From 4a6f7bfb116148221d46b9f28d979b8bf7138816 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Wed, 5 Jun 2024 23:47:14 -0500
Subject: [PATCH 01/19] basic auto-naming

---
 NAMESPACE                    |  1 +
 R/epi_df.R                   | 27 ++++++++++++++++++++++++++-
 man/as_epi_df.Rd             | 10 +++++++++-
 tests/testthat/test-epi_df.R | 16 ++++++++++++++++
 4 files changed, 52 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index b4cafc83..edbaf137 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -100,6 +100,7 @@ importFrom(checkmate,test_subset)
 importFrom(checkmate,vname)
 importFrom(cli,cat_line)
 importFrom(cli,cli_abort)
+importFrom(cli,cli_inform)
 importFrom(cli,cli_vec)
 importFrom(cli,cli_warn)
 importFrom(cli,format_message)
diff --git a/R/epi_df.R b/R/epi_df.R
index f4df1604..6ac1b7db 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -256,9 +256,34 @@ as_epi_df.epi_df <- function(x, ...) {
 #'   (stored in its attributes); if this fails, then the current day-time will
 #'   be used.
 #' @importFrom rlang .data
+#' @importFrom cli cli_inform
 #' @export
 as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
-                             additional_metadata = list(), ...) {
+                             additional_metadata = list(),
+                             substitutions = NULL, ...) {
+  # possible standard substitutions
+  if (!("time_value" %in% names(x))) {
+    if (("forecast_date" %in% names(x)) && ("target_date" %in% names(x))) {
+      cli_abort("both `forecast_date` and `target_date` are present without a `time_value`
+column, so it is ambiguous which to choose as `time_value`.")
+    }
+    name_substitutions <- substitutions %||% c(
+      time_value = "date",
+      time_value = "forecast_date",
+      time_value = "target_date",
+      time_value = "dates",
+      time_value = "time_values",
+      time_value = "forecast_dates",
+      time_value = "target_dates"
+    )
+    x <- tryCatch(x %>% rename(any_of(name_substitutions)),
+      error = function(cond) {
+        cli_abort("There are multiple `time_value` candidate columns.
+Either `rename` on yourself or drop some.")
+      }
+    )
+    cli_inform("inferring `time_value` column.")
+  }
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
       "Columns `geo_value` and `time_value` must be present in `x`."
diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
index 40c0a1c5..82bd8882 100644
--- a/man/as_epi_df.Rd
+++ b/man/as_epi_df.Rd
@@ -12,7 +12,15 @@ as_epi_df(x, ...)
 
 \method{as_epi_df}{epi_df}(x, ...)
 
-\method{as_epi_df}{tbl_df}(x, geo_type, time_type, as_of, additional_metadata = list(), ...)
+\method{as_epi_df}{tbl_df}(
+  x,
+  geo_type,
+  time_type,
+  as_of,
+  additional_metadata = list(),
+  substitutions = NULL,
+  ...
+)
 
 \method{as_epi_df}{data.frame}(x, geo_type, time_type, as_of, additional_metadata = list(), ...)
 
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 8cfb4408..8ffc9820 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -46,6 +46,22 @@ test_that("as_epi_df errors when additional_metadata is not a list", {
   )
 })
 
+test_that("as_epi_df works for nonstandard input", {
+  tib <- tibble::tibble(
+    x = 1:10, y = 1:10,
+    date = rep(seq(as.Date("2020-01-01"), by = 1, length.out = 5), times = 2),
+    geo_value = rep(c("ca", "hi"), each = 5)
+  )
+  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
+
+  tib <- tib %>% rename(forecast_date = date)
+  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
+  tib %>% rename(any_of(name_substitutions))
+
+  tib <- tib %>% mutate(target_date = 20 + forecast_date)
+  expect_error(tib_epi_df <- tib %>% as_epi_df())
+})
+
 # select fixes
 
 tib <- tibble::tibble(

From 284daaf93465ea92f58f4631da339a6c866150c6 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 7 Jun 2024 16:04:39 -0500
Subject: [PATCH 02/19] geo_value and version, separate functions, more ex

---
 NAMESPACE                     |   1 +
 R/archive.R                   |   3 +
 R/epi_df.R                    |  29 ++--------
 R/utils.R                     | 106 ++++++++++++++++++++++++++++++++++
 man/as_epi_df.Rd              |   2 +-
 man/guess_time_column_name.Rd |  12 ++++
 man/upcase_snake_case.Rd      |  16 +++++
 7 files changed, 144 insertions(+), 25 deletions(-)
 create mode 100644 man/guess_time_column_name.Rd
 create mode 100644 man/upcase_snake_case.Rd

diff --git a/NAMESPACE b/NAMESPACE
index edbaf137..f0b01e82 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -187,6 +187,7 @@ importFrom(tibble,as_tibble)
 importFrom(tibble,new_tibble)
 importFrom(tibble,validate_tibble)
 importFrom(tidyr,unnest)
+importFrom(tidyselect,any_of)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
diff --git a/R/archive.R b/R/archive.R
index 464d68ef..8488cbfa 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -456,6 +456,9 @@ as_epi_archive <- function(
     clobberable_versions_start = NULL,
     versions_end = NULL) {
   assert_data_frame(x)
+  x <- guess_time_column_name(x)
+  x <- guess_geo_column_name(x)
+  x <- guess_version_column_name(x)
   if (!test_subset(c("geo_value", "time_value", "version"), names(x))) {
     cli_abort(
       "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
diff --git a/R/epi_df.R b/R/epi_df.R
index 6ac1b7db..712c4b0e 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -256,34 +256,15 @@ as_epi_df.epi_df <- function(x, ...) {
 #'   (stored in its attributes); if this fails, then the current day-time will
 #'   be used.
 #' @importFrom rlang .data
+#' @importFrom tidyselect any_of
 #' @importFrom cli cli_inform
 #' @export
 as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
                              additional_metadata = list(),
-                             substitutions = NULL, ...) {
-  # possible standard substitutions
-  if (!("time_value" %in% names(x))) {
-    if (("forecast_date" %in% names(x)) && ("target_date" %in% names(x))) {
-      cli_abort("both `forecast_date` and `target_date` are present without a `time_value`
-column, so it is ambiguous which to choose as `time_value`.")
-    }
-    name_substitutions <- substitutions %||% c(
-      time_value = "date",
-      time_value = "forecast_date",
-      time_value = "target_date",
-      time_value = "dates",
-      time_value = "time_values",
-      time_value = "forecast_dates",
-      time_value = "target_dates"
-    )
-    x <- tryCatch(x %>% rename(any_of(name_substitutions)),
-      error = function(cond) {
-        cli_abort("There are multiple `time_value` candidate columns.
-Either `rename` on yourself or drop some.")
-      }
-    )
-    cli_inform("inferring `time_value` column.")
-  }
+                             ...) {
+  # possible standard substitutions for time_value
+  x <- guess_time_column_name(x)
+  x <- guess_geo_column_name(x)
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
       "Columns `geo_value` and `time_value` must be present in `x`."
diff --git a/R/utils.R b/R/utils.R
index b2098e9b..39f97a36 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -448,6 +448,112 @@ guess_time_type <- function(time_value) {
   return("custom")
 }
 
