot2::aes(y = .data$.response), color = .base_color)
+  }
+  
+  if (".facets" %in% names(object)) {
+    p <- p + ggplot2::facet_wrap(~.facets, scales = "free_y") +
+      ggplot2::ylab(names(vars))
+    if (.facet_by == "all") p <- p + ggplot2::ylab("")
+  } else if ((length(vars) > 1 && .facet_by == ".response")) {
+    p <- p + ggplot2::facet_wrap(~.response_name, scales = "free_y") +
+      ggplot2::ylab("")
+  } else {
+    p <- p + ggplot2::ylab(names(vars))
+  }
+  p
+}

From cc58ddc1d935374a26cd18ce899f76dd14151472 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:42:11 -0800
Subject: [PATCH 06/27] document()

---
 NAMESPACE              |  8 +++++++
 man/autoplot.epi_df.Rd | 54 ++++++++++++++++++++++++++++++++++++++++++
 man/epi_keys.Rd        | 20 ++++++++++++++++
 man/reexports.Rd       |  3 +++
 4 files changed, 85 insertions(+)
 create mode 100644 man/autoplot.epi_df.Rd
 create mode 100644 man/epi_keys.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 4f9b8151..eb88c7a4 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,10 +8,15 @@ S3method(as_epi_df,tbl_df)
 S3method(as_epi_df,tbl_ts)
 S3method(as_tibble,epi_df)
 S3method(as_tsibble,epi_df)
+S3method(autoplot,epi_df)
 S3method(dplyr_col_modify,col_modify_recorder_df)
 S3method(dplyr_col_modify,epi_df)
 S3method(dplyr_reconstruct,epi_df)
 S3method(dplyr_row_slice,epi_df)
+S3method(epi_keys,data.frame)
+S3method(epi_keys,default)
+S3method(epi_keys,epi_archive)
+S3method(epi_keys,epi_df)
 S3method(epix_truncate_versions_after,epi_archive)
 S3method(epix_truncate_versions_after,grouped_epi_archive)
 S3method(group_by,epi_archive)
@@ -33,11 +38,13 @@ export(arrange)
 export(as_epi_archive)
 export(as_epi_df)
 export(as_tsibble)
+export(autoplot)
 export(detect_outlr)
 export(detect_outlr_rm)
 export(detect_outlr_stl)
 export(epi_archive)
 export(epi_cor)
+export(epi_keys)
 export(epi_slide)
 export(epix_as_of)
 export(epix_merge)
@@ -85,6 +92,7 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,ungroup)
+importFrom(ggplot2,autoplot)
 importFrom(lubridate,days)
 importFrom(lubridate,weeks)
 importFrom(magrittr,"%>%")
diff --git a/man/autoplot.epi_df.Rd b/man/autoplot.epi_df.Rd
new file mode 100644
index 00000000..134a83fe
--- /dev/null
+++ b/man/autoplot.epi_df.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoplot.R
+\name{autoplot.epi_df}
+\alias{autoplot.epi_df}
+\title{Automatically plot an epi_df}
+\usage{
+\method{autoplot}{epi_df}(
+  object,
+  ...,
+  .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
+  .facet_by = c(".response", "other_keys", "all_keys", "geo_value", "all", "none"),
+  .base_color = "#3A448F",
+  .max_facets = Inf
+)
+}
+\arguments{
+\item{object}{An \code{epi_df}}
+
+\item{...}{<\code{\link[=dplyr_tidy_select]{tidy-select}}> One or more unquoted
+expressions separated by commas. Variable names can be used as if they
+were positions in the data frame, so expressions like \code{x:y} can
+be used to select a range of variables.}
+
+\item{.color_by}{Which variables should determine the color(s) used to plot
+lines. Options include:
+\itemize{
+\item \code{all_keys} - the default uses the interaction of any key variables
+including the \code{geo_value}
+\item \code{geo_value} - \code{geo_value} only
+\item \code{other_keys} - any available keys that are not \code{geo_value}
+\item \code{.response} - the numeric variables (same as the y-axis)
+\item \code{all} - uses the interaction of all keys and numeric variables
+\item \code{none} - no coloring aesthetic is applied
+}}
+
+\item{.facet_by}{Similar to \code{.color_by} except that the default is to display
+each numeric variable on a separate facet}
+
+\item{.base_color}{Lines will be shown with this color. For example, with a
+single numeric variable and faceting by \code{geo_value}, all locations would
+share the same color line.}
+
+\item{.max_facets}{Cut down of the number of facets displayed. Especially
+useful for testing when there are many \code{geo_value}'s or keys.}
+}
+\description{
+Automatically plot an epi_df
+}
+\examples{
+autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
+autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
+autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+  .facet_by = "geo_value")
+}
diff --git a/man/epi_keys.Rd b/man/epi_keys.Rd
new file mode 100644
index 00000000..8026fc14
--- /dev/null
+++ b/man/epi_keys.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/epi_keys.R
+\name{epi_keys}
+\alias{epi_keys}
+\title{Grab any keys associated to an epi_df}
+\usage{
+epi_keys(x, ...)
+}
+\arguments{
+\item{x}{a data.frame, tibble, or epi_df}
+
+\item{...}{additional arguments passed on to methods}
+}
+\value{
+If an \code{epi_df}, this returns all "keys". Otherwise \code{NULL}
+}
+\description{
+Grab any keys associated to an epi_df
+}
+\keyword{internal}
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 46e961d9..fdda2925 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -14,6 +14,7 @@
 \alias{rename}
 \alias{slice}
 \alias{unnest}
+\alias{autoplot}
 \title{Objects exported from other packages}
 \keyword{internal}
 \description{
@@ -23,6 +24,8 @@ below to see their documentation.
 \describe{
   \item{dplyr}{\code{\link[dplyr]{arrange}}, \code{\link[dplyr]{filter}}, \code{\link[dplyr]{group_by}}, \code{\link[dplyr:group_map]{group_modify}}, \code{\link[dplyr]{mutate}}, \code{\link[dplyr]{relocate}}, \code{\link[dplyr]{rename}}, \code{\link[dplyr]{slice}}, \code{\link[dplyr:group_by]{ungroup}}}
 
+  \item{ggplot2}{\code{\link[ggplot2]{autoplot}}}
+
   \item{tidyr}{\code{\link[tidyr]{unnest}}}
 
   \item{tsibble}{\code{\link[tsibble:as-tsibble]{as_tsibble}}}

From d29b79fdf348ef09f480ab575cef4d39857f12af Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Mon, 27 Nov 2023 15:59:35 -0800
Subject: [PATCH 07/27] add new functions to pkgdown

---
 _pkgdown.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index bba3ea8d..00110b01 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -66,10 +66,13 @@ reference:
   - archive_cases_dv_subset
   - incidence_num_outlier_example
   - contains("jhu_csse")
+- title: Basic automatic plotting
+  contents:
+  - autoplot.epi_df
 - title: internal
   contents:
   - epiprocess
   - max_version_with_row_in
   - next_after
   - guess_period
-
+  - epi_keys

From becc554277869496bf600bb9e332b1c20cc9cc8d Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Fri, 19 Jan 2024 11:43:15 -0800
Subject: [PATCH 08/27] style: run styler

---
 R/autoplot.R  | 44 +++++++++++++++++++++++---------------------
 R/utils-arg.R |  3 +--
 R/utils.R     |  2 +-
 3 files changed, 25 insertions(+), 24 deletions(-)

diff --git a/R/autoplot.R b/R/autoplot.R
index 8263818d..6c6bf5eb 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -28,8 +28,10 @@
 #' @examples
 #' autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
 #' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
-#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
-#'   .facet_by = "geo_value")
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av,
+#'   .color_by = "none",
+#'   .facet_by = "geo_value"
+#' )
 autoplot.epi_df <- function(
     object, ...,
     .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
@@ -38,15 +40,15 @@ autoplot.epi_df <- function(
     .max_facets = Inf) {
   .color_by <- match.arg(.color_by)
   .facet_by <- match.arg(.facet_by)
-  
+
   arg_is_scalar(.max_facets)
   if (is.finite(.max_facets)) arg_is_int(.max_facets)
   arg_is_chr_scalar(.base_color)
-  
+
   ek <- epi_keys(object)
   mv <- setdiff(names(object), ek)
   ek <- kill_time_value(ek)
-  
+
   # --- check for numeric variables
   allowed <- purrr::map_lgl(object[mv], is.numeric)
   if (length(allowed) == 0) {
@@ -72,7 +74,7 @@ autoplot.epi_df <- function(
       vars <- vars[ok]
     }
   }
-  
+
   # --- create a viable df to plot
   pos <- tidyselect::eval_select(
     rlang::expr(c("time_value", ek, names(vars))), object
@@ -89,25 +91,25 @@ autoplot.epi_df <- function(
   all_keys <- rlang::syms(as.list(ek))
   other_keys <- rlang::syms(as.list(setdiff(ek, "geo_value")))
   all_avail <- rlang::syms(as.list(c(ek, ".response_name")))
-  
+
   object <- object %>%
     dplyr::mutate(
       .colours = switch(.color_by,
-                        all_keys = interaction(!!!all_keys, sep = "/"),
-                        geo_value = geo_value,
-                        other_keys = interaction(!!!other_keys, sep = "/"),
-                        all = interaction(!!!all_avail, sep = "/"),
-                        NULL
+        all_keys = interaction(!!!all_keys, sep = "/"),
+        geo_value = geo_value,
+        other_keys = interaction(!!!other_keys, sep = "/"),
+        all = interaction(!!!all_avail, sep = "/"),
+        NULL
       ),
       .facets = switch(.facet_by,
-                       all_keys = interaction(!!!all_keys, sep = "/"),
-                       geo_value = as.factor(geo_value),
-                       other_keys = interaction(!!!other_keys, sep = "/"),
-                       all = interaction(!!!all_avail, sep = "/"),
-                       NULL
+        all_keys = interaction(!!!all_keys, sep = "/"),
+        geo_value = as.factor(geo_value),
+        other_keys = interaction(!!!other_keys, sep = "/"),
+        all = interaction(!!!all_avail, sep = "/"),
+        NULL
       )
     )
-  
+
   if (.max_facets < Inf && ".facets" %in% names(object)) {
     n_facets <- nlevels(object$.facets)
     if (n_facets > .max_facets) {
@@ -119,10 +121,10 @@ autoplot.epi_df <- function(
       }
     }
   }
-  
+
   p <- ggplot2::ggplot(object, ggplot2::aes(x = .data$time_value)) +
     ggplot2::theme_bw()
-  
+
   if (".colours" %in% names(object)) {
     p <- p + ggplot2::geom_line(
       ggplot2::aes(y = .data$.response, colour = .data$.colours),
@@ -139,7 +141,7 @@ autoplot.epi_df <- function(
     p <- p +
       ggplot2::geom_line(ggplot2::aes(y = .data$.response), color = .base_color)
   }
-  
+
   if (".facets" %in% names(object)) {
     p <- p + ggplot2::facet_wrap(~.facets, scales = "free_y") +
       ggplot2::ylab(names(vars))
diff --git a/R/utils-arg.R b/R/utils-arg.R
index b5700b6d..dca21646 100644
--- a/R/utils-arg.R
+++ b/R/utils-arg.R
@@ -2,7 +2,7 @@ handle_arg_list <- function(..., tests) {
   values <- list(...)
   names <- eval(substitute(alist(...)))
   names <- purrr::map(names, deparse)
-  
+
   purrr::walk2(names, values, tests)
 }
 
