Update revision_summary

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epiprocess
 Type: Package
 Title: Tools for basic signal processing in epidemiology
-Version: 0.10.1
+Version: 0.10.2
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "lcbrooks+github@andrew.cmu.edu", role = c("aut", "cre")),
@@ -103,5 +103,6 @@ Collate:
     'reexports.R'
     'revision_analysis.R'
     'slide.R'
+    'time-utils.R'
     'utils.R'
     'utils_pipe.R'

NAMESPACE

@@ -96,13 +96,15 @@ export(time_column_names)
 export(ungroup)
 export(unnest)
 export(validate_epi_archive)
+export(vec_position_lag)
 export(version_column_names)
 import(epidatasets)
 importFrom(checkmate,anyInfinite)
 importFrom(checkmate,anyMissing)
 importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_class)
+importFrom(checkmate,assert_count)
 importFrom(checkmate,assert_data_frame)
 importFrom(checkmate,assert_false)
 importFrom(checkmate,assert_function)
@@ -195,6 +197,7 @@ importFrom(rlang,caller_arg)
 importFrom(rlang,caller_env)
 importFrom(rlang,check_dots_empty)
 importFrom(rlang,check_dots_empty0)
+importFrom(rlang,dots_n)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,env)
@@ -235,5 +238,10 @@ importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
 importFrom(utils,capture.output)
 importFrom(utils,tail)
+importFrom(vctrs,obj_check_vector)
+importFrom(vctrs,vec_c)
+importFrom(vctrs,vec_cast)
 importFrom(vctrs,vec_data)
 importFrom(vctrs,vec_equal)
+importFrom(vctrs,vec_size)
+importFrom(vctrs,vec_slice)

R/archive.R

@@ -369,6 +369,23 @@ removed_by_compactify <- function(df, keys, tolerance) {
     )) # nolint: object_usage_linter
 }
 
+#' Lag entries in a vctrs-style vector by their position in the vector
+#'
+#' @importFrom checkmate assert_count
+#' @importFrom vctrs obj_check_vector vec_slice vec_size
+#' @keywords internal
+#' @importFrom vctrs vec_c vec_slice vec_size
+#' @export
+vec_position_lag <- function(x, n) {
+  obj_check_vector(x)
+  assert_count(n)
+  if (length(x) == 0L) {
+    x
+  } else {
+    vec_c(rep(NA, n), vec_slice(x, seq_len(vec_size(x) - 1L)))
+  }
+}
+
 #' Checks to see if a value in a vector is LOCF
 #' @description
 #' LOCF meaning last observation carried forward. lags the vector by 1, then
@@ -378,8 +395,8 @@ removed_by_compactify <- function(df, keys, tolerance) {
 #' @importFrom dplyr lag if_else near
 #' @keywords internal
 is_locf <- function(vec, tolerance) { # nolint: object_usage_linter
-  lag_vec <- dplyr::lag(vec)
-  if (typeof(vec) == "double") {
+  lag_vec <- vec_position_lag(vec, 1L)
+  if (inherits(vec, "numeric")) { # (no matrix/array/general support)
     res <- if_else(
       !is.na(vec) & !is.na(lag_vec),
       near(vec, lag_vec, tol = tolerance),

R/epiprocess-package.R

@@ -32,6 +32,6 @@ utils::globalVariables(c(
   ".x", ".group_key", ".ref_time_value", "resid",
   "fitted", ".response", "geo_value", "time_value",
   "value", ".real", "lag", "max_value", "min_value",
-  "median_value", "spread", "rel_spread", "time_to",
-  "time_near_latest", "n_revisions", "min_lag", "max_lag"
+  "median_value", "spread", "rel_spread", "lag_to",
+  "lag_near_latest", "n_revisions", "min_lag", "max_lag"
 ))

R/key_colnames.R

@@ -27,7 +27,16 @@
 #' @keywords internal
 #' @export
 key_colnames <- function(x, ..., exclude = character()) {
-  UseMethod("key_colnames")
+  provided_args <- rlang::call_args_names(rlang::call_match())
+  if ("extra_keys" %in% provided_args) {
+    lifecycle::deprecate_soft("0.9.6", "key_colnames(extra_keys=)", "key_colnames(other_keys=)")
+    redispatch <- function(..., extra_keys) {
+      key_colnames(..., other_keys = extra_keys)
+    }
+    redispatch(x, ..., exclude = exclude)
+  } else {
+    UseMethod("key_colnames")
+  }
 }
 
 #' @rdname key_colnames
@@ -44,7 +53,7 @@ key_colnames.data.frame <- function(x, ...,
   assert_character(time_keys)
   assert_character(other_keys)
   assert_character(exclude)
-  keys = c(geo_keys, other_keys, time_keys)
+  keys <- c(geo_keys, other_keys, time_keys)
   if (!all(keys %in% names(x))) {
     cli_abort(c(
       "Some of the specified key columns aren't present in `x`",
@@ -67,11 +76,13 @@ key_colnames.epi_df <- function(x, ...,
   check_dots_empty0(...)
   if (!identical(geo_keys, "geo_value")) {
     cli_abort('If `x` is an `epi_df`, then `geo_keys` must be `"geo_value"`',
-              class = "epiprocess__key_colnames__mismatched_geo_keys")
+      class = "epiprocess__key_colnames__mismatched_geo_keys"
+    )
   }
   if (!identical(time_keys, "time_value")) {
     cli_abort('If `x` is an `epi_df`, then `time_keys` must be `"time_value"`',
-              class = "epiprocess__key_colnames__mismatched_time_keys")
+      class = "epiprocess__key_colnames__mismatched_time_keys"
+    )
   }
   expected_other_keys <- attr(x, "metadata")$other_keys
   if (is.null(other_keys)) {