+#'  given a vector of characters, add the same values, but upcased, e.g.
+#'   "date" -> c("date", "Date")
+#'   "target_date" -> c("target_date", "Target_Date")
+#' @keywords internal
+upcase_snake_case <- function(x) {
+  X <- strsplit(x, "_") %>%
+    map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
+    unlist()
+  c(x, X)
+}
+
+#' given an arbitrary
+#' @keywords internal
+guess_time_column_name <- function(x, substitutions = NULL) {
+  if (!("time_value" %in% names(x))) {
+    if (is.null(substitutions)) {
+      substitutions <- c(
+        time_value = "date",
+        time_value = "time",
+        time_value = "datetime",
+        time_value = "dateTime",
+        tmie_value = "date_time",
+        time_value = "forecast_date",
+        time_value = "target_date",
+        time_value = "week",
+        time_value = "day",
+        time_value = "epiweek",
+        time_value = "month",
+        time_value = "year",
+        time_value = "yearmon",
+        time_value = "yearMon",
+        time_value = "dates",
+        time_value = "time_values",
+        time_value = "forecast_dates",
+        time_value = "target_dates"
+      )
+      substitutions <- upcase_snake_case(substitutions)
+    }
+    strsplit(name_substitutions, "_") %>%
+      map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
+      unlist()
+    x <- tryCatch(x %>% rename(any_of(name_substitutions)),
+      error = function(cond) {
+        cli_abort("There are multiple `time_value` candidate columns.
+Either `rename` some yourself or drop some.")
+      }
+    )
+    cli_inform("inferring `time_value` column.")
+  }
+  return(x)
+}
+
+
+#' @keywords internal
+guess_geo_column_name <- function(x, substitutions = NULL) {
+  if (!("time_value" %in% names(x))) {
+    substitutions <- substitutions %||% c(
+      geo_value = "geo_values",
+      geo_value = "geo_id",
+      geo_value = "geos",
+      geo_value = "location",
+      geo_value = "jurisdiction",
+      geo_value = "fips",
+      geo_value = "zip",
+      geo_value = "county",
+      geo_value = "hrr",
+      geo_value = "msa",
+      geo_value = "state",
+      geo_value = "province",
+      geo_value = "nation",
+      geo_value = "states",
+      geo_value = "provinces",
+      geo_value = "counties"
+    )
+    substitutions <- upcase_snake_case(substitutions)
+    x <- tryCatch(x %>% rename(any_of(substitutions)),
+      error = function(cond) {
+        cli_abort("There are multiple `geo_value` candidate columns.
+Either `rename` some yourself or drop some.")
+      }
+    )
+    cli_inform("inferring `time_value` column.")
+  }
+  return(x)
+}
+
+guess_version_column_name <- function(x, substitutions = NULL) {
+  if (!("version" %in% names(x))) {
+    if (is.null(substitutions)) {
+      substitutions <- c(
+        version = "issue",
+        version = "release"
+      )
+      substitutions <- upcase_snake_case(substitutions)
+    }
+    x <- tryCatch(x %>% rename(any_of(substitutions)),
+      error = function(cond) {
+        cli_abort("There are multiple `geo_value` candidate columns.
+Either `rename` some yourself or drop some.")
+      }
+    )
+    cli_inform("inferring `time_value` column.")
+  }
+  return(x)
+}
+
 ##########
 
 
diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
index 82bd8882..22faa265 100644
--- a/man/as_epi_df.Rd
+++ b/man/as_epi_df.Rd
@@ -17,8 +17,8 @@ as_epi_df(x, ...)
   geo_type,
   time_type,
   as_of,
+  other_keys = character(0),
   additional_metadata = list(),
-  substitutions = NULL,
   ...
 )
 
diff --git a/man/guess_time_column_name.Rd b/man/guess_time_column_name.Rd
new file mode 100644
index 00000000..45a173b6
--- /dev/null
+++ b/man/guess_time_column_name.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{guess_time_column_name}
+\alias{guess_time_column_name}
+\title{given an arbitrary}
+\usage{
+guess_time_column_name(x, substitutions = NULL)
+}
+\description{
+given an arbitrary
+}
+\keyword{internal}
diff --git a/man/upcase_snake_case.Rd b/man/upcase_snake_case.Rd
new file mode 100644
index 00000000..398f6a0b
--- /dev/null
+++ b/man/upcase_snake_case.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{upcase_snake_case}
+\alias{upcase_snake_case}
+\title{given a vector of characters, add the same values, but upcased, e.g.
+"date" -> c("date", "Date")
+"target_date" -> c("target_date", "Target_Date")}
+\usage{
+upcase_snake_case(x)
+}
+\description{
+given a vector of characters, add the same values, but upcased, e.g.
+"date" -> c("date", "Date")
+"target_date" -> c("target_date", "Target_Date")
+}
+\keyword{internal}

From 6b361da54d06a7c317581b6d56c8d061fbef4bae Mon Sep 17 00:00:00 2001
From: dsweber2 <dsweber2@users.noreply.github.com>
Date: Fri, 7 Jun 2024 21:06:52 +0000
Subject: [PATCH 03/19] docs: document (GHA)

---
 man/as_epi_df.Rd | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
index 22faa265..40c0a1c5 100644
--- a/man/as_epi_df.Rd
+++ b/man/as_epi_df.Rd
@@ -12,15 +12,7 @@ as_epi_df(x, ...)
 
 \method{as_epi_df}{epi_df}(x, ...)
 
-\method{as_epi_df}{tbl_df}(
-  x,
-  geo_type,
-  time_type,
-  as_of,
-  other_keys = character(0),
-  additional_metadata = list(),
-  ...
-)
+\method{as_epi_df}{tbl_df}(x, geo_type, time_type, as_of, additional_metadata = list(), ...)
 
 \method{as_epi_df}{data.frame}(x, geo_type, time_type, as_of, additional_metadata = list(), ...)
 

From 3276e9e5d6eacc45773c41ad0db4aaa308ee312d Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 7 Jun 2024 17:31:58 -0500
Subject: [PATCH 04/19] errant renamed variables

---
 R/utils.R                    | 4 ++--
 tests/testthat/test-epi_df.R | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 39f97a36..e52c0da9 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -486,10 +486,10 @@ guess_time_column_name <- function(x, substitutions = NULL) {
       )
       substitutions <- upcase_snake_case(substitutions)
     }
-    strsplit(name_substitutions, "_") %>%
+    strsplit(substitutions, "_") %>%
       map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
       unlist()
-    x <- tryCatch(x %>% rename(any_of(name_substitutions)),
+    x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
         cli_abort("There are multiple `time_value` candidate columns.
 Either `rename` some yourself or drop some.")
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 8ffc9820..c6a304bd 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -56,7 +56,6 @@ test_that("as_epi_df works for nonstandard input", {
 
   tib <- tib %>% rename(forecast_date = date)
   expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
-  tib %>% rename(any_of(name_substitutions))
 
   tib <- tib %>% mutate(target_date = 20 + forecast_date)
   expect_error(tib_epi_df <- tib %>% as_epi_df())

From 00ce1da71e00db14efd78345b436c1b12d9aa69d Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Mon, 24 Jun 2024 19:05:44 -0500
Subject: [PATCH 05/19] More tests, `...` tidyselect, doc as_epi_df, more
 values

---
 R/archive.R                   |  3 ++-
 R/epi_df.R                    | 19 ++++++++++++-------
 R/utils.R                     | 20 ++++++++++++++------
 man/as_epi_df.Rd              | 16 ++++++++++------
 man/guess_time_column_name.Rd |  4 ++--
 tests/testthat/test-epi_df.R  |  9 +++++++++
 6 files changed, 49 insertions(+), 22 deletions(-)

diff --git a/R/archive.R b/R/archive.R
index 8488cbfa..83806eef 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -454,8 +454,9 @@ as_epi_archive <- function(
     additional_metadata = NULL,
     compactify = NULL,
     clobberable_versions_start = NULL,
-    versions_end = NULL) {
+    versions_end = NULL, ...) {
   assert_data_frame(x)
+  x <- rename(x, ...)
   x <- guess_time_column_name(x)
   x <- guess_geo_column_name(x)
   x <- guess_version_column_name(x)
diff --git a/R/epi_df.R b/R/epi_df.R
index 712c4b0e..c7554b33 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -249,12 +249,16 @@ as_epi_df.epi_df <- function(x, ...) {
 