@@ -60,4 +60,3 @@ arg_is_chr_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
   arg_is_chr(..., allow_null = allow_null, allow_na = allow_na)
   arg_is_scalar(..., allow_null = allow_null, allow_na = allow_na)
 }
-
diff --git a/R/utils.R b/R/utils.R
index 787da5bd..f0a586d7 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -481,7 +481,7 @@ quiet <- function(x) {
 ##########
 
 # Create an auto-named list
-enlist = function(...) {
+enlist <- function(...) {
   # converted to thin wrapper around
   rlang::dots_list(
     ...,

From ede6c9c92440eb2c3f9659a3f112880e8807e482 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Fri, 19 Jan 2024 11:56:01 -0800
Subject: [PATCH 09/27] rename epi_keys to key_colnames

---
 R/epi_keys.R     | 42 ------------------------------------------
 R/key_colnames.R | 44 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+), 42 deletions(-)
 delete mode 100644 R/epi_keys.R
 create mode 100644 R/key_colnames.R

diff --git a/R/epi_keys.R b/R/epi_keys.R
deleted file mode 100644
index 324b4eff..00000000
--- a/R/epi_keys.R
+++ /dev/null
@@ -1,42 +0,0 @@
-#' Grab any keys associated to an epi_df
-#'
-#' @param x a data.frame, tibble, or epi_df
-#' @param ... additional arguments passed on to methods
-#'
-#' @return If an `epi_df`, this returns all "keys". Otherwise `NULL`
-#' @keywords internal
-#' @export
-epi_keys <- function(x, ...) {
-  UseMethod("epi_keys")
-}
-
-#' @export
-epi_keys.default <- function(x, ...) {
-  character(0L)
-}
-
-#' @export
-epi_keys.data.frame <- function(x, other_keys = character(0L), ...) {
-  arg_is_chr(other_keys, allow_empty = TRUE)
-  nm <- c("time_value", "geo_value", other_keys)
-  intersect(nm, names(x))
-}
-
-#' @export
-epi_keys.epi_df <- function(x, ...) {
-  c("time_value", "geo_value", attr(x, "metadata")$other_keys)
-}
-
-#' @export
-epi_keys.epi_archive <- function(x, ...) {
-  c("time_value", "geo_value", attr(x, "metadata")$other_keys)
-}
-
-kill_time_value <- function(v) {
-  arg_is_chr(v)
-  v[v != "time_value"]
-}
-
-epi_keys_only <- function(x, ...) {
-  kill_time_value(epi_keys(x, ...))
-}
diff --git a/R/key_colnames.R b/R/key_colnames.R
new file mode 100644
index 00000000..91be7ab6
--- /dev/null
+++ b/R/key_colnames.R
@@ -0,0 +1,44 @@
+#' Grab any keys associated to an epi_df
+#'
+#' @param x a data.frame, tibble, or epi_df
+#' @param ... additional arguments passed on to methods
+#'
+#' @return If an `epi_df`, this returns all "keys". Otherwise `NULL`
+#' @keywords internal
+#' @export
+key_colnames <- function(x, ...) {
+  UseMethod("key_colnames")
+}
+
+#' @export
+key_colnames.default <- function(x, ...) {
+  character(0L)
+}
+
+#' @export
+key_colnames.data.frame <- function(x, other_keys = character(0L), ...) {
+  arg_is_chr(other_keys, allow_empty = TRUE)
+  nm <- c("time_value", "geo_value", other_keys)
+  intersect(nm, colnames(x))
+}
+
+#' @export
+key_colnames.epi_df <- function(x, ...) {
+  other_keys <- attr(x, "metadata")$other_keys
+  c("time_value", "geo_value", other_keys)
+}
+
+#' @export
+key_colnames.epi_archive <- function(x, ...) {
+  other_keys <- attr(x, "metadata")$other_keys
+  c("time_value", "geo_value", other_keys)
+}
+
+kill_time_value <- function(v) {
+  arg_is_chr(v)
+  v[v != "time_value"]
+}
+
+key_colnames_only <- function(x, ...) {
+  kill_time_value(key_colnames(x, ...))
+}

From 989ee8c84994e97fc3aa0c4322adecccd8a6148c Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Fri, 19 Jan 2024 15:23:05 -0800
Subject: [PATCH 10/27] rename based on review

---
 DESCRIPTION                          |  2 +-
 NAMESPACE                            | 10 ++---
 R/autoplot.R                         | 18 ++++----
 man/as_epi_archive.Rd                | 56 +++++++++++++++----------
 man/as_epi_df.Rd                     | 44 ++++++++++++--------
 man/autoplot.epi_df.Rd               |  9 +++-
 man/detect_outlr.Rd                  | 62 +++++++++++++++++-----------
 man/detect_outlr_rm.Rd               |  7 ++--
 man/detect_outlr_stl.Rd              |  7 ++--
 man/epi_archive.Rd                   | 18 ++++----
 man/epi_cor.Rd                       | 48 ++++++++++++---------
 man/epi_slide.Rd                     | 22 ++++++----
 man/epix_as_of.Rd                    | 25 +++++++----
 man/epix_merge.Rd                    | 10 ++---
 man/epix_slide.Rd                    | 55 +++++++++++++-----------
 man/group_by.epi_archive.Rd          | 48 ++++++++++++---------
 man/growth_rate.Rd                   | 12 +++---
 man/is_epi_archive.Rd                |  4 +-
 man/{epi_keys.Rd => key_colnames.Rd} |  8 ++--
 19 files changed, 273 insertions(+), 192 deletions(-)
 rename man/{epi_keys.Rd => key_colnames.Rd} (76%)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3ce7b860..211c5212 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -76,12 +76,12 @@ Collate:
     'correlation.R'
     'data.R'
     'epi_df.R'
-    'epi_keys.R'
     'epiprocess.R'
     'group_by_epi_df_methods.R'
     'methods-epi_archive.R'
     'grouped_epi_archive.R'
     'growth_rate.R'
+    'key_colnames.R'
     'methods-epi_df.R'
     'outliers.R'
     'reexports.R'
diff --git a/NAMESPACE b/NAMESPACE
index 9b2134ae..a843813d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,10 +13,6 @@ S3method(dplyr_col_modify,col_modify_recorder_df)
 S3method(dplyr_col_modify,epi_df)
 S3method(dplyr_reconstruct,epi_df)
 S3method(dplyr_row_slice,epi_df)
-S3method(epi_keys,data.frame)
-S3method(epi_keys,default)
-S3method(epi_keys,epi_archive)
-S3method(epi_keys,epi_df)
 S3method(epix_truncate_versions_after,epi_archive)
 S3method(epix_truncate_versions_after,grouped_epi_archive)
 S3method(group_by,epi_archive)
@@ -25,6 +21,10 @@ S3method(group_by,grouped_epi_archive)
 S3method(group_by_drop_default,grouped_epi_archive)
 S3method(group_modify,epi_df)
 S3method(groups,grouped_epi_archive)
+S3method(key_colnames,data.frame)
+S3method(key_colnames,default)
+S3method(key_colnames,epi_archive)
+S3method(key_colnames,epi_df)
 S3method(next_after,Date)
 S3method(next_after,integer)
 S3method(print,epi_df)
@@ -45,7 +45,6 @@ export(detect_outlr_rm)
 export(detect_outlr_stl)
 export(epi_archive)
 export(epi_cor)
-export(epi_keys)
 export(epi_slide)
 export(epix_as_of)
 export(epix_merge)
@@ -58,6 +57,7 @@ export(growth_rate)
 export(is_epi_archive)
 export(is_epi_df)
 export(is_grouped_epi_archive)
+export(key_colnames)
 export(max_version_with_row_in)
 export(mutate)
 export(new_epi_df)
diff --git a/R/autoplot.R b/R/autoplot.R
index 6c6bf5eb..bcd0b54d 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -22,7 +22,7 @@
 #' @param .max_facets Cut down of the number of facets displayed. Especially
 #'   useful for testing when there are many `geo_value`'s or keys.
 #'
-#' @return
+#' @return A ggplot object
 #' @export
 #'
 #' @examples
@@ -45,12 +45,12 @@ autoplot.epi_df <- function(
   if (is.finite(.max_facets)) arg_is_int(.max_facets)
   arg_is_chr_scalar(.base_color)
 
-  ek <- epi_keys(object)
-  mv <- setdiff(names(object), ek)
-  ek <- kill_time_value(ek)
+  key_cols <- key_colnames(object)
+  non_key_cols <- setdiff(names(object), key_cols)
+  geo_and_other_keys <- kill_time_value(key_cols)
 
   # --- check for numeric variables
-  allowed <- purrr::map_lgl(object[mv], is.numeric)
+  allowed <- purrr::map_lgl(object[non_key_cols], is.numeric)
   if (length(allowed) == 0) {
     cli::cli_abort("No numeric variables were available to plot automatically.")
   }
@@ -77,7 +77,7 @@ autoplot.epi_df <- function(
 
   # --- create a viable df to plot
   pos <- tidyselect::eval_select(
-    rlang::expr(c("time_value", ek, names(vars))), object
+    rlang::expr(c("time_value", geo_and_other_keys, names(vars))), object
   )
   if (length(vars) > 1) {
     object <- tidyr::pivot_longer(
@@ -88,9 +88,9 @@ autoplot.epi_df <- function(
   } else {
     object <- dplyr::rename(object[pos], .response := !!names(vars))
   }
-  all_keys <- rlang::syms(as.list(ek))
-  other_keys <- rlang::syms(as.list(setdiff(ek, "geo_value")))
-  all_avail <- rlang::syms(as.list(c(ek, ".response_name")))
+  all_keys <- rlang::syms(as.list(geo_and_other_keys))
+  other_keys <- rlang::syms(as.list(setdiff(geo_and_other_keys, "geo_value")))
+  all_avail <- rlang::syms(as.list(c(geo_and_other_keys, ".response_name")))
 
   object <- object %>%
     dplyr::mutate(
diff --git a/man/as_epi_archive.Rd b/man/as_epi_archive.Rd
index e3604341..93b10736 100644
--- a/man/as_epi_archive.Rd
+++ b/man/as_epi_archive.Rd
@@ -99,32 +99,44 @@ would be equivalent to:
 # Simple ex. with necessary keys
 tib <- tibble::tibble(
   geo_value = rep(c("ca", "hi"), each = 5),
-  time_value = rep(seq(as.Date("2020-01-01"), 
-                       by = 1, length.out = 5), times = 2),
-  version = rep(seq(as.Date("2020-01-02"), 
-                    by = 1, length.out = 5), times = 2),
+  time_value = rep(seq(as.Date("2020-01-01"),
+    by = 1, length.out = 5
+  ), times = 2),
+  version = rep(seq(as.Date("2020-01-02"),
+    by = 1, length.out = 5
+  ), times = 2),
   value = rnorm(10, mean = 2, sd = 1)
 )
 
-toy_epi_archive <- tib \%>\% as_epi_archive(geo_type = "state", 
-                                          time_type = "day")
-toy_epi_archive 
+toy_epi_archive <- tib \%>\% as_epi_archive(
+  geo_type = "state",
+  time_type = "day"
+)
+toy_epi_archive
 