 #' @method as_epi_df tbl_df
 #' @describeIn as_epi_df The input tibble `x` must contain the columns
-#'   `geo_value` and `time_value`. All other columns will be preserved as is,
-#'   and treated as measured variables. If `as_of` is missing, then the function
-#'   will try to guess it from an `as_of`, `issue`, or `version` column of `x`
-#'   (if any of these are present), or from as an `as_of` field in its metadata
-#'   (stored in its attributes); if this fails, then the current day-time will
-#'   be used.
+#'   `geo_value` and `time_value`, or column names that uniquely map onto these
+#'   (e.g. `date` or `province`). Alternatively, you can specify the conversion
+#'   explicitly (`time_value = someWeirdColumnName`). All other columns not
+#'   specified as `other_keys` will be preserved as is, and treated as measured
+#'   variables.
+#'
+#'  If `as_of` is missing, then the function will try to guess it from an
+#'   `as_of`, `issue`, or `version` column of `x` (if any of these are present),
+#'   or from as an `as_of` field in its metadata (stored in its attributes); if
+#'   this fails, then the current day-time will be used.
 #' @importFrom rlang .data
 #' @importFrom tidyselect any_of
 #' @importFrom cli cli_inform
@@ -263,11 +267,12 @@ as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
                              additional_metadata = list(),
                              ...) {
   # possible standard substitutions for time_value
+  x <- rename(x, ...)
   x <- guess_time_column_name(x)
   x <- guess_geo_column_name(x)
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
-      "Columns `geo_value` and `time_value` must be present in `x`."
+      "Either columns `geo_value` and `time_value` must be present in `x`, or related columns (see the internal functions `guess_time_column_name()` and/or `guess_geo_column_name()` for a complete list)."
     )
   }
 
diff --git a/R/utils.R b/R/utils.R
index e52c0da9..bce158dd 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -459,7 +459,7 @@ upcase_snake_case <- function(x) {
   c(x, X)
 }
 
-#' given an arbitrary
+#' rename potential time_value columns
 #' @keywords internal
 guess_time_column_name <- function(x, substitutions = NULL) {
   if (!("time_value" %in% names(x))) {
@@ -473,12 +473,14 @@ guess_time_column_name <- function(x, substitutions = NULL) {
         time_value = "forecast_date",
         time_value = "target_date",
         time_value = "week",
-        time_value = "day",
         time_value = "epiweek",
         time_value = "month",
+        time_value = "mon",
         time_value = "year",
         time_value = "yearmon",
+        time_value = "yearmonth",
         time_value = "yearMon",
+        time_value = "yearMonth",
         time_value = "dates",
         time_value = "time_values",
         time_value = "forecast_dates",
@@ -495,7 +497,9 @@ guess_time_column_name <- function(x, substitutions = NULL) {
 Either `rename` some yourself or drop some.")
       }
     )
-    cli_inform("inferring `time_value` column.")
+    if (any(substitutions != "")) {
+      cli_inform("inferring `time_value` column.")
+    }
   }
   return(x)
 }
@@ -529,7 +533,9 @@ guess_geo_column_name <- function(x, substitutions = NULL) {
 Either `rename` some yourself or drop some.")
       }
     )
-    cli_inform("inferring `time_value` column.")
+    if (any(substitutions != "")) {
+      cli_inform("inferring `geo_value` column.")
+    }
   }
   return(x)
 }
@@ -545,11 +551,13 @@ guess_version_column_name <- function(x, substitutions = NULL) {
     }
     x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
-        cli_abort("There are multiple `geo_value` candidate columns.
+        cli_abort("There are multiple `version` candidate columns.
 Either `rename` some yourself or drop some.")
       }
     )
-    cli_inform("inferring `time_value` column.")
+    if (any(substitutions != "")) {
+      cli_inform("inferring `version` column.")
+    }
   }
   return(x)
 }
diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd
index 40c0a1c5..98cdbb83 100644
--- a/man/as_epi_df.Rd
+++ b/man/as_epi_df.Rd
@@ -55,12 +55,16 @@ examples.
 \item \code{as_epi_df(epi_df)}: Simply returns the \code{epi_df} object unchanged.
 
 \item \code{as_epi_df(tbl_df)}: The input tibble \code{x} must contain the columns
-\code{geo_value} and \code{time_value}. All other columns will be preserved as is,
-and treated as measured variables. If \code{as_of} is missing, then the function
-will try to guess it from an \code{as_of}, \code{issue}, or \code{version} column of \code{x}
-(if any of these are present), or from as an \code{as_of} field in its metadata
-(stored in its attributes); if this fails, then the current day-time will
-be used.
+\code{geo_value} and \code{time_value}, or column names that uniquely map onto these
+(e.g. \code{date} or \code{province}). Alternatively, you can specify the conversion
+explicitly (\code{time_value = someWeirdColumnName}). All other columns not
+specified as \code{other_keys} will be preserved as is, and treated as measured
+variables.
+
+If \code{as_of} is missing, then the function will try to guess it from an
+\code{as_of}, \code{issue}, or \code{version} column of \code{x} (if any of these are present),
+or from as an \code{as_of} field in its metadata (stored in its attributes); if
+this fails, then the current day-time will be used.
 
 \item \code{as_epi_df(data.frame)}: Works analogously to \code{as_epi_df.tbl_df()}.
 
diff --git a/man/guess_time_column_name.Rd b/man/guess_time_column_name.Rd
index 45a173b6..f09a0e6e 100644
--- a/man/guess_time_column_name.Rd
+++ b/man/guess_time_column_name.Rd
@@ -2,11 +2,11 @@
 % Please edit documentation in R/utils.R
 \name{guess_time_column_name}
 \alias{guess_time_column_name}
-\title{given an arbitrary}
+\title{rename potential time_value columns}
 \usage{
 guess_time_column_name(x, substitutions = NULL)
 }
 \description{
-given an arbitrary
+rename potential time_value columns
 }
 \keyword{internal}
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index c6a304bd..e7f092fd 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -53,6 +53,15 @@ test_that("as_epi_df works for nonstandard input", {
     geo_value = rep(c("ca", "hi"), each = 5)
   )
   expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
+  expect_no_error(tib_epi_df <- tib %>% as_epi_df(time_value = date, geo_value = geo_value))
+  expect_error(expect_message(
+    tib %>% rename(awefa = geo_value) %>% as_epi_df(),
+    regexp = "inferring `time_value` column."
+  ))
+  expect_no_error(expect_message(
+    tib %>% rename(awefa = geo_value) %>% as_epi_df(geo_value = awefa),
+    regexp = "inferring `time_value` column."
+  ))
 
   tib <- tib %>% rename(forecast_date = date)
   expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))

From 287edd7608632bbbf0d3a8cb3fcedd6e6f9d46bc Mon Sep 17 00:00:00 2001
From: dsweber2 <dsweber2@users.noreply.github.com>
Date: Tue, 25 Jun 2024 00:08:36 +0000
Subject: [PATCH 06/19] docs: document (GHA)

---
 man/epi_archive.Rd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index 97ff6af0..d95e6eb5 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -37,7 +37,8 @@ as_epi_archive(
   additional_metadata = NULL,
   compactify = NULL,
   clobberable_versions_start = NULL,
-  versions_end = NULL
+  versions_end = NULL,
+  ...
 )
 }
 \arguments{

From 75c62c2bacc9bea2b35b67498de85acbe04421d8 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 25 Jun 2024 10:47:03 -0500
Subject: [PATCH 07/19] remove `forecast_date` as a default

---
 R/utils.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index bce158dd..d008f1b3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -470,7 +470,6 @@ guess_time_column_name <- function(x, substitutions = NULL) {
         time_value = "datetime",
         time_value = "dateTime",
         tmie_value = "date_time",
-        time_value = "forecast_date",
         time_value = "target_date",
         time_value = "week",
         time_value = "epiweek",
@@ -483,7 +482,6 @@ guess_time_column_name <- function(x, substitutions = NULL) {
         time_value = "yearMonth",
         time_value = "dates",
         time_value = "time_values",
-        time_value = "forecast_dates",
         time_value = "target_dates"
       )
       substitutions <- upcase_snake_case(substitutions)

From 952e0e24b6b769edaf042bb7116fe464d2b9645d Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 25 Jun 2024 10:55:02 -0500
Subject: [PATCH 08/19] happier linter

---
 R/epi_df.R               | 3 ++-
 R/utils.R                | 6 +++---
 man/upcase_snake_case.Rd | 2 +-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/epi_df.R b/R/epi_df.R
index c7554b33..5c84e90f 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -272,7 +272,8 @@ as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
   x <- guess_geo_column_name(x)
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
-      "Either columns `geo_value` and `time_value` must be present in `x`, or related columns (see the internal functions `guess_time_column_name()` and/or `guess_geo_column_name()` for a complete list)."
+      "Either columns `geo_value` and `time_value` must be present in `x`, or related columns (see the internal
+ functions `guess_time_column_name()` and/or `guess_geo_column_name()` for a complete list)."
     )
   }
 
diff --git a/R/utils.R b/R/utils.R
index d008f1b3..c00205a3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -452,11 +452,11 @@ guess_time_type <- function(time_value) {
 #'   "date" -> c("date", "Date")
 #'   "target_date" -> c("target_date", "Target_Date")
 #' @keywords internal
-upcase_snake_case <- function(x) {
-  X <- strsplit(x, "_") %>%
+upcase_snake_case <- function(vec) {
+  VEC <- strsplit(vec, "_") %>%
     map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
     unlist()
-  c(x, X)
+  c(vec, VEC)
 }
 
 #' rename potential time_value columns
diff --git a/man/upcase_snake_case.Rd b/man/upcase_snake_case.Rd
index 398f6a0b..31ecb768 100644
--- a/man/upcase_snake_case.Rd
+++ b/man/upcase_snake_case.Rd
@@ -6,7 +6,7 @@
 "date" -> c("date", "Date")
 "target_date" -> c("target_date", "Target_Date")}
 \usage{
-upcase_snake_case(x)
+upcase_snake_case(vec)
 }
 \description{
 given a vector of characters, add the same values, but upcased, e.g.

From e3feab6255bdf9eee54256823e524409c25537a6 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 25 Jun 2024 15:34:40 -0500
Subject: [PATCH 09/19] wrong test, better too many columns error

---
 R/archive.R                  |  1 +
 R/utils.R                    | 10 +++++-----
 man/epi_archive.Rd           |  2 ++
 tests/testthat/test-epi_df.R |  4 ++--
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/R/archive.R b/R/archive.R
index 83806eef..b9c29b63 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -442,6 +442,7 @@ validate_epi_archive <- function(
 
 #' `as_epi_archive` converts a data frame, data table, or tibble into an
 #' `epi_archive` object.
+#' @param ... used for specifying column names, such as `version = release_date`
 #'
 #' @rdname epi_archive
 #'
diff --git a/R/utils.R b/R/utils.R
index c00205a3..d2fa3ab4 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -453,10 +453,10 @@ guess_time_type <- function(time_value) {
 #'   "target_date" -> c("target_date", "Target_Date")
 #' @keywords internal
 upcase_snake_case <- function(vec) {
-  VEC <- strsplit(vec, "_") %>%
+  upper_vec <- strsplit(vec, "_") %>%
     map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
     unlist()
-  c(vec, VEC)
+  c(vec, upper_vec)
 }
 
 #' rename potential time_value columns
@@ -491,7 +491,7 @@ guess_time_column_name <- function(x, substitutions = NULL) {
       unlist()
     x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
-        cli_abort("There are multiple `time_value` candidate columns.
+        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
 Either `rename` some yourself or drop some.")
       }
     )
@@ -527,7 +527,7 @@ guess_geo_column_name <- function(x, substitutions = NULL) {
     substitutions <- upcase_snake_case(substitutions)
     x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
-        cli_abort("There are multiple `geo_value` candidate columns.
+        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
 Either `rename` some yourself or drop some.")
       }
     )
@@ -549,7 +549,7 @@ guess_version_column_name <- function(x, substitutions = NULL) {
     }
     x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
-        cli_abort("There are multiple `version` candidate columns.
+        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
 Either `rename` some yourself or drop some.")
       }
     )
diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index d95e6eb5..943d8e11 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -90,6 +90,8 @@ beyond \code{max(x$version)}, but they all contained empty updates. (The default
 value of \code{clobberable_versions_start} does not fully trust these empty
 updates, and assumes that any version \verb{>= max(x$version)} could be
 clobbered.) If \code{nrow(x) == 0}, then this argument is mandatory.}
+
+\item{...}{used for specifying column names, such as \code{version = release_date}}
 }
 \value{
 An \code{epi_archive} object.
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index e7f092fd..1ccb0bec 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -63,10 +63,10 @@ test_that("as_epi_df works for nonstandard input", {
     regexp = "inferring `time_value` column."
   ))
 
-  tib <- tib %>% rename(forecast_date = date)
+  tib <- tib %>% rename(target_date = date)
   expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
 
-  tib <- tib %>% mutate(target_date = 20 + forecast_date)
+  tib <- tib %>% mutate(Time = 20 + target_date)
   expect_error(tib_epi_df <- tib %>% as_epi_df())
 })
 

From ad70c69ad97d3924bac72f12f666c0492b287786 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Mon, 8 Jul 2024 12:36:14 -0500
Subject: [PATCH 10/19] minor refactor to make col name subs accessible

---
 NAMESPACE                     |   3 +
 R/archive.R                   |   6 +-
 R/epi_df.R                    |   4 +-
 R/utils.R                     | 139 ++++++++++++++--------------------
 man/geo_column_names.Rd       |  12 +++
 man/guess_column_name.Rd      |  17 +++++
 man/guess_time_column_name.Rd |  12 ---
 man/time_column_names.Rd      |  12 +++
 man/version_column_names.Rd   |  12 +++
 tests/testthat/test-archive.R |   8 +-
 tests/testthat/test-epi_df.R  |   4 +-
 11 files changed, 122 insertions(+), 107 deletions(-)
 create mode 100644 man/geo_column_names.Rd
 create mode 100644 man/guess_column_name.Rd
 delete mode 100644 man/guess_time_column_name.Rd
 create mode 100644 man/time_column_names.Rd
 create mode 100644 man/version_column_names.Rd

diff --git a/NAMESPACE b/NAMESPACE
index f0b01e82..dcbc151e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -61,6 +61,7 @@ export(epix_merge)
 export(epix_slide)
 export(epix_truncate_versions_after)
 export(filter)
+export(geo_column_names)
 export(group_by)
 export(group_modify)
 export(growth_rate)
@@ -75,9 +76,11 @@ export(next_after)
 export(relocate)
 export(rename)
 export(slice)
+export(time_column_names)
 export(ungroup)
 export(unnest)
 export(validate_epi_archive)
+export(version_column_names)
 importFrom(checkmate,anyInfinite)
 importFrom(checkmate,anyMissing)
 importFrom(checkmate,assert)
diff --git a/R/archive.R b/R/archive.R
index b9c29b63..2adccb5f 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -458,9 +458,9 @@ as_epi_archive <- function(
     versions_end = NULL, ...) {
   assert_data_frame(x)
   x <- rename(x, ...)
-  x <- guess_time_column_name(x)
-  x <- guess_geo_column_name(x)
-  x <- guess_version_column_name(x)
+  x <- guess_column_name(x, "time_value", time_column_names())
+  x <- guess_column_name(x, "geo_value", geo_column_names())
+  x <- guess_column_name(x, "version", version_column_names())
   if (!test_subset(c("geo_value", "time_value", "version"), names(x))) {
     cli_abort(
       "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
diff --git a/R/epi_df.R b/R/epi_df.R
index 5c84e90f..2cb68138 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -268,8 +268,8 @@ as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
                              ...) {
   # possible standard substitutions for time_value
   x <- rename(x, ...)
-  x <- guess_time_column_name(x)
-  x <- guess_geo_column_name(x)
+  x <- guess_column_name(x, "time_value", time_column_names())
+  x <- guess_column_name(x, "geo_value", geo_column_names())
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
       "Either columns `geo_value` and `time_value` must be present in `x`, or related columns (see the internal
diff --git a/R/utils.R b/R/utils.R
index d2fa3ab4..e65c5fea 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -459,102 +459,73 @@ upcase_snake_case <- function(vec) {
   c(vec, upper_vec)
 }
 