 # Ex. with an additional key for county
-df <- data.frame (geo_value  = c(replicate(2, "ca"), replicate(2, "fl")),
-                 county = c(1, 3, 2, 5),
-                 time_value = c("2020-06-01",
-                                "2020-06-02",
-                                "2020-06-01",
-                                "2020-06-02"),
-                 version = c("2020-06-02",
-                             "2020-06-03",
-                             "2020-06-02",
-                             "2020-06-03"),
-                 cases = c(1, 2, 3, 4),
-                 cases_rate = c(0.01, 0.02, 0.01, 0.05))
+df <- data.frame(
+  geo_value = c(replicate(2, "ca"), replicate(2, "fl")),
+  county = c(1, 3, 2, 5),
+  time_value = c(
+    "2020-06-01",
+    "2020-06-02",
+    "2020-06-01",
+    "2020-06-02"
+  ),
+  version = c(
+    "2020-06-02",
+    "2020-06-03",
+    "2020-06-02",
+    "2020-06-03"
+  ),
+  cases = c(1, 2, 3, 4),
+  cases_rate = c(0.01, 0.02, 0.01, 0.05)
+)
 
-x <- df \%>\% as_epi_archive(geo_type = "state",
-                           time_type = "day",
-                           other_keys = "county")
+x <- df \%>\% as_epi_archive(
+  geo_type = "state",
+  time_type = "day",
+  other_keys = "county"
+)
 }
diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
index 851aed7e..40c0a1c5 100644
--- a/man/as_epi_df.Rd
+++ b/man/as_epi_df.Rd
@@ -76,19 +76,22 @@ the \code{tbl_ts} class is dropped, and any key variables (other than
 
 ex1_input <- tibble::tibble(
   geo_value = rep(c("ca", "fl", "pa"), each = 3),
-  county_code = c("06059","06061","06067",
-                  "12111","12113","12117",
-                  "42101", "42103","42105"),
+  county_code = c(
+    "06059", "06061", "06067",
+    "12111", "12113", "12117",
+    "42101", "42103", "42105"
+  ),
   time_value = rep(seq(as.Date("2020-06-01"), as.Date("2020-06-03"),
-                       by = "day"), length.out = length(geo_value)),
+    by = "day"
+  ), length.out = length(geo_value)),
   value = 1:length(geo_value) + 0.01 * rnorm(length(geo_value))
-) \%>\% 
+) \%>\%
   tsibble::as_tsibble(index = time_value, key = c(geo_value, county_code))
 
 # The `other_keys` metadata (`"county_code"` in this case) is automatically
 # inferred from the `tsibble`'s `key`:
 ex1 <- as_epi_df(x = ex1_input, geo_type = "state", time_type = "day", as_of = "2020-06-03")
-attr(ex1,"metadata")[["other_keys"]]
+attr(ex1, "metadata")[["other_keys"]]
 
 
 
@@ -102,17 +105,21 @@ ex2_input <- tibble::tibble(
   state = rep(c("ca", "fl", "pa"), each = 3), # misnamed
   pol = rep(c("blue", "swing", "swing"), each = 3), # extra key
   reported_date = rep(seq(as.Date("2020-06-01"), as.Date("2020-06-03"),
-                          by = "day"), length.out = length(state)), # misnamed
+    by = "day"
+  ), length.out = length(state)), # misnamed
   value = 1:length(state) + 0.01 * rnorm(length(state))
-) 
+)
 
 print(ex2_input)
 
-ex2 <- ex2_input \%>\% dplyr::rename(geo_value = state, time_value = reported_date) \%>\%
-  as_epi_df(geo_type = "state", as_of = "2020-06-03", 
-            additional_metadata = list(other_keys = "pol")) 
+ex2 <- ex2_input \%>\%
+  dplyr::rename(geo_value = state, time_value = reported_date) \%>\%
+  as_epi_df(
+    geo_type = "state", as_of = "2020-06-03",
+    additional_metadata = list(other_keys = "pol")
+  )
 
-attr(ex2,"metadata")
+attr(ex2, "metadata")
 
 
 
@@ -120,17 +127,18 @@ attr(ex2,"metadata")
 
 ex3_input <- jhu_csse_county_level_subset \%>\%
   dplyr::filter(time_value > "2021-12-01", state_name == "Massachusetts") \%>\%
-  dplyr::slice_tail(n = 6) 
+  dplyr::slice_tail(n = 6)
 
-ex3 <- ex3_input \%>\% 
+ex3 <- ex3_input \%>\%
   tsibble::as_tsibble() \%>\% # needed to add the additional metadata
   # add 2 extra keys
   dplyr::mutate(
-    state = rep("MA",6),
-    pol = rep(c("blue", "swing", "swing"), each = 2)) \%>\% 
-  # the 2 extra keys we added have to be specified in the other_keys 
+    state = rep("MA", 6),
+    pol = rep(c("blue", "swing", "swing"), each = 2)
+  ) \%>\%
+  # the 2 extra keys we added have to be specified in the other_keys
   # component of additional_metadata.
   as_epi_df(additional_metadata = list(other_keys = c("state", "pol")))
 
-attr(ex3,"metadata")
+attr(ex3, "metadata")
 }
diff --git a/man/autoplot.epi_df.Rd b/man/autoplot.epi_df.Rd
index 134a83fe..68aef0c4 100644
--- a/man/autoplot.epi_df.Rd
+++ b/man/autoplot.epi_df.Rd
@@ -43,12 +43,17 @@ share the same color line.}
 \item{.max_facets}{Cut down of the number of facets displayed. Especially
 useful for testing when there are many \code{geo_value}'s or keys.}
 }
+\value{
+A ggplot object
+}
 \description{
 Automatically plot an epi_df
 }
 \examples{
 autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
 autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
-autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
-  .facet_by = "geo_value")
+autoplot(jhu_csse_daily_subset, case_rate_7d_av,
+  .color_by = "none",
+  .facet_by = "geo_value"
+)
 }
diff --git a/man/detect_outlr.Rd b/man/detect_outlr.Rd
index 4aa0b79c..3a793ebf 100644
--- a/man/detect_outlr.Rd
+++ b/man/detect_outlr.Rd
@@ -64,29 +64,43 @@ For convenience, the outlier detection method can be specified (in the
 STL decomposition.
 }
 \examples{
- detection_methods = dplyr::bind_rows(
-   dplyr::tibble(method = "rm",
-          args = list(list(detect_negatives = TRUE,
-                           detection_multiplier = 2.5)),
-          abbr = "rm"),
-   dplyr::tibble(method = "stl",
-          args = list(list(detect_negatives = TRUE,
-                           detection_multiplier = 2.5,
-                           seasonal_period = 7)),
-          abbr = "stl_seasonal"),
-   dplyr::tibble(method = "stl",
-          args = list(list(detect_negatives = TRUE,
-                           detection_multiplier = 2.5,
-                           seasonal_period = NULL)),
-          abbr = "stl_nonseasonal"))
+detection_methods <- dplyr::bind_rows(
+  dplyr::tibble(
+    method = "rm",
+    args = list(list(
+      detect_negatives = TRUE,
+      detection_multiplier = 2.5
+    )),
+    abbr = "rm"
+  ),
+  dplyr::tibble(
+    method = "stl",
+    args = list(list(
+      detect_negatives = TRUE,
+      detection_multiplier = 2.5,
+      seasonal_period = 7
+    )),
+    abbr = "stl_seasonal"
+  ),
+  dplyr::tibble(
+    method = "stl",
+    args = list(list(
+      detect_negatives = TRUE,
+      detection_multiplier = 2.5,
+      seasonal_period = NULL
+    )),
+    abbr = "stl_nonseasonal"
+  )
+)
 
- x <- incidence_num_outlier_example \%>\%
-   dplyr::select(geo_value,time_value,cases) \%>\%
-   as_epi_df() \%>\%
-   group_by(geo_value) \%>\%
-   mutate(outlier_info  = detect_outlr(
-     x = time_value, y = cases,
-     methods = detection_methods,
-     combiner = "median")) \%>\%
-   unnest(outlier_info)
+x <- incidence_num_outlier_example \%>\%
+  dplyr::select(geo_value, time_value, cases) \%>\%
+  as_epi_df() \%>\%
+  group_by(geo_value) \%>\%
+  mutate(outlier_info = detect_outlr(
+    x = time_value, y = cases,
+    methods = detection_methods,
+    combiner = "median"
+  )) \%>\%
+  unnest(outlier_info)
 }
diff --git a/man/detect_outlr_rm.Rd b/man/detect_outlr_rm.Rd
index 3efae55d..0d011619 100644
--- a/man/detect_outlr_rm.Rd
+++ b/man/detect_outlr_rm.Rd
@@ -59,10 +59,11 @@ terms of multiples of the rolling interquartile range (IQR).
 \examples{
 # Detect outliers based on a rolling median
 incidence_num_outlier_example \%>\%
-  dplyr::select(geo_value,time_value,cases) \%>\%
+  dplyr::select(geo_value, time_value, cases) \%>\%
   as_epi_df() \%>\%
   group_by(geo_value) \%>\%
-  mutate(outlier_info  = detect_outlr_rm(
-    x = time_value, y = cases)) \%>\%
+  mutate(outlier_info = detect_outlr_rm(
+    x = time_value, y = cases
+  )) \%>\%
   unnest(outlier_info)
 }
diff --git a/man/detect_outlr_stl.Rd b/man/detect_outlr_stl.Rd
index 7e724a4e..34a550d5 100644
--- a/man/detect_outlr_stl.Rd
+++ b/man/detect_outlr_stl.Rd
@@ -78,11 +78,12 @@ are exactly as in \code{detect_outlr_rm()}.
 \examples{
 # Detects outliers based on a seasonal-trend decomposition using LOESS
 incidence_num_outlier_example \%>\%
-  dplyr::select(geo_value,time_value,cases) \%>\%
+  dplyr::select(geo_value, time_value, cases) \%>\%
   as_epi_df() \%>\%
   group_by(geo_value) \%>\%
-  mutate(outlier_info  = detect_outlr_stl(
+  mutate(outlier_info = detect_outlr_stl(
     x = time_value, y = cases,
-    seasonal_period = 7 )) \%>\% # weekly seasonality for daily data
+    seasonal_period = 7
+  )) \%>\% # weekly seasonality for daily data
   unnest(outlier_info)
 }
diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index f328eb44..6a25b2af 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -100,16 +100,20 @@ are documented in the wrapper function \code{\link[=epix_slide]{epix_slide()}}.
 \examples{
 tib <- tibble::tibble(
   geo_value = rep(c("ca", "hi"), each = 5),
-  time_value = rep(seq(as.Date("2020-01-01"), 
-                       by = 1, length.out = 5), times = 2),
-  version = rep(seq(as.Date("2020-01-02"), 
-                    by = 1, length.out = 5), times = 2),
+  time_value = rep(seq(as.Date("2020-01-01"),
+    by = 1, length.out = 5
+  ), times = 2),
+  version = rep(seq(as.Date("2020-01-02"),
+    by = 1, length.out = 5
+  ), times = 2),
   value = rnorm(10, mean = 2, sd = 1)
 )
 