-#' rename potential time_value columns
-#' @keywords internal
-guess_time_column_name <- function(x, substitutions = NULL) {
-  if (!("time_value" %in% names(x))) {
-    if (is.null(substitutions)) {
-      substitutions <- c(
-        time_value = "date",
-        time_value = "time",
-        time_value = "datetime",
-        time_value = "dateTime",
-        tmie_value = "date_time",
-        time_value = "target_date",
-        time_value = "week",
-        time_value = "epiweek",
-        time_value = "month",
-        time_value = "mon",
-        time_value = "year",
-        time_value = "yearmon",
-        time_value = "yearmonth",
-        time_value = "yearMon",
-        time_value = "yearMonth",
-        time_value = "dates",
-        time_value = "time_values",
-        time_value = "target_dates"
-      )
-      substitutions <- upcase_snake_case(substitutions)
-    }
-    strsplit(substitutions, "_") %>%
-      map(function(name) paste0(toupper(substr(name, 1, 1)), substr(name, 2, nchar(name)), collapse = "_")) %>%
-      unlist()
-    x <- tryCatch(x %>% rename(any_of(substitutions)),
-      error = function(cond) {
-        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
-Either `rename` some yourself or drop some.")
-      }
-    )
-    if (any(substitutions != "")) {
-      cli_inform("inferring `time_value` column.")
-    }
-  }
-  return(x)
+#' potential time_value columns
+#' @description
+#' the full list of potential substitutions for the `time_value` column name:
+#' `r time_column_names()`
+#' @export
+time_column_names <- function() {
+  substitutions <- c(
+    "time_value", "date", "time", "datetime", "dateTime", "date_time", "target_date",
+    "week", "epiweek", "month", "mon", "year", "yearmon", "yearmonth",
+    "yearMon", "yearMonth", "dates", "time_values", "target_dates", "time_Value"
+  )
+  substitutions <- upcase_snake_case(substitutions)
+  names(substitutions) <- rep("time_value", length(substitutions))
+  return(substitutions)
+}
+#
+#' potential geo_value columns
+#' @description
+#' the full list of potential substitutions for the `geo_value` column name:
+#' `r geo_column_names()`
+#' @export
+geo_column_names <- function() {
+  substitutions <- c(
+    "geo_value", "geo_values", "geo_id", "geos", "location", "jurisdiction", "fips", "zip",
+    "county", "hrr", "msa", "state", "province", "nation", "states",
+    "provinces", "counties", "geo_Value"
+  )
+  substitutions <- upcase_snake_case(substitutions)
+  names(substitutions) <- rep("geo_value", length(substitutions))
+  return(substitutions)
 }
 
+#' potential version columns
+#' @description
+#' the full list of potential substitutions for the `version` column name:
+#' `r version_column_names()`
+#' @export
+version_column_names <- function() {
+  substitutions <- c(
+    "version", "issue", "release"
+  )
+  substitutions <- upcase_snake_case(substitutions)
+  names(substitutions) <- rep("version", length(substitutions))
+  return(substitutions)
+}
 
+#' rename potential time_value columns
+#'
+#' @description
+#' potentially renames
+#' @param x the tibble to potentially rename
+#' @param substitions a named vector. the potential substitions, with every name `time_value`
 #' @keywords internal
-guess_geo_column_name <- function(x, substitutions = NULL) {
-  if (!("time_value" %in% names(x))) {
-    substitutions <- substitutions %||% c(
-      geo_value = "geo_values",
-      geo_value = "geo_id",
-      geo_value = "geos",
-      geo_value = "location",
-      geo_value = "jurisdiction",
-      geo_value = "fips",
-      geo_value = "zip",
-      geo_value = "county",
-      geo_value = "hrr",
-      geo_value = "msa",
-      geo_value = "state",
-      geo_value = "province",
-      geo_value = "nation",
-      geo_value = "states",
-      geo_value = "provinces",
-      geo_value = "counties"
-    )
-    substitutions <- upcase_snake_case(substitutions)
+guess_column_name <- function(x, column_name, substitutions) {
+  if (!(column_name %in% names(x))) {
     x <- tryCatch(x %>% rename(any_of(substitutions)),
       error = function(cond) {
         cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
 Either `rename` some yourself or drop some.")
       }
     )
-    if (any(substitutions != "")) {
-      cli_inform("inferring `geo_value` column.")
+    # if none of the names are in substitutions, and `column_name` isn't a column, we're missing a relevant column
+    if (!any(names(x) %in% substitutions)) {
+      cli_abort("There is no {column_name} column or similar name. See e.g. [`time_column_name()`] for a complete list")
     }
-  }
-  return(x)
-}
-
-guess_version_column_name <- function(x, substitutions = NULL) {
-  if (!("version" %in% names(x))) {
-    if (is.null(substitutions)) {
-      substitutions <- c(
-        version = "issue",
-        version = "release"
-      )
-      substitutions <- upcase_snake_case(substitutions)
-    }
-    x <- tryCatch(x %>% rename(any_of(substitutions)),
-      error = function(cond) {
-        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
-Either `rename` some yourself or drop some.")
-      }
-    )
     if (any(substitutions != "")) {
-      cli_inform("inferring `version` column.")
+      cli_inform("inferring {column_name} column.")
     }
   }
   return(x)
diff --git a/man/geo_column_names.Rd b/man/geo_column_names.Rd
new file mode 100644
index 00000000..4b3810dc
--- /dev/null
+++ b/man/geo_column_names.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{geo_column_names}
+\alias{geo_column_names}
+\title{potential geo_value columns}
+\usage{
+geo_column_names()
+}
+\description{
+the full list of potential substitutions for the \code{geo_value} column name:
+geo_value, geo_values, geo_id, geos, location, jurisdiction, fips, zip, county, hrr, msa, state, province, nation, states, provinces, counties, geo_Value, Geo_Value, Geo_Values, Geo_Id, Geos, Location, Jurisdiction, Fips, Zip, County, Hrr, Msa, State, Province, Nation, States, Provinces, Counties, Geo_Value
+}
diff --git a/man/guess_column_name.Rd b/man/guess_column_name.Rd
new file mode 100644
index 00000000..f03a7b80
--- /dev/null
+++ b/man/guess_column_name.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{guess_column_name}
+\alias{guess_column_name}
+\title{rename potential time_value columns}
+\usage{
+guess_column_name(x, column_name, substitutions)
+}
+\arguments{
+\item{x}{the tibble to potentially rename}
+
+\item{substitions}{a named vector. the potential substitions, with every name \code{time_value}}
+}
+\description{
+potentially renames
+}
+\keyword{internal}
diff --git a/man/guess_time_column_name.Rd b/man/guess_time_column_name.Rd
deleted file mode 100644
index f09a0e6e..00000000
--- a/man/guess_time_column_name.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{guess_time_column_name}
-\alias{guess_time_column_name}
-\title{rename potential time_value columns}
-\usage{
-guess_time_column_name(x, substitutions = NULL)
-}
-\description{
-rename potential time_value columns
-}
-\keyword{internal}
diff --git a/man/time_column_names.Rd b/man/time_column_names.Rd
new file mode 100644
index 00000000..2e2db6b5
--- /dev/null
+++ b/man/time_column_names.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{time_column_names}
+\alias{time_column_names}
+\title{potential time_value columns}
+\usage{
+time_column_names()
+}
+\description{
+the full list of potential substitutions for the \code{time_value} column name:
+time_value, date, time, datetime, dateTime, date_time, target_date, week, epiweek, month, mon, year, yearmon, yearmonth, yearMon, yearMonth, dates, time_values, target_dates, time_Value, Time_Value, Date, Time, Datetime, DateTime, Date_Time, Target_Date, Week, Epiweek, Month, Mon, Year, Yearmon, Yearmonth, YearMon, YearMonth, Dates, Time_Values, Target_Dates, Time_Value
+}
diff --git a/man/version_column_names.Rd b/man/version_column_names.Rd
new file mode 100644
index 00000000..75ee2315
--- /dev/null
+++ b/man/version_column_names.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{version_column_names}
+\alias{version_column_names}
+\title{potential version columns}
+\usage{
+version_column_names()
+}
+\description{
+the full list of potential substitutions for the \code{version} column name:
+version, issue, release, Version, Issue, Release
+}
diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index 1291e3c7..218baf46 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -8,13 +8,13 @@ dt <- archive_cases_dv_subset$DT
 
 test_that("data.frame must contain geo_value, time_value and version columns", {
   expect_error(as_epi_archive(select(dt, -geo_value), compactify = FALSE),
-    regexp = "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
+    regexp = "There is no geo_value column or similar name"
   )
-  expect_error(as_epi_archive(select(dt, -time_value), compactify = FALSE),
-    regexp = "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
+  expect_error(expect_message(as_epi_archive(select(dt, -time_value), compactify = FALSE)),
+    regexp = "There is no time_value column or similar name"
   )
   expect_error(as_epi_archive(select(dt, -version), compactify = FALSE),
-    regexp = "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
+    regexp = "There is no version column or similar name"
   )
 })
 
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 1ccb0bec..25a2dc59 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -56,11 +56,11 @@ test_that("as_epi_df works for nonstandard input", {
   expect_no_error(tib_epi_df <- tib %>% as_epi_df(time_value = date, geo_value = geo_value))
   expect_error(expect_message(
     tib %>% rename(awefa = geo_value) %>% as_epi_df(),
-    regexp = "inferring `time_value` column."
+    regexp = "inferring "
   ))
   expect_no_error(expect_message(
     tib %>% rename(awefa = geo_value) %>% as_epi_df(geo_value = awefa),
-    regexp = "inferring `time_value` column."
+    regexp = "inferring"
   ))
 
   tib <- tib %>% rename(target_date = date)

From edbf1acdfb2c862efd2e0e4a043c3b062b9280a9 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Mon, 8 Jul 2024 12:37:24 -0500
Subject: [PATCH 11/19] Nat's suggestions

---
 R/archive.R        | 6 ++++--
 R/epi_df.R         | 4 ++--
 man/epi_archive.Rd | 3 ++-
 man/new_epi_df.Rd  | 3 +--
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/archive.R b/R/archive.R
index 2adccb5f..1fd40d73 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -442,7 +442,8 @@ validate_epi_archive <- function(
 
 #' `as_epi_archive` converts a data frame, data table, or tibble into an
 #' `epi_archive` object.
-#' @param ... used for specifying column names, such as `version = release_date`
+#' @param ... used for specifying column names, as in [`dplyr::rename`]. For
+#'   example `version = release_date`
 #'
 #' @rdname epi_archive
 #'
@@ -463,7 +464,8 @@ as_epi_archive <- function(
   x <- guess_column_name(x, "version", version_column_names())
   if (!test_subset(c("geo_value", "time_value", "version"), names(x))) {
     cli_abort(
-      "Columns `geo_value`, `time_value`, and `version` must be present in `x`."
+      "Either columns `geo_value`, `time_value`, and `version` must be present in `x`, or related columns (see the internal
+ functions `guess_time_column_name()`, `guess_geo_column_name()` and/or `guess_geo_version_name()` for complete list)."
     )
   }
   if (anyMissing(x$version)) {
diff --git a/R/epi_df.R b/R/epi_df.R
index 2cb68138..e3c77e96 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -95,7 +95,7 @@ NULL
 #'
 #' @export
 new_epi_df <- function(x = tibble::tibble(), geo_type, time_type, as_of,
-                       additional_metadata = list(), ...) {
+                       additional_metadata = list()) {
   assert_data_frame(x)
   assert_list(additional_metadata)
 
@@ -279,7 +279,7 @@ as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
 
   new_epi_df(
     x, geo_type, time_type, as_of,
-    additional_metadata, ...
+    additional_metadata
   )
 }
 
diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index 943d8e11..19ab1d1e 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -91,7 +91,8 @@ value of \code{clobberable_versions_start} does not fully trust these empty
 updates, and assumes that any version \verb{>= max(x$version)} could be
 clobbered.) If \code{nrow(x) == 0}, then this argument is mandatory.}
 
-\item{...}{used for specifying column names, such as \code{version = release_date}}
+\item{...}{used for specifying column names, as in \code{\link[dplyr:rename]{dplyr::rename}}. For
+example \code{version = release_date}}
 }
 \value{
 An \code{epi_archive} object.
diff --git a/man/new_epi_df.Rd b/man/new_epi_df.Rd
index 7182c222..934a716e 100644
--- a/man/new_epi_df.Rd
+++ b/man/new_epi_df.Rd
@@ -9,8 +9,7 @@ new_epi_df(
   geo_type,
   time_type,
   as_of,
-  additional_metadata = list(),
-  ...
+  additional_metadata = list()
 )
 }
 \arguments{

From d19d1a5e2538ffa77af429062399cf4e3b2c61ef Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 9 Jul 2024 11:39:55 -0500
Subject: [PATCH 12/19] avoid arg prefix-completion for versions_end

---
 R/archive.R                   |  3 ++-
 tests/testthat/test-archive.R | 18 ++++++++++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/R/archive.R b/R/archive.R
index 1fd40d73..6137cc72 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -456,7 +456,8 @@ as_epi_archive <- function(
     additional_metadata = NULL,
     compactify = NULL,
     clobberable_versions_start = NULL,
-    versions_end = NULL, ...) {
+    .versions_end = NULL, ...,
+    versions_end = .versions_end) {
   assert_data_frame(x)
   x <- rename(x, ...)
   x <- guess_column_name(x, "time_value", time_column_names())
diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index 218baf46..c606b664 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -18,6 +18,24 @@ test_that("data.frame must contain geo_value, time_value and version columns", {
   )
 })
 
+test_that("as_epi_archive custom name mapping works correctly", {
+  # custom name works correctly
+  suppressWarnings(expect_equal(
+      as_epi_archive(rename(dt, weirdName = version), version = weirdName),
+    as_epi_archive(dt)
+  ))
+  suppressWarnings(expect_equal(
+    as_epi_archive(rename(dt, weirdName = geo_value), geo_value = weirdName),
+    as_epi_archive(dt)
+  ))
+  suppressWarnings(expect_equal(
+      as_epi_archive(rename(dt, weirdName = time_value), time_value = weirdName),
+    as_epi_archive(dt)
+  ))
+
+  expect_error(as_epi_archive(rename(dt, weirdName = version), version = weirdName, version = time_value), "Names must be unique")
+})
+
 test_that("other_keys can only contain names of the data.frame columns", {
   expect_error(as_epi_archive(dt, other_keys = "xyz", compactify = FALSE),
     regexp = "`other_keys` must be contained in the column names of `x`."

From f6904f27beb35ff933423f280d2784fc5208491b Mon Sep 17 00:00:00 2001
From: dsweber2 <dsweber2@users.noreply.github.com>
Date: Tue, 9 Jul 2024 16:49:18 +0000
Subject: [PATCH 13/19] style: styler (GHA)

---
 tests/testthat/test-archive.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index c606b664..1858da86 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -21,7 +21,7 @@ test_that("data.frame must contain geo_value, time_value and version columns", {
 test_that("as_epi_archive custom name mapping works correctly", {
   # custom name works correctly
   suppressWarnings(expect_equal(
-      as_epi_archive(rename(dt, weirdName = version), version = weirdName),
+    as_epi_archive(rename(dt, weirdName = version), version = weirdName),
     as_epi_archive(dt)
   ))
   suppressWarnings(expect_equal(
@@ -29,7 +29,7 @@ test_that("as_epi_archive custom name mapping works correctly", {
     as_epi_archive(dt)
   ))
   suppressWarnings(expect_equal(
-      as_epi_archive(rename(dt, weirdName = time_value), time_value = weirdName),
+    as_epi_archive(rename(dt, weirdName = time_value), time_value = weirdName),
     as_epi_archive(dt)
   ))
 

From 76388e2052def411b22b6d7ff89791dbc6de83fd Mon Sep 17 00:00:00 2001
From: dsweber2 <dsweber2@users.noreply.github.com>
Date: Tue, 9 Jul 2024 16:49:21 +0000
Subject: [PATCH 14/19] docs: document (GHA)

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

diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index 19ab1d1e..a813c6de 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -37,8 +37,9 @@ as_epi_archive(
   additional_metadata = NULL,
   compactify = NULL,
   clobberable_versions_start = NULL,
-  versions_end = NULL,
-  ...
+  .versions_end = NULL,
+  ...,
+  versions_end = .versions_end
 )
 }
 \arguments{