-toy_epi_archive <- tib \%>\% epi_archive$new(geo_type = "state", 
-                                           time_type = "day")
-toy_epi_archive 
+toy_epi_archive <- tib \%>\% epi_archive$new(
+  geo_type = "state",
+  time_type = "day"
+)
+toy_epi_archive
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/epi_cor.Rd b/man/epi_cor.Rd
index 6b2279db..fb56073f 100644
--- a/man/epi_cor.Rd
+++ b/man/epi_cor.Rd
@@ -58,30 +58,38 @@ grouping by geo value, time value, or any other variables. See the
 for examples.
 }
 \examples{
- 
+
 # linear association of case and death rates on any given day
-epi_cor(x = jhu_csse_daily_subset, 
-        var1 = case_rate_7d_av, 
-        var2 = death_rate_7d_av, 
-        cor_by = "time_value")
+epi_cor(
+  x = jhu_csse_daily_subset,
+  var1 = case_rate_7d_av,
+  var2 = death_rate_7d_av,
+  cor_by = "time_value"
+)
 
 # correlation of death rates and lagged case rates
-epi_cor(x = jhu_csse_daily_subset, 
-        var1 = case_rate_7d_av, 
-        var2 = death_rate_7d_av, 
-        cor_by = time_value, 
-        dt1 = -2)
+epi_cor(
+  x = jhu_csse_daily_subset,
+  var1 = case_rate_7d_av,
+  var2 = death_rate_7d_av,
+  cor_by = time_value,
+  dt1 = -2
+)
 
-# correlation grouped by location 
-epi_cor(x = jhu_csse_daily_subset, 
-        var1 = case_rate_7d_av, 
-        var2 = death_rate_7d_av, 
-        cor_by = geo_value)
+# correlation grouped by location
+epi_cor(
+  x = jhu_csse_daily_subset,
+  var1 = case_rate_7d_av,
+  var2 = death_rate_7d_av,
+  cor_by = geo_value
+)
 
 # correlation grouped by location and incorporates lagged cases rates
-epi_cor(x = jhu_csse_daily_subset, 
-        var1 = case_rate_7d_av, 
-        var2 = death_rate_7d_av, 
-        cor_by = geo_value, 
-        dt1 = -2)
+epi_cor(
+  x = jhu_csse_daily_subset,
+  var1 = case_rate_7d_av,
+  var2 = death_rate_7d_av,
+  cor_by = geo_value,
+  dt1 = -2
+)
 }
diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd
index 33c3a7fb..668be9ff 100644
--- a/man/epi_slide.Rd
+++ b/man/epi_slide.Rd
@@ -156,9 +156,9 @@ through the \code{new_col_name} argument.
 # slide a 7-day trailing average formula on cases
 jhu_csse_daily_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide(cases_7dav = mean(cases), before = 6) \%>\% 
+  epi_slide(cases_7dav = mean(cases), before = 6) \%>\%
   # rmv a nonessential var. to ensure new col is printed
-  dplyr::select(-death_rate_7d_av) 
+  dplyr::select(-death_rate_7d_av)
 
 # slide a 7-day leading average
 jhu_csse_daily_subset \%>\%
@@ -170,21 +170,25 @@ jhu_csse_daily_subset \%>\%
 # slide a 7-day centre-aligned average
 jhu_csse_daily_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide(cases_7dav = mean(cases), before = 3, after = 3) \%>\% 
+  epi_slide(cases_7dav = mean(cases), before = 3, after = 3) \%>\%
   # rmv a nonessential var. to ensure new col is printed
-  dplyr::select(-death_rate_7d_av) 
+  dplyr::select(-death_rate_7d_av)
 
 # slide a 14-day centre-aligned average
 jhu_csse_daily_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide(cases_7dav = mean(cases), before = 6, after = 7) \%>\% 
+  epi_slide(cases_7dav = mean(cases), before = 6, after = 7) \%>\%
   # rmv a nonessential var. to ensure new col is printed
-  dplyr::select(-death_rate_7d_av) 
+  dplyr::select(-death_rate_7d_av)
 
 # nested new columns
 jhu_csse_daily_subset \%>\%
   group_by(geo_value) \%>\%
-  epi_slide(a = data.frame(cases_2dav = mean(cases),
-                           cases_2dma = mad(cases)),
-            before = 1, as_list_col = TRUE)
+  epi_slide(
+    a = data.frame(
+      cases_2dav = mean(cases),
+      cases_2dma = mad(cases)
+    ),
+    before = 1, as_list_col = TRUE
+  )
 }
diff --git a/man/epix_as_of.Rd b/man/epix_as_of.Rd
index 51884597..9a0a53ce 100644
--- a/man/epix_as_of.Rd
+++ b/man/epix_as_of.Rd
@@ -55,14 +55,18 @@ in the future.
 }
 \examples{
 # warning message of data latency shown
-epix_as_of(x = archive_cases_dv_subset,
-           max_version = max(archive_cases_dv_subset$DT$version))
+epix_as_of(
+  x = archive_cases_dv_subset,
+  max_version = max(archive_cases_dv_subset$DT$version)
+)
 
 
 range(archive_cases_dv_subset$DT$version) # 2020-06-02 -- 2021-12-01
 
-epix_as_of(x = archive_cases_dv_subset,
-           max_version = as.Date("2020-06-12"))
+epix_as_of(
+  x = archive_cases_dv_subset,
+  max_version = as.Date("2020-06-12")
+)
 
 # When fetching a snapshot as of the latest version with update data in the
 # archive, a warning is issued by default, as this update data might not yet
@@ -72,10 +76,15 @@ epix_as_of(x = archive_cases_dv_subset,
 # based on database queries, the latest available update might still be
 # subject to change, but previous versions should be finalized). We can
 # muffle such warnings with the following pattern:
-withCallingHandlers({
-  epix_as_of(x = archive_cases_dv_subset,
-             max_version = max(archive_cases_dv_subset$DT$version))
-}, epiprocess__snapshot_as_of_clobberable_version = function(wrn) invokeRestart("muffleWarning"))
+withCallingHandlers(
+  {
+    epix_as_of(
+      x = archive_cases_dv_subset,
+      max_version = max(archive_cases_dv_subset$DT$version)
+    )
+  },
+  epiprocess__snapshot_as_of_clobberable_version = function(wrn) invokeRestart("muffleWarning")
+)
 # Since R 4.0, there is a `globalCallingHandlers` function that can be used
 # to globally toggle these warnings.
 
diff --git a/man/epix_merge.Rd b/man/epix_merge.Rd
index 09f67fa2..53dea071 100644
--- a/man/epix_merge.Rd
+++ b/man/epix_merge.Rd
@@ -60,13 +60,13 @@ be clobbered in either input archive.
 \examples{
 # create two example epi_archive datasets
 x <- archive_cases_dv_subset$DT \%>\%
-  dplyr::select(geo_value,time_value,version,case_rate_7d_av) \%>\%
-  as_epi_archive(compactify=TRUE)
+  dplyr::select(geo_value, time_value, version, case_rate_7d_av) \%>\%
+  as_epi_archive(compactify = TRUE)
 y <- archive_cases_dv_subset$DT \%>\%
-  dplyr::select(geo_value,time_value,version,percent_cli) \%>\%
-  as_epi_archive(compactify=TRUE)
+  dplyr::select(geo_value, time_value, version, percent_cli) \%>\%
+  as_epi_archive(compactify = TRUE)
 # merge results stored in a third object:
-xy = epix_merge(x, y)
+xy <- epix_merge(x, y)
 # vs. mutating x to hold the merge result:
 x$merge(y)
 
diff --git a/man/epix_slide.Rd b/man/epix_slide.Rd
index d94460af..3ac55a18 100644
--- a/man/epix_slide.Rd
+++ b/man/epix_slide.Rd
@@ -193,17 +193,20 @@ library(dplyr)
 
 # Reference time points for which we want to compute slide values:
 ref_time_values <- seq(as.Date("2020-06-01"),
-                       as.Date("2020-06-15"),
-                       by = "1 day")
+  as.Date("2020-06-15"),
+  by = "1 day"
+)
 
 # A simple (but not very useful) example (see the archive vignette for a more
 # realistic one):
 archive_cases_dv_subset \%>\%
   group_by(geo_value) \%>\%
-  epix_slide(f = ~ mean(.x$case_rate_7d_av),
-             before = 2,
-             ref_time_values = ref_time_values,
-             new_col_name = 'case_rate_7d_av_recent_av') \%>\%
+  epix_slide(
+    f = ~ mean(.x$case_rate_7d_av),
+    before = 2,
+    ref_time_values = ref_time_values,
+    new_col_name = "case_rate_7d_av_recent_av"
+  ) \%>\%
   ungroup()
 # We requested time windows that started 2 days before the corresponding time
 # values. The actual number of `time_value`s in each computation depends on
@@ -221,23 +224,24 @@ archive_cases_dv_subset \%>\%
 # Examining characteristics of the data passed to each computation with
 # `all_versions=FALSE`.
 archive_cases_dv_subset \%>\%
- group_by(geo_value) \%>\%
- epix_slide(
-   function(x, gk, rtv) {
-     tibble(
-       time_range = if(nrow(x) == 0L) {
-         "0 `time_value`s"
-       } else {
-         sprintf("\%s -- \%s", min(x$time_value), max(x$time_value))
-       },
-       n = nrow(x),
-       class1 = class(x)[[1L]]
-     )
-   },
-   before = 5, all_versions = FALSE,
-   ref_time_values = ref_time_values, names_sep=NULL) \%>\%
- ungroup() \%>\%
- arrange(geo_value, time_value)
+  group_by(geo_value) \%>\%
+  epix_slide(
+    function(x, gk, rtv) {
+      tibble(
+        time_range = if (nrow(x) == 0L) {
+          "0 `time_value`s"
+        } else {
+          sprintf("\%s -- \%s", min(x$time_value), max(x$time_value))
+        },
+        n = nrow(x),
+        class1 = class(x)[[1L]]
+      )
+    },
+    before = 5, all_versions = FALSE,
+    ref_time_values = ref_time_values, names_sep = NULL
+  ) \%>\%
+  ungroup() \%>\%
+  arrange(geo_value, time_value)
 
 # --- Advanced: ---
 
@@ -259,7 +263,7 @@ archive_cases_dv_subset \%>\%
           toString(min(x$DT$version))
         },
         versions_end = x$versions_end,
-        time_range = if(nrow(x$DT) == 0L) {
+        time_range = if (nrow(x$DT) == 0L) {
           "0 `time_value`s"
         } else {
           sprintf("\%s -- \%s", min(x$DT$time_value), max(x$DT$time_value))
@@ -269,7 +273,8 @@ archive_cases_dv_subset \%>\%
       )
     },
     before = 5, all_versions = TRUE,
-    ref_time_values = ref_time_values, names_sep=NULL) \%>\%
+    ref_time_values = ref_time_values, names_sep = NULL
+  ) \%>\%
   ungroup() \%>\%
   # Focus on one geo_value so we can better see the columns above:
   filter(geo_value == "ca") \%>\%
diff --git a/man/group_by.epi_archive.Rd b/man/group_by.epi_archive.Rd
index aee0a07b..5e867bf3 100644
--- a/man/group_by.epi_archive.Rd
+++ b/man/group_by.epi_archive.Rd
@@ -93,7 +93,7 @@ to \code{group_by_drop_default.default} (but there is a dedicated method for
 }
 \examples{
 
-grouped_archive = archive_cases_dv_subset \%>\% group_by(geo_value)
+grouped_archive <- archive_cases_dv_subset \%>\% group_by(geo_value)
 
 # `print` for metadata and method listing:
 grouped_archive \%>\% print()
@@ -102,10 +102,12 @@ grouped_archive \%>\% print()
 
 archive_cases_dv_subset \%>\%
   group_by(geo_value) \%>\%
-  epix_slide(f = ~ mean(.x$case_rate_7d_av),
-             before = 2,
-             ref_time_values = as.Date("2020-06-11") + 0:2,
-             new_col_name = 'case_rate_3d_av') \%>\%
+  epix_slide(
+    f = ~ mean(.x$case_rate_7d_av),
+    before = 2,
+    ref_time_values = as.Date("2020-06-11") + 0:2,
+    new_col_name = "case_rate_3d_av"
+  ) \%>\%
   ungroup()
 
 # -----------------------------------------------------------------
@@ -113,34 +115,42 @@ archive_cases_dv_subset \%>\%
 # Advanced: some other features of dplyr grouping are implemented:
 
 library(dplyr)
-toy_archive =
+toy_archive <-
   tribble(
-    ~geo_value,  ~age_group,  ~time_value,     ~version, ~value,
-          "us",     "adult", "2000-01-01", "2000-01-02",    121,
-          "us", "pediatric", "2000-01-02", "2000-01-03",      5, # (addition)
-          "us",     "adult", "2000-01-01", "2000-01-03",    125, # (revision)
-          "us",     "adult", "2000-01-02", "2000-01-03",    130  # (addition)
+    ~geo_value, ~age_group, ~time_value, ~version, ~value,
+    "us", "adult", "2000-01-01", "2000-01-02", 121,
+    "us", "pediatric", "2000-01-02", "2000-01-03", 5, # (addition)
+    "us", "adult", "2000-01-01", "2000-01-03", 125, # (revision)
+    "us", "adult", "2000-01-02", "2000-01-03", 130 # (addition)
+  ) \%>\%
+  mutate(
+    age_group = ordered(age_group, c("pediatric", "adult")),
+    time_value = as.Date(time_value),
+    version = as.Date(version)
   ) \%>\%
-  mutate(age_group = ordered(age_group, c("pediatric", "adult")),
-         time_value = as.Date(time_value),
-         version = as.Date(version)) \%>\%
   as_epi_archive(other_keys = "age_group")
 
 # The following are equivalent:
 toy_archive \%>\% group_by(geo_value, age_group)
-toy_archive \%>\% group_by(geo_value) \%>\% group_by(age_group, .add=TRUE)
-grouping_cols = c("geo_value", "age_group")
+toy_archive \%>\%
+  group_by(geo_value) \%>\%
+  group_by(age_group, .add = TRUE)
+grouping_cols <- c("geo_value", "age_group")
 toy_archive \%>\% group_by(across(all_of(grouping_cols)))
 
 # And these are equivalent:
 toy_archive \%>\% group_by(geo_value)
-toy_archive \%>\% group_by(geo_value, age_group) \%>\% ungroup(age_group)
+toy_archive \%>\%
+  group_by(geo_value, age_group) \%>\%
+  ungroup(age_group)
 
 # To get the grouping variable names as a `list` of `name`s (a.k.a. symbols):
-toy_archive \%>\% group_by(geo_value) \%>\% groups()
+toy_archive \%>\%
+  group_by(geo_value) \%>\%
+  groups()
 
 toy_archive \%>\%
-  group_by(geo_value, age_group, .drop=FALSE) \%>\%
+  group_by(geo_value, age_group, .drop = FALSE) \%>\%
   epix_slide(f = ~ sum(.x$value), before = 20) \%>\%
   ungroup()
 
diff --git a/man/growth_rate.Rd b/man/growth_rate.Rd
index 203d5d7d..7a3f1151 100644
--- a/man/growth_rate.Rd
+++ b/man/growth_rate.Rd
@@ -136,12 +136,12 @@ user.
 
 \examples{
 # COVID cases growth rate by state using default method relative change
-jhu_csse_daily_subset \%>\% 
-  group_by(geo_value) \%>\% 
-  mutate(cases_gr = growth_rate(x = time_value,  y = cases))
+jhu_csse_daily_subset \%>\%
+  group_by(geo_value) \%>\%
+  mutate(cases_gr = growth_rate(x = time_value, y = cases))
 
 # Log scale, degree 4 polynomial and 6-fold cross validation
-jhu_csse_daily_subset \%>\% 
-  group_by(geo_value) \%>\% 
-  mutate(gr_poly = growth_rate( x = time_value, y = cases, log_scale = TRUE,  ord = 4,  k = 6))
+jhu_csse_daily_subset \%>\%
+  group_by(geo_value) \%>\%
+  mutate(gr_poly = growth_rate(x = time_value, y = cases, log_scale = TRUE, ord = 4, k = 6))
 }
diff --git a/man/is_epi_archive.Rd b/man/is_epi_archive.Rd
index 5b133004..2beb3a8c 100644
--- a/man/is_epi_archive.Rd
+++ b/man/is_epi_archive.Rd
@@ -25,9 +25,9 @@ is_epi_archive(archive_cases_dv_subset) # TRUE
 # By default, grouped_epi_archives don't count as epi_archives, as they may
 # support a different set of operations from regular `epi_archives`. This
 # behavior can be controlled by `grouped_okay`.
-grouped_archive = archive_cases_dv_subset$group_by(geo_value)
+grouped_archive <- archive_cases_dv_subset$group_by(geo_value)
 is_epi_archive(grouped_archive) # FALSE
-is_epi_archive(grouped_archive, grouped_okay=TRUE) # TRUE
+is_epi_archive(grouped_archive, grouped_okay = TRUE) # TRUE
 
 }
 \seealso{
diff --git a/man/epi_keys.Rd b/man/key_colnames.Rd
similarity index 76%
rename from man/epi_keys.Rd
rename to man/key_colnames.Rd
index 8026fc14..fbaa3c11 100644
--- a/man/epi_keys.Rd
+++ b/man/key_colnames.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/epi_keys.R
-\name{epi_keys}
-\alias{epi_keys}
+% Please edit documentation in R/key_colnames.R
+\name{key_colnames}
+\alias{key_colnames}
 \title{Grab any keys associated to an epi_df}
 \usage{
-epi_keys(x, ...)
+key_colnames(x, ...)
 }
 \arguments{
 \item{x}{a data.frame, tibble, or epi_df}

From 3c68f1db0676b48197c38b1806443402074a97f0 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Fri, 19 Jan 2024 15:34:08 -0800
Subject: [PATCH 11/27] pkgdown fix

---
 _pkgdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 1d9b1955..1b11ee6f 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -91,4 +91,4 @@ reference:
           - max_version_with_row_in
           - next_after
           - guess_period
-          - epi_keys
+          - key_colnames

From f6464c02c6406a68f4cbffe4043c5cdb288f2303 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Thu, 25 Jan 2024 08:43:51 -0800
Subject: [PATCH 12/27] bugfix: add missing arg_is_numeric

---
 R/utils-arg.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/R/utils-arg.R b/R/utils-arg.R
index dca21646..b48a3642 100644
--- a/R/utils-arg.R
+++ b/R/utils-arg.R
@@ -24,6 +24,17 @@ arg_is_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
   )
 }
 
+arg_is_numeric <- function(..., allow_null = FALSE) {
+  handle_arg_list(
+    ...,
+    tests = function(name, value) {
+      if (!(is.numeric(value) | (is.null(value) & allow_null))) {
+        cli::cli_abort("All {.val {name}} must numeric.")
+      }
+    }
+  )
+}
+
 arg_is_int <- function(..., allow_null = FALSE) {
   arg_is_numeric(..., allow_null = allow_null)
   handle_arg_list(

From b3d876d85a077fe606700ca3bd9643458bac5d92 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Thu, 25 Jan 2024 09:05:37 -0800
Subject: [PATCH 13/27] bugfix: remove ability to plot non-numeric vars

---
 R/autoplot.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/autoplot.R b/R/autoplot.R
index bcd0b54d..c193e01f 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -32,6 +32,12 @@
 #'   .color_by = "none",
 #'   .facet_by = "geo_value"
 #' )
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+#'   .base_color = "red", .facet_by = "geo_value")
+#' 
+#' # .base_color specification won't have any effect due .color_by default
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av,
+#'   .base_color = "red", .facet_by = "geo_value") 
 autoplot.epi_df <- function(
     object, ...,
     .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
@@ -51,6 +57,7 @@ autoplot.epi_df <- function(
 
   # --- check for numeric variables
   allowed <- purrr::map_lgl(object[non_key_cols], is.numeric)
+  allowed <- allowed[allowed]
   if (length(allowed) == 0) {
     cli::cli_abort("No numeric variables were available to plot automatically.")
   }

From b1a2eef72b6898e08dcff0d33705f65e4d7901ea Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Thu, 25 Jan 2024 09:09:21 -0800
Subject: [PATCH 14/27] remove unused

---
 R/key_colnames.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/key_colnames.R b/R/key_colnames.R
index 91be7ab6..158c5a86 100644
--- a/R/key_colnames.R
+++ b/R/key_colnames.R
@@ -38,7 +38,3 @@ kill_time_value <- function(v) {
   arg_is_chr(v)
   v[v != "time_value"]
 }
-
-key_colnames_only <- function(x, ...) {
-  kill_time_value(key_colnames(x, ...))
-}

From d30fc8542f5f7e11a9b19055200e41c42458f424 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Thu, 25 Jan 2024 09:17:03 -0800
Subject: [PATCH 15/27] redocument

---
 man/autoplot.epi_df.Rd | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/man/autoplot.epi_df.Rd b/man/autoplot.epi_df.Rd
index 68aef0c4..df30528e 100644
--- a/man/autoplot.epi_df.Rd
+++ b/man/autoplot.epi_df.Rd
@@ -56,4 +56,10 @@ autoplot(jhu_csse_daily_subset, case_rate_7d_av,
   .color_by = "none",
   .facet_by = "geo_value"
 )
+autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+  .base_color = "red", .facet_by = "geo_value")
+
+# .base_color specification won't have any effect due .color_by default
+autoplot(jhu_csse_daily_subset, case_rate_7d_av,
+  .base_color = "red", .facet_by = "geo_value") 
 }

From f2927136333e46ee6448463f8903fe5d1f3c930d Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 25 Jan 2024 15:26:06 -0500
Subject: [PATCH 16/27] class warnings and errors