From 500a952f4101c52bba297317698a58a60e805946 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 12 Jul 2024 11:39:05 -0500
Subject: [PATCH 15/19] formatting

---
 R/archive.R                   | 8 ++++++--
 man/epi_archive.Rd            | 4 ++++
 tests/testthat/test-archive.R | 4 +++-
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/R/archive.R b/R/archive.R
index 6137cc72..91f5d4a7 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -444,6 +444,9 @@ validate_epi_archive <- function(
 #' `epi_archive` object.
 #' @param ... used for specifying column names, as in [`dplyr::rename`]. For
 #'   example `version = release_date`
+#' @param .versions_end location based versions_end, used to avoid prefix
+#'   `version = issue` from being assigned to `versions_end` instead of being
+#'   used to rename columns.
 #'
 #' @rdname epi_archive
 #'
@@ -465,8 +468,9 @@ as_epi_archive <- function(
   x <- guess_column_name(x, "version", version_column_names())
   if (!test_subset(c("geo_value", "time_value", "version"), names(x))) {
     cli_abort(
-      "Either columns `geo_value`, `time_value`, and `version` must be present in `x`, or related columns (see the internal
- functions `guess_time_column_name()`, `guess_geo_column_name()` and/or `guess_geo_version_name()` for complete list)."
+      "Either columns `geo_value`, `time_value`, and `version` must be present in `x`,
+or related columns (see the internal functions `guess_time_column_name()`,
+`guess_geo_column_name()` and/or `guess_geo_version_name()` for complete list)."
     )
   }
   if (anyMissing(x$version)) {
diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd
index a813c6de..99203052 100644
--- a/man/epi_archive.Rd
+++ b/man/epi_archive.Rd
@@ -92,6 +92,10 @@ value of \code{clobberable_versions_start} does not fully trust these empty
 updates, and assumes that any version \verb{>= max(x$version)} could be
 clobbered.) If \code{nrow(x) == 0}, then this argument is mandatory.}
 
+\item{.versions_end}{location based versions_end, used to avoid prefix
+\code{version = issue} from being assigned to \code{versions_end} instead of being
+used to rename columns.}
+
 \item{...}{used for specifying column names, as in \code{\link[dplyr:rename]{dplyr::rename}}. For
 example \code{version = release_date}}
 }
diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index 1858da86..54501a31 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -33,7 +33,9 @@ test_that("as_epi_archive custom name mapping works correctly", {
     as_epi_archive(dt)
   ))
 
-  expect_error(as_epi_archive(rename(dt, weirdName = version), version = weirdName, version = time_value), "Names must be unique")
+  expect_error(as_epi_archive(rename(dt, weirdName = version),
+    version = weirdName, version = time_value
+  ), "Names must be unique")
 })
 
 test_that("other_keys can only contain names of the data.frame columns", {

From 1b84d010aad36f046d5828cf2044a8f368fbfd62 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 12 Jul 2024 15:33:57 -0500
Subject: [PATCH 16/19] template needed changing

---
 R/epi_df.R                    |  1 +
 R/utils.R                     |  2 +-
 man-roxygen/epi_df-params.R   |  1 -
 man/guess_column_name.Rd      |  2 +-
 man/new_epi_df.Rd             |  2 --
 tests/testthat/test-archive.R | 10 +++++++---
 6 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/R/epi_df.R b/R/epi_df.R
index e3c77e96..d8b399fb 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -162,6 +162,7 @@ new_epi_df <- function(x = tibble::tibble(), geo_type, time_type, as_of,
 #' guide](https://cmu-delphi.github.io/epiprocess/articles/epiprocess.html) for
 #' examples.
 #'
+#' @param ... Additional arguments passed to methods.
 #' @template epi_df-params
 #'
 #' @export
diff --git a/R/utils.R b/R/utils.R
index e65c5fea..24da3995 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -510,7 +510,7 @@ version_column_names <- function() {
 #' @description
 #' potentially renames
 #' @param x the tibble to potentially rename
-#' @param substitions a named vector. the potential substitions, with every name `time_value`
+#' @param substitutions a named vector. the potential substitions, with every name `time_value`
 #' @keywords internal
 guess_column_name <- function(x, column_name, substitutions) {
   if (!(column_name %in% names(x))) {
diff --git a/man-roxygen/epi_df-params.R b/man-roxygen/epi_df-params.R
index 54d8c2d2..59c51603 100644
--- a/man-roxygen/epi_df-params.R
+++ b/man-roxygen/epi_df-params.R
@@ -15,5 +15,4 @@
 #'   `as_of` fields; named entries from the passed list will be included as
 #'   well. If your tibble has additional keys, be sure to specify them as a
 #'   character vector in the `other_keys` component of `additional_metadata`.
-#' @param ... Additional arguments passed to methods.
 #' @return An `epi_df` object.
diff --git a/man/guess_column_name.Rd b/man/guess_column_name.Rd
index f03a7b80..d4aa09b7 100644
--- a/man/guess_column_name.Rd
+++ b/man/guess_column_name.Rd
@@ -9,7 +9,7 @@ guess_column_name(x, column_name, substitutions)
 \arguments{
 \item{x}{the tibble to potentially rename}
 
-\item{substitions}{a named vector. the potential substitions, with every name \code{time_value}}
+\item{substitutions}{a named vector. the potential substitions, with every name \code{time_value}}
 }
 \description{
 potentially renames
diff --git a/man/new_epi_df.Rd b/man/new_epi_df.Rd
index 934a716e..8010b700 100644
--- a/man/new_epi_df.Rd
+++ b/man/new_epi_df.Rd
@@ -34,8 +34,6 @@ then the current day-time will be used.}
 \code{as_of} fields; named entries from the passed list will be included as
 well. If your tibble has additional keys, be sure to specify them as a
 character vector in the \code{other_keys} component of \code{additional_metadata}.}
-
-\item{...}{Additional arguments passed to methods.}
 }
 \value{
 An \code{epi_df} object.
diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index 54501a31..679e4dbd 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -33,9 +33,13 @@ test_that("as_epi_archive custom name mapping works correctly", {
     as_epi_archive(dt)
   ))
 
-  expect_error(as_epi_archive(rename(dt, weirdName = version),
-    version = weirdName, version = time_value
-  ), "Names must be unique")
+  expect_error(
+    as_epi_archive(
+      rename(dt, weirdName = version),
+      version = weirdName,
+      version = time_value
+    ), "Names must be unique"
+  )
 })
 
 test_that("other_keys can only contain names of the data.frame columns", {

From c59af46b494d88c587a7c386d779ed714eb0824c Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 12 Jul 2024 16:48:34 -0500
Subject: [PATCH 17/19] pkgdown fix for new functions, apparently

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

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 4930c9f5..b95a6386 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -63,6 +63,7 @@ reference:
     desc: Details on `epi_df` format, and basic functionality.
   - contents:
       - matches("epi_df")
+      - matches("column_names")
   - title: "`epi_*()` functions"
     desc: Functions that act on `epi_df` objects.
   - contents:

From 7d99e6df8f10cd592f4c72cd37cf404f18984eec Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 19 Jul 2024 15:21:27 -0500
Subject: [PATCH 18/19] recs from Nat, local checks passing