---
 R/autoplot.R  | 12 ++++++++----
 R/utils-arg.R | 31 +++++++++++++++++++++++--------
 2 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/R/autoplot.R b/R/autoplot.R
index c193e01f..ef0878a1 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -59,25 +59,29 @@ autoplot.epi_df <- function(
   allowed <- purrr::map_lgl(object[non_key_cols], is.numeric)
   allowed <- allowed[allowed]
   if (length(allowed) == 0) {
-    cli::cli_abort("No numeric variables were available to plot automatically.")
+    cli::cli_abort("No numeric variables were available to plot automatically.",
+      class = "epiprocess__no_numeric_vars_available")
   }
   vars <- tidyselect::eval_select(rlang::expr(c(...)), object)
   if (rlang::is_empty(vars)) { # find them automatically if unspecified
     vars <- tidyselect::eval_select(names(allowed)[1], object)
     cli::cli_warn(
-      "Plot variable was unspecified. Automatically selecting {.var {names(allowed)[1]}}."
+      "Plot variable was unspecified. Automatically selecting {.var {names(allowed)[1]}}.",
+      class = "epiprocess__unspecified_plot_var"
     )
   } else { # if variables were specified, ensure that they are numeric
     ok <- names(vars) %in% names(allowed)
     if (!any(ok)) {
       cli::cli_abort(
-        "None of the requested variables {.var {names(vars)}} are numeric."
+        "None of the requested variables {.var {names(vars)}} are numeric.",
+        class = "epiprocess__all_requested_vars_not_numeric"
       )
     } else if (!all(ok)) {
       cli::cli_warn(c(
         "Only the requested variables {.var {names(vars)[ok]}} are numeric.",
         i = "`autoplot()` cannot display {.var {names(vars)[!ok]}}."
-      ))
+      ),
+      class = "epiprocess__some_requested_vars_not_numeric")
       vars <- vars[ok]
     }
   }
diff --git a/R/utils-arg.R b/R/utils-arg.R
index b48a3642..dc761e55 100644
--- a/R/utils-arg.R
+++ b/R/utils-arg.R
@@ -11,12 +11,15 @@ arg_is_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
     ...,
     tests = function(name, value) {
       if (length(value) > 1 | (!allow_null & length(value) == 0)) {
-        cli::cli_abort("Argument {.val {name}} must be of length 1.")
+        cli::cli_abort("Argument {.val {name}} must be of length 1.",
+          class = "epiprocess__value_not_length_1"
+        )
       }
       if (!is.null(value)) {
         if (is.na(value) & !allow_na) {
           cli::cli_abort(
-            "Argument {.val {name}} must not be a missing value ({.val {NA}})."
+            "Argument {.val {name}} must not be a missing value ({.val {NA}}).",
+            class = "epiprocess__value_is_na"
           )
         }
       }
@@ -29,7 +32,9 @@ arg_is_numeric <- function(..., allow_null = FALSE) {
     ...,
     tests = function(name, value) {
       if (!(is.numeric(value) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must numeric.")
+        cli::cli_abort("All {.val {name}} must be numeric.",
+          class = "epiprocess__value_is_null_or_not_numeric"
+        )
       }
     }
   )
@@ -41,7 +46,9 @@ arg_is_int <- function(..., allow_null = FALSE) {
     ...,
     tests = function(name, value) {
       if (!(all(value %% 1 == 0) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must be whole positive number(s).")
+        cli::cli_abort("All {.val {name}} must be whole positive number(s).",
+          class = "epiprocess__some_decimal_or_negative_elements"
+        )
       }
     }
   )
@@ -52,16 +59,24 @@ arg_is_chr <- function(..., allow_null = FALSE, allow_na = FALSE, allow_empty =
     ...,
     tests = function(name, value) {
       if (is.null(value) & !allow_null) {
-        cli::cli_abort("Argument {.val {name}} may not be `NULL`.")
+        cli::cli_abort("Argument {.val {name}} may not be `NULL`.",
+          class = "epiprocess__value_is_null"
+        )
       }
       if (any(is.na(value)) & !allow_na) {
-        cli::cli_abort("Argument {.val {name}} must not contain any missing values ({.val {NA}}).")
+        cli::cli_abort("Argument {.val {name}} must not contain any missing values ({.val {NA}}).",
+          class = "epiprocess__some_na_elements"
+        )
       }
       if (!is.null(value) & (length(value) == 0L & !allow_empty)) {
-        cli::cli_abort("Argument {.val {name}} must have length > 0.")
+        cli::cli_abort("Argument {.val {name}} must have length > 0.",
+          class = "epiprocess__value_length_0"
+        )
       }
       if (!(is.character(value) | is.null(value) | all(is.na(value)))) {
-        cli::cli_abort("Argument {.val {name}} must be of character type.")
+        cli::cli_abort("Argument {.val {name}} must be of character type.",
+          class = "epiprocess__not_character_type"
+        )
       }
     }
   )

From 42da7860f4990dcaee5b4bf1ed7af7663db33bcf Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 25 Jan 2024 16:11:42 -0500
Subject: [PATCH 17/27] test autoplot warnings and errors

---
 tests/testthat/test-autoplot.R | 87 ++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 tests/testthat/test-autoplot.R

diff --git a/tests/testthat/test-autoplot.R b/tests/testthat/test-autoplot.R
new file mode 100644
index 00000000..ba3f8d53
--- /dev/null
+++ b/tests/testthat/test-autoplot.R
@@ -0,0 +1,87 @@
+library(dplyr)
+
+d <- as.Date("2020-01-01")
+
+raw_df_chr <- dplyr::bind_rows(
+  dplyr::tibble(geo_value = "ak", time_value = d + 1:5, value = "a"),
+  dplyr::tibble(geo_value = "al", time_value = d + 1:5, value = "d")
+)
+ungrouped_chr <- as_epi_df(raw_df_chr, as_of = d + 6)
+grouped_chr <- ungrouped_chr %>%
+  group_by(geo_value)
+
+raw_df_num <- dplyr::bind_rows(
+  dplyr::tibble(geo_value = "ak", time_value = d + 1:5, value = 11:15),
+  dplyr::tibble(geo_value = "al", time_value = d + 1:5, value = 1:5)
+)
+ungrouped_num <- as_epi_df(raw_df_num, as_of = d + 6)
+grouped_num <- ungrouped_num %>%
+  group_by(geo_value)
+
+test_that("autoplot fails if no non-key columns are numeric", {
+  expect_error(autoplot(ungrouped_chr),
+    class = "epiprocess__no_numeric_vars_available"
+  )
+
+  # Multiple non-numeric columns
+  testdf <- mutate(ungrouped_chr, value2 = "d")
+  expect_error(autoplot(testdf),
+    class = "epiprocess__no_numeric_vars_available"
+  )
+
+  expect_error(autoplot(grouped_chr),
+    class = "epiprocess__no_numeric_vars_available"
+  )
+
+  # A numeric column is available, but is a key not a value.
+  testdf <- mutate(raw_df_chr, key1 = c(1:5, 5:9)) %>%
+    as_tsibble(index = time_value, key = c(geo_value, key1)) %>%
+    as_epi_df(as_of = d + 6)
+  expect_error(autoplot(testdf),
+    class = "epiprocess__no_numeric_vars_available"
+  )
+})
+
+test_that("autoplot warns when a variable is not specified, and lists the auto-selected column", {
+  expect_warning(autoplot(ungrouped_num),
+    regexp = ".*selecting `value`[.]",
+    class = "epiprocess__unspecified_plot_var"
+  )
+
+  expect_warning(autoplot(grouped_num),
+    regexp = ".*selecting `value`[.]",
+    class = "epiprocess__unspecified_plot_var"
+  )
+})
+
+test_that("autoplot errors when all specified columns are not numeric, and lists column names", {
+  expect_error(autoplot(ungrouped_chr, value),
+    regexp = ".*value.*",
+    class = "epiprocess__all_requested_vars_not_numeric"
+  )
+
+  testdf <- mutate(ungrouped_chr, value2 = "d")
+  expect_error(autoplot(testdf, value, value2),
+    regexp = ".*variables `value` and `value2` are.*",
+    class = "epiprocess__all_requested_vars_not_numeric"
+  )
+
+  expect_error(autoplot(grouped_chr, value),
+    regexp = ".*variables `value` are.*",
+    class = "epiprocess__all_requested_vars_not_numeric"
+  )
+})
+
+test_that("autoplot warns when some specified columns are not numeric, and lists column names", {
+  testdf <- mutate(ungrouped_num, value2 = "d")
+  expect_warning(autoplot(testdf, value, value2),
+    regexp = ".*`value` are numeric.*cannot display `value2`.*",
+    class = "epiprocess__some_requested_vars_not_numeric"
+  )
+
+  testdf <- mutate(grouped_num, value2 = "d")
+  expect_warning(autoplot(testdf, value, value2),
+    regexp = ".*`value` are numeric.*cannot display `value2`.*",
+    class = "epiprocess__some_requested_vars_not_numeric"
+  )
+})

From 7cd1d258b1293e071c5186323d2d2d5eb3f9e146 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 25 Jan 2024 16:28:33 -0500
Subject: [PATCH 18/27] raise 'plot automatically' error only when dots are
 empty because user didn't pass col names

---
 R/autoplot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/autoplot.R b/R/autoplot.R
index ef0878a1..d5fe871f 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -58,7 +58,7 @@ autoplot.epi_df <- function(
   # --- check for numeric variables
   allowed <- purrr::map_lgl(object[non_key_cols], is.numeric)
   allowed <- allowed[allowed]
-  if (length(allowed) == 0) {
+  if (length(allowed) == 0 && rlang::dots_n(...) == 0L) {
     cli::cli_abort("No numeric variables were available to plot automatically.",
       class = "epiprocess__no_numeric_vars_available")
   }

From 9409ae7730c6e71505b57d0e170677ab70cd5b07 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 25 Jan 2024 16:41:17 -0500
Subject: [PATCH 19/27] wrap cols list in all_of to suppress warning

Using an external vector in selections was deprecated in tidyselect 1.1.0.
i Please use `all_of()` or `any_of()` instead.
  # Was:
  data %>% select(geo_and_other_keys)

  # Now:
  data %>% select(all_of(geo_and_other_keys))
---
 R/autoplot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/autoplot.R b/R/autoplot.R
index d5fe871f..34bf55e0 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -88,7 +88,7 @@ autoplot.epi_df <- function(
 
   # --- create a viable df to plot
   pos <- tidyselect::eval_select(
-    rlang::expr(c("time_value", geo_and_other_keys, names(vars))), object
+    rlang::expr(c("time_value", tidyselect::all_of(geo_and_other_keys), names(vars))), object
   )
   if (length(vars) > 1) {
     object <- tidyr::pivot_longer(

From 39f3704c968c6db223d4947db1bf0957684be920 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 26 Jan 2024 11:56:39 -0500
Subject: [PATCH 20/27] check int positive

---
 R/utils-arg.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils-arg.R b/R/utils-arg.R
index dc761e55..85331dd6 100644
--- a/R/utils-arg.R
+++ b/R/utils-arg.R
@@ -45,7 +45,7 @@ arg_is_int <- function(..., allow_null = FALSE) {
   handle_arg_list(
     ...,
     tests = function(name, value) {
-      if (!(all(value %% 1 == 0) | (is.null(value) & allow_null))) {
+      if (!( (all(value %% 1 == 0) && all(value > 0)) | (is.null(value) & allow_null))) {
         cli::cli_abort("All {.val {name}} must be whole positive number(s).",
           class = "epiprocess__some_decimal_or_negative_elements"
         )

From 2e301ad568459976f8de63085efc60a64f7dd5bd Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 25 Jan 2024 17:42:29 -0500
Subject: [PATCH 21/27] test utils-arg