---
 R/archive.R                   |  7 ++++---
 R/epi_df.R                    |  6 ++++--
 R/utils.R                     | 36 +++++++++++++++++++++++++----------
 tests/testthat/test-archive.R | 32 ++++++++++++++++++-------------
 tests/testthat/test-epi_df.R  | 27 ++++++++++++++++++--------
 5 files changed, 72 insertions(+), 36 deletions(-)

diff --git a/R/archive.R b/R/archive.R
index 91f5d4a7..780279b0 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -468,9 +468,10 @@ as_epi_archive <- function(
   x <- guess_column_name(x, "version", version_column_names())
   if (!test_subset(c("geo_value", "time_value", "version"), names(x))) {
     cli_abort(
-      "Either columns `geo_value`, `time_value`, and `version` must be present in `x`,
-or related columns (see the internal functions `guess_time_column_name()`,
-`guess_geo_column_name()` and/or `guess_geo_version_name()` for complete list)."
+      "Either columns `geo_value`, `time_value`, and `version`, or related columns
+      (see the internal functions `guess_time_column_name()`,
+      `guess_geo_column_name()` and/or `guess_geo_version_name()` for complete
+      list) must be present in `x`."
     )
   }
   if (anyMissing(x$version)) {
diff --git a/R/epi_df.R b/R/epi_df.R
index d8b399fb..707944f6 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -273,8 +273,10 @@ as_epi_df.tbl_df <- function(x, geo_type, time_type, as_of,
   x <- guess_column_name(x, "geo_value", geo_column_names())
   if (!test_subset(c("geo_value", "time_value"), names(x))) {
     cli_abort(
-      "Either columns `geo_value` and `time_value` must be present in `x`, or related columns (see the internal
- functions `guess_time_column_name()` and/or `guess_geo_column_name()` for a complete list)."
+      "Either columns `geo_value` and `time_value` or related columns
+       (see the internal functions `guess_time_column_name()` and/or
+       `guess_geo_column_name()` for a complete list)
+       must be present in `x`."
     )
   }
 
diff --git a/R/utils.R b/R/utils.R
index 24da3995..9396070d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -512,21 +512,37 @@ version_column_names <- function() {
 #' @param x the tibble to potentially rename
 #' @param substitutions a named vector. the potential substitions, with every name `time_value`
 #' @keywords internal
+#' @importFrom cli cli_inform cli_abort
+#' @importFrom dplyr rename
 guess_column_name <- function(x, column_name, substitutions) {
   if (!(column_name %in% names(x))) {
-    x <- tryCatch(x %>% rename(any_of(substitutions)),
-      error = function(cond) {
-        cli_abort("{names(x)[names(x) %in% substitutions]} are both/all valid substitutions.
-Either `rename` some yourself or drop some.")
-      }
-    )
     # if none of the names are in substitutions, and `column_name` isn't a column, we're missing a relevant column
     if (!any(names(x) %in% substitutions)) {
-      cli_abort("There is no {column_name} column or similar name. See e.g. [`time_column_name()`] for a complete list")
-    }
-    if (any(substitutions != "")) {
-      cli_inform("inferring {column_name} column.")
+      cli_abort(
+        "There is no {column_name} column or similar name.
+         See e.g. [`time_column_name()`] for a complete list",
+        class = "epiprocess__guess_column__multiple_substitution_error"
+      )
     }
+
+    tryCatch(
+      {
+        x <- x %>% rename(any_of(substitutions))
+        cli_inform(
+          "inferring {column_name} column.",
+          class = "epiprocess__guess_column_inferring_inform"
+        )
+        return(x)
+      },
+      error = function(cond) {
+        cli_abort(
+          "{intersect(names(x), substitutions)}
+           are both/all valid substitutions for {column_name}.
+           Either `rename` some yourself or drop some.",
+          class = "epiprocess__guess_column__multiple_substitution_error"
+        )
+      }
+    )
   }
   return(x)
 }
diff --git a/tests/testthat/test-archive.R b/tests/testthat/test-archive.R
index 679e4dbd..d437c983 100644
--- a/tests/testthat/test-archive.R
+++ b/tests/testthat/test-archive.R
@@ -10,7 +10,7 @@ test_that("data.frame must contain geo_value, time_value and version columns", {
   expect_error(as_epi_archive(select(dt, -geo_value), compactify = FALSE),
     regexp = "There is no geo_value column or similar name"
   )
-  expect_error(expect_message(as_epi_archive(select(dt, -time_value), compactify = FALSE)),
+  expect_error(as_epi_archive(select(dt, -time_value), compactify = FALSE),
     regexp = "There is no time_value column or similar name"
   )
   expect_error(as_epi_archive(select(dt, -version), compactify = FALSE),
@@ -20,18 +20,24 @@ test_that("data.frame must contain geo_value, time_value and version columns", {
 
 test_that("as_epi_archive custom name mapping works correctly", {
   # custom name works correctly
-  suppressWarnings(expect_equal(
-    as_epi_archive(rename(dt, weirdName = version), version = weirdName),
-    as_epi_archive(dt)
-  ))
-  suppressWarnings(expect_equal(
-    as_epi_archive(rename(dt, weirdName = geo_value), geo_value = weirdName),
-    as_epi_archive(dt)
-  ))
-  suppressWarnings(expect_equal(
-    as_epi_archive(rename(dt, weirdName = time_value), time_value = weirdName),
-    as_epi_archive(dt)
-  ))
+  expect_equal(
+    as_epi_archive(rename(dt, weirdName = version),
+      version = weirdName, compactify = TRUE
+    ),
+    as_epi_archive(dt, compactify = TRUE)
+  )
+  expect_equal(
+    as_epi_archive(rename(dt, weirdName = geo_value),
+      geo_value = weirdName, compactify = TRUE
+    ),
+    as_epi_archive(dt, compactify = TRUE)
+  )
+  expect_equal(
+    as_epi_archive(rename(dt, weirdName = time_value),
+      time_value = weirdName, compactify = TRUE
+    ),
+    as_epi_archive(dt, compactify = TRUE)
+  )
 
   expect_error(
     as_epi_archive(
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 25a2dc59..1c5e527f 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -52,22 +52,33 @@ test_that("as_epi_df works for nonstandard input", {
     date = rep(seq(as.Date("2020-01-01"), by = 1, length.out = 5), times = 2),
     geo_value = rep(c("ca", "hi"), each = 5)
   )
-  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
+  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()),
+    class = "epiprocess__guess_column_inferring_inform"
+  )
   expect_no_error(tib_epi_df <- tib %>% as_epi_df(time_value = date, geo_value = geo_value))
-  expect_error(expect_message(
-    tib %>% rename(awefa = geo_value) %>% as_epi_df(),
-    regexp = "inferring "
-  ))
+  expect_error(
+    expect_message(
+      tib %>%
+        rename(awefa = geo_value) %>%
+        as_epi_df(),
+      class = "epiprocess__guess_column_inferring_inform"
+    ),
+    class = "epiprocess__guess_column__multiple_substitution_error"
+  )
   expect_no_error(expect_message(
     tib %>% rename(awefa = geo_value) %>% as_epi_df(geo_value = awefa),
-    regexp = "inferring"
+    class = "epiprocess__guess_column_inferring_inform"
   ))
 
   tib <- tib %>% rename(target_date = date)
-  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()))
+  expect_message(expect_no_error(tib_epi_df <- tib %>% as_epi_df()),
+    class = "epiprocess__guess_column_inferring_inform"
+  )
 
   tib <- tib %>% mutate(Time = 20 + target_date)
-  expect_error(tib_epi_df <- tib %>% as_epi_df())
+  expect_error(tib_epi_df <- tib %>% as_epi_df(),
+    class = "epiprocess__guess_column__multiple_substitution_error"
+  )
 })
 
 # select fixes

From 243c45e9c949653dc6b89608dd68c1722a5fb1a7 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Fri, 19 Jul 2024 15:43:37 -0500
Subject: [PATCH 19/19] desc, news

---
 DESCRIPTION | 2 +-
 NEWS.md     | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ac188dc9..21dda4f5 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.7.12
+Version: 0.7.13
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", email = "lcbrooks@andrew.cmu.edu", role = c("aut", "cre")),
diff --git a/NEWS.md b/NEWS.md
index ed9dea40..7be31506 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -40,6 +40,11 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 - Improved documentation web site landing page's introduction.
 - Fixed documentation referring to old `epi_slide()` interface (#466, thanks
   @XuedaShen!).
+- `as_epi_df` and `as_epi_archive` now support arguments to specify column names
+  e.g.  `as_epi_df(some_tibble, geo_value=state)`. In addition, there is a list
+  of default conversions, see `time_column_names`  for a list of columns that
+  will automatically be recognized and converted to  `time_value` column (there
+  are similar functions for `geo` and `version`).
 
 ## Cleanup
 - Resolved some linting messages in package checks (#468).