---
 tests/testthat/test-utils-arg.R | 80 +++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 tests/testthat/test-utils-arg.R

diff --git a/tests/testthat/test-utils-arg.R b/tests/testthat/test-utils-arg.R
new file mode 100644
index 00000000..ab29e061
--- /dev/null
+++ b/tests/testthat/test-utils-arg.R
@@ -0,0 +1,80 @@
+test_that("arg_is_scalar basic behavior", {
+  expect_no_error(arg_is_scalar(d = 1, "a", 2, c = c("1"), a = list(2)))
+
+  expect_error(arg_is_scalar(c(3, 5, 5)),
+    class = "epiprocess__value_not_length_1"
+  )
+
+  expect_no_error(arg_is_scalar(NULL, allow_null = TRUE))
+  expect_error(arg_is_scalar(NULL),
+    class = "epiprocess__value_not_length_1"
+  )
+
+  expect_no_error(arg_is_scalar(NA, allow_na = TRUE))
+  expect_error(arg_is_scalar(NA),
+    class = "epiprocess__value_is_na"
+  )
+})
+
+test_that("arg_is_numeric basic behavior", {
+  expect_no_error(arg_is_numeric(c = 1.25, b = 2:5, 1, c(2.22, 2.12)))
+
+  for (val in list(list(1), "a", list(NULL))) {
+    expect_error(arg_is_numeric(val),
+      class = "epiprocess__value_is_null_or_not_numeric"
+    )
+  }
+
+  expect_no_error(arg_is_numeric(1, c(1.255, 2.33, 3), NULL, allow_null = TRUE))
+  expect_error(arg_is_numeric(1, c(1.255, 2.33, 3), NULL),
+    class = "epiprocess__value_is_null_or_not_numeric"
+  )
+})
+
+test_that("arg_is_int basic behavior", {
+  expect_no_error(arg_is_int(c = 1, 1, 3, b = 2:5))
+  expect_no_error(arg_is_int(NULL, 1, allow_null = TRUE))
+
+  for (val in list(1.25, -(1:3))) {
+    expect_error(arg_is_int(val),
+      class = "epiprocess__some_decimal_or_negative_elements"
+    )
+  }
+})
+
+test_that("arg_is_chr basic behavior", {
+  expect_no_error(arg_is_chr(c = c("a", "value"), d = "a", "d"))
+
+  expect_no_error(arg_is_chr(NULL, allow_null = TRUE)) #
+  for (val in list(NULL)) {
+    expect_error(arg_is_chr(val), #
+      class = "epiprocess__value_is_null"
+    )
+  }
+
+  expect_no_error(arg_is_chr(NA, c(NA, NA, NA), c(NA, "a"), allow_na = TRUE))
+  for (val in list(NA, c(NA, NA, NA), c(NA, "a"))) {
+    expect_error(arg_is_chr(val),
+      class = "epiprocess__some_na_elements"
+    )
+  }
+
+  expect_no_error(arg_is_chr(c("a", "value"), character(0), list(), allow_empty = TRUE))
+  for (val in list(character(0), list())) {
+    expect_error(arg_is_chr(val),
+      class = "epiprocess__value_length_0"
+    )
+  }
+
+  for (val in list(c(5, 4), list(5, 4), 5)) {
+    expect_error(arg_is_chr(val),
+      class = "epiprocess__not_character_type"
+    )
+  }
+})
+
+test_that("arg_is_chr_scalar basic behavior", {
+  expect_no_error(arg_is_chr_scalar("a", "b", c = "c"))
+  expect_no_error(arg_is_chr_scalar(c = "c"))
+})
+

From 0bb93e2d1af009ca9acb50bb05456ee62772a938 Mon Sep 17 00:00:00 2001
From: Dmitry Shemetov <dshemetov@ucdavis.edu>
Date: Fri, 26 Jan 2024 10:46:30 -0800
Subject: [PATCH 22/27] refactor: use checkmate checks

---
 DESCRIPTION            |  2 +-
 NAMESPACE              |  4 +++
 R/autoplot.R           | 13 ++++----
 R/key_colnames.R       |  6 ++--
 R/utils-arg.R          | 73 ------------------------------------------
 man/autoplot.epi_df.Rd |  4 +--
 6 files changed, 18 insertions(+), 84 deletions(-)
 delete mode 100644 R/utils-arg.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 211c5212..14437481 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,6 +26,7 @@ Description: This package introduces a common data structure for epidemiological
 License: MIT + file LICENSE
 Copyright: file inst/COPYRIGHTS
 Imports:
+    checkmate,
     cli,
     data.table,
     dplyr (>= 1.0.0),
@@ -86,6 +87,5 @@ Collate:
     'outliers.R'
     'reexports.R'
     'slide.R'
-    'utils-arg.R'
     'utils.R'
     'utils_pipe.R'
diff --git a/NAMESPACE b/NAMESPACE
index a843813d..23140464 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -68,6 +68,10 @@ export(slice)
 export(ungroup)
 export(unnest)
 importFrom(R6,R6Class)
+importFrom(checkmate,anyInfinite)
+importFrom(checkmate,assert)
+importFrom(checkmate,assert_character)
+importFrom(checkmate,assert_int)
 importFrom(data.table,":=")
 importFrom(data.table,address)
 importFrom(data.table,as.data.table)
diff --git a/R/autoplot.R b/R/autoplot.R
index c193e01f..73bcaf0b 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -25,6 +25,8 @@
 #' @return A ggplot object
 #' @export
 #'
+#' @importFrom checkmate assert assert_int anyInfinite assert_character
+#'
 #' @examples
 #' autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
 #' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
@@ -32,12 +34,12 @@
 #'   .color_by = "none",
 #'   .facet_by = "geo_value"
 #' )
-#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+#' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none",
 #'   .base_color = "red", .facet_by = "geo_value")
-#' 
+#'
 #' # .base_color specification won't have any effect due .color_by default
 #' autoplot(jhu_csse_daily_subset, case_rate_7d_av,
-#'   .base_color = "red", .facet_by = "geo_value") 
+#'   .base_color = "red", .facet_by = "geo_value")
 autoplot.epi_df <- function(
     object, ...,
     .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
@@ -47,9 +49,8 @@ autoplot.epi_df <- function(
   .color_by <- match.arg(.color_by)
   .facet_by <- match.arg(.facet_by)
 
-  arg_is_scalar(.max_facets)
-  if (is.finite(.max_facets)) arg_is_int(.max_facets)
-  arg_is_chr_scalar(.base_color)
+  assert(anyInfinite(.max_facets), assert_int(.max_facets), combine = "or")
+  assert_character(.base_color, len = 1)
 
   key_cols <- key_colnames(object)
   non_key_cols <- setdiff(names(object), key_cols)
diff --git a/R/key_colnames.R b/R/key_colnames.R
index 158c5a86..0d34f5f4 100644
--- a/R/key_colnames.R
+++ b/R/key_colnames.R
@@ -15,9 +15,10 @@ key_colnames.default <- function(x, ...) {
   character(0L)
 }
 
+#' @importFrom checkmate assert_character
 #' @export
 key_colnames.data.frame <- function(x, other_keys = character(0L), ...) {
-  arg_is_chr(other_keys, allow_empty = TRUE)
+  assert_character(other_keys)
   nm <- c("time_value", "geo_value", other_keys)
   intersect(nm, colnames(x))
 }
@@ -34,7 +35,8 @@ key_colnames.epi_archive <- function(x, ...) {
   c("time_value", "geo_value", other_keys)
 }
 
+#' @importFrom checkmate assert_character
 kill_time_value <- function(v) {
-  arg_is_chr(v)
+  assert_character(v)
   v[v != "time_value"]
 }
diff --git a/R/utils-arg.R b/R/utils-arg.R
deleted file mode 100644
index b48a3642..00000000
--- a/R/utils-arg.R
+++ /dev/null
@@ -1,73 +0,0 @@
-handle_arg_list <- function(..., tests) {
-  values <- list(...)
-  names <- eval(substitute(alist(...)))
-  names <- purrr::map(names, deparse)
-
-  purrr::walk2(names, values, tests)
-}
-
-arg_is_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (length(value) > 1 | (!allow_null & length(value) == 0)) {
-        cli::cli_abort("Argument {.val {name}} must be of length 1.")
-      }
-      if (!is.null(value)) {
-        if (is.na(value) & !allow_na) {
-          cli::cli_abort(
-            "Argument {.val {name}} must not be a missing value ({.val {NA}})."
-          )
-        }
-      }
-    }
-  )
-}
-
-arg_is_numeric <- function(..., allow_null = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (!(is.numeric(value) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must numeric.")
-      }
-    }
-  )
-}
-
-arg_is_int <- function(..., allow_null = FALSE) {
-  arg_is_numeric(..., allow_null = allow_null)
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (!(all(value %% 1 == 0) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must be whole positive number(s).")
-      }
-    }
-  )
-}
-
-arg_is_chr <- function(..., allow_null = FALSE, allow_na = FALSE, allow_empty = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (is.null(value) & !allow_null) {
-        cli::cli_abort("Argument {.val {name}} may not be `NULL`.")
-      }
-      if (any(is.na(value)) & !allow_na) {
-        cli::cli_abort("Argument {.val {name}} must not contain any missing values ({.val {NA}}).")
-      }
-      if (!is.null(value) & (length(value) == 0L & !allow_empty)) {
-        cli::cli_abort("Argument {.val {name}} must have length > 0.")
-      }
-      if (!(is.character(value) | is.null(value) | all(is.na(value)))) {
-        cli::cli_abort("Argument {.val {name}} must be of character type.")
-      }
-    }
-  )
-}
-
-arg_is_chr_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
-  arg_is_chr(..., allow_null = allow_null, allow_na = allow_na)
-  arg_is_scalar(..., allow_null = allow_null, allow_na = allow_na)
-}
diff --git a/man/autoplot.epi_df.Rd b/man/autoplot.epi_df.Rd
index df30528e..a87bc8ca 100644
--- a/man/autoplot.epi_df.Rd
+++ b/man/autoplot.epi_df.Rd
@@ -56,10 +56,10 @@ autoplot(jhu_csse_daily_subset, case_rate_7d_av,
   .color_by = "none",
   .facet_by = "geo_value"
 )
-autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none", 
+autoplot(jhu_csse_daily_subset, case_rate_7d_av, .color_by = "none",
   .base_color = "red", .facet_by = "geo_value")
 
 # .base_color specification won't have any effect due .color_by default
 autoplot(jhu_csse_daily_subset, case_rate_7d_av,
-  .base_color = "red", .facet_by = "geo_value") 
+  .base_color = "red", .facet_by = "geo_value")
 }

From 8671c0c554fa4e99da96292ad3ef0634e379e612 Mon Sep 17 00:00:00 2001
From: Dmitry Shemetov <dshemetov@ucdavis.edu>
Date: Fri, 26 Jan 2024 15:20:52 -0800
Subject: [PATCH 23/27] refactor: move checkmate imports to one place

---
 R/autoplot.R     | 2 --
 R/epiprocess.R   | 1 +
 R/key_colnames.R | 2 --
 3 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/autoplot.R b/R/autoplot.R
index 73bcaf0b..a6cf99bc 100644
--- a/R/autoplot.R
+++ b/R/autoplot.R
@@ -25,8 +25,6 @@
 #' @return A ggplot object
 #' @export
 #'
-#' @importFrom checkmate assert assert_int anyInfinite assert_character
-#'
 #' @examples
 #' autoplot(jhu_csse_daily_subset, cases, death_rate_7d_av)
 #' autoplot(jhu_csse_daily_subset, case_rate_7d_av, .facet_by = "geo_value")
diff --git a/R/epiprocess.R b/R/epiprocess.R
index bbdcf4f3..79f9635d 100644
--- a/R/epiprocess.R
+++ b/R/epiprocess.R
@@ -4,6 +4,7 @@
 #' measured over space and time, and offers associated utilities to perform
 #' basic signal processing tasks.
 #'
+#' @importFrom checkmate assert assert_character assert_int anyInfinite
 #' @docType package
 #' @name epiprocess
 NULL
diff --git a/R/key_colnames.R b/R/key_colnames.R
index 0d34f5f4..99d8a9ed 100644
--- a/R/key_colnames.R
+++ b/R/key_colnames.R
@@ -15,7 +15,6 @@ key_colnames.default <- function(x, ...) {
   character(0L)
 }
 
-#' @importFrom checkmate assert_character
 #' @export
 key_colnames.data.frame <- function(x, other_keys = character(0L), ...) {
   assert_character(other_keys)
@@ -35,7 +34,6 @@ key_colnames.epi_archive <- function(x, ...) {
   c("time_value", "geo_value", other_keys)
 }
 
-#' @importFrom checkmate assert_character
 kill_time_value <- function(v) {
   assert_character(v)
   v[v != "time_value"]

From 1d45d65d78e495dfa424f6e16918d97fd52135ae Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 29 Jan 2024 11:47:00 -0500
Subject: [PATCH 24/27] utils-arg removed in #410, so no longer need to test

---
 R/utils-arg.R                   | 88 ---------------------------------
 tests/testthat/test-utils-arg.R | 80 ------------------------------
 2 files changed, 168 deletions(-)
 delete mode 100644 R/utils-arg.R
 delete mode 100644 tests/testthat/test-utils-arg.R

diff --git a/R/utils-arg.R b/R/utils-arg.R
deleted file mode 100644
index 85331dd6..00000000
--- a/R/utils-arg.R
+++ /dev/null
@@ -1,88 +0,0 @@
-handle_arg_list <- function(..., tests) {
-  values <- list(...)
-  names <- eval(substitute(alist(...)))
-  names <- purrr::map(names, deparse)
-
-  purrr::walk2(names, values, tests)
-}
-
-arg_is_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (length(value) > 1 | (!allow_null & length(value) == 0)) {
-        cli::cli_abort("Argument {.val {name}} must be of length 1.",
-          class = "epiprocess__value_not_length_1"
-        )
-      }
-      if (!is.null(value)) {
-        if (is.na(value) & !allow_na) {
-          cli::cli_abort(
-            "Argument {.val {name}} must not be a missing value ({.val {NA}}).",
-            class = "epiprocess__value_is_na"
-          )
-        }
-      }
-    }
-  )
-}
-
-arg_is_numeric <- function(..., allow_null = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (!(is.numeric(value) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must be numeric.",
-          class = "epiprocess__value_is_null_or_not_numeric"
-        )
-      }
-    }
-  )
-}
-
-arg_is_int <- function(..., allow_null = FALSE) {
-  arg_is_numeric(..., allow_null = allow_null)
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (!( (all(value %% 1 == 0) && all(value > 0)) | (is.null(value) & allow_null))) {
-        cli::cli_abort("All {.val {name}} must be whole positive number(s).",
-          class = "epiprocess__some_decimal_or_negative_elements"
-        )
-      }
-    }
-  )
-}
-
-arg_is_chr <- function(..., allow_null = FALSE, allow_na = FALSE, allow_empty = FALSE) {
-  handle_arg_list(
-    ...,
-    tests = function(name, value) {
-      if (is.null(value) & !allow_null) {
-        cli::cli_abort("Argument {.val {name}} may not be `NULL`.",
-          class = "epiprocess__value_is_null"
-        )
-      }
-      if (any(is.na(value)) & !allow_na) {
-        cli::cli_abort("Argument {.val {name}} must not contain any missing values ({.val {NA}}).",
-          class = "epiprocess__some_na_elements"
-        )
-      }
-      if (!is.null(value) & (length(value) == 0L & !allow_empty)) {
-        cli::cli_abort("Argument {.val {name}} must have length > 0.",
-          class = "epiprocess__value_length_0"
-        )
-      }
-      if (!(is.character(value) | is.null(value) | all(is.na(value)))) {
-        cli::cli_abort("Argument {.val {name}} must be of character type.",
-          class = "epiprocess__not_character_type"
-        )
-      }
-    }
-  )
-}
-
-arg_is_chr_scalar <- function(..., allow_null = FALSE, allow_na = FALSE) {
-  arg_is_chr(..., allow_null = allow_null, allow_na = allow_na)
-  arg_is_scalar(..., allow_null = allow_null, allow_na = allow_na)
-}
diff --git a/tests/testthat/test-utils-arg.R b/tests/testthat/test-utils-arg.R
deleted file mode 100644
index ab29e061..00000000
--- a/tests/testthat/test-utils-arg.R
+++ /dev/null
@@ -1,80 +0,0 @@
-test_that("arg_is_scalar basic behavior", {
-  expect_no_error(arg_is_scalar(d = 1, "a", 2, c = c("1"), a = list(2)))
-
-  expect_error(arg_is_scalar(c(3, 5, 5)),
-    class = "epiprocess__value_not_length_1"
-  )
-
-  expect_no_error(arg_is_scalar(NULL, allow_null = TRUE))
-  expect_error(arg_is_scalar(NULL),
-    class = "epiprocess__value_not_length_1"
-  )
-
-  expect_no_error(arg_is_scalar(NA, allow_na = TRUE))
-  expect_error(arg_is_scalar(NA),
-    class = "epiprocess__value_is_na"
-  )
-})
-
-test_that("arg_is_numeric basic behavior", {
-  expect_no_error(arg_is_numeric(c = 1.25, b = 2:5, 1, c(2.22, 2.12)))
-
-  for (val in list(list(1), "a", list(NULL))) {
-    expect_error(arg_is_numeric(val),
-      class = "epiprocess__value_is_null_or_not_numeric"
-    )
-  }
-
-  expect_no_error(arg_is_numeric(1, c(1.255, 2.33, 3), NULL, allow_null = TRUE))
-  expect_error(arg_is_numeric(1, c(1.255, 2.33, 3), NULL),
-    class = "epiprocess__value_is_null_or_not_numeric"
-  )
-})
-
-test_that("arg_is_int basic behavior", {
-  expect_no_error(arg_is_int(c = 1, 1, 3, b = 2:5))
-  expect_no_error(arg_is_int(NULL, 1, allow_null = TRUE))
-
-  for (val in list(1.25, -(1:3))) {
-    expect_error(arg_is_int(val),
-      class = "epiprocess__some_decimal_or_negative_elements"
-    )
-  }
-})
-
-test_that("arg_is_chr basic behavior", {
-  expect_no_error(arg_is_chr(c = c("a", "value"), d = "a", "d"))
-
-  expect_no_error(arg_is_chr(NULL, allow_null = TRUE)) #
-  for (val in list(NULL)) {
-    expect_error(arg_is_chr(val), #
-      class = "epiprocess__value_is_null"
-    )
-  }
-
-  expect_no_error(arg_is_chr(NA, c(NA, NA, NA), c(NA, "a"), allow_na = TRUE))
-  for (val in list(NA, c(NA, NA, NA), c(NA, "a"))) {
-    expect_error(arg_is_chr(val),
-      class = "epiprocess__some_na_elements"
-    )
-  }
-
-  expect_no_error(arg_is_chr(c("a", "value"), character(0), list(), allow_empty = TRUE))
-  for (val in list(character(0), list())) {
-    expect_error(arg_is_chr(val),
-      class = "epiprocess__value_length_0"
-    )
-  }
-
-  for (val in list(c(5, 4), list(5, 4), 5)) {
-    expect_error(arg_is_chr(val),
-      class = "epiprocess__not_character_type"
-    )
-  }
-})
-
-test_that("arg_is_chr_scalar basic behavior", {
-  expect_no_error(arg_is_chr_scalar("a", "b", c = "c"))
-  expect_no_error(arg_is_chr_scalar(c = "c"))
-})
-

From a53e98154327a6f4e9583f2c6c9d4b03269f8e54 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Tue, 6 Feb 2024 09:38:39 -0800
Subject: [PATCH 25/27] roxygen note

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c014ad78..7f36ad7c 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -67,7 +67,7 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
     R (>= 2.10)
 URL: https://cmu-delphi.github.io/epiprocess/

From ab96bad5b9ca67ee02aa0e49d630f6795897bf25 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Tue, 6 Feb 2024 09:45:38 -0800
Subject: [PATCH 26/27] redocument

---
 NAMESPACE         |  1 +
 man/epiprocess.Rd | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 23140464..5a1ddfa0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -72,6 +72,7 @@ importFrom(checkmate,anyInfinite)
 importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_int)
+importFrom(cli,cli_inform)
 importFrom(data.table,":=")
 importFrom(data.table,address)
 importFrom(data.table,as.data.table)
diff --git a/man/epiprocess.Rd b/man/epiprocess.Rd
index 9d501aeb..7c3ecd8a 100644
--- a/man/epiprocess.Rd
+++ b/man/epiprocess.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/epiprocess.R
 \docType{package}
 \name{epiprocess}
+\alias{epiprocess-package}
 \alias{epiprocess}
 \title{epiprocess: Tools for basic signal processing in epidemiology}
 \description{
@@ -9,3 +10,36 @@ This package introduces a common data structure for epidemiological data sets
 measured over space and time, and offers associated utilities to perform
 basic signal processing tasks.
 }
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://cmu-delphi.github.io/epiprocess/}
+}
+
+}
+\author{
+\strong{Maintainer}: Ryan Tibshirani \email{ryantibs@cmu.edu}
+
+Authors:
+\itemize{
+  \item Logan Brooks
+  \item Daniel McDonald
+  \item Evan Ray
+}
+
+Other contributors:
+\itemize{
+  \item Jacob Bien [contributor]
+  \item Rafael Catoia [contributor]
+  \item Nat DeFries [contributor]
+  \item Rachel Lobay [contributor]
+  \item Ken Mawer [contributor]
+  \item Chloe You [contributor]
+  \item Quang Nguyen [contributor]
+  \item Dmitry Shemetov [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]
+}
+
+}

From c84d67859fc07abd830011b997f57b596fff08f3 Mon Sep 17 00:00:00 2001
From: "Daniel J. McDonald" <dajmcdon@gmail.com>
Date: Tue, 6 Feb 2024 09:46:49 -0800
Subject: [PATCH 27/27] fix: follow instructions for @docType deprecated error

---
 R/epiprocess.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/epiprocess.R b/R/epiprocess.R
index 79f9635d..254ebd01 100644
--- a/R/epiprocess.R
+++ b/R/epiprocess.R
@@ -5,7 +5,6 @@
 #' basic signal processing tasks.
 #'
 #' @importFrom checkmate assert assert_character assert_int anyInfinite
-#' @docType package
 #' @name epiprocess
-NULL
+"_PACKAGE"
 utils::globalVariables(c(".x", ".group_key", ".ref_time_value"))