wip lint: maybe bug fix

.lintr

@@ -5,5 +5,6 @@ linters: linters_with_defaults(
   )
 exclusions: list(
   "renv",
-  "venv"
+  "venv",
+  "instr/templates/"
   )

R/arx_classifier.R

@@ -58,13 +58,16 @@ arx_classifier <- function(
   if (args_list$adjust_latency == "none") {
     forecast_date_default <- max(epi_data$time_value)
     if (!is.null(args_list$forecast_date) && args_list$forecast_date != forecast_date_default) {
-      cli_warn("The specified forecast date {args_list$forecast_date} doesn't match the date from which the forecast is occurring {forecast_date}.")
+      cli_warn(
+        "The specified forecast date {args_list$forecast_date} doesn't match the date from which the forecast
+        is occurring {forecast_date}."
+      )
     }
   } else {
     forecast_date_default <- attributes(epi_data)$metadata$as_of
   }
-  forecast_date <- args_list$forecast_date %||% forecast_date_default
-  target_date <- args_list$target_date %||% (forecast_date + args_list$ahead)
+  args_list$forecast_date <- args_list$forecast_date %||% forecast_date_default
+  args_list$target_date <- args_list$target_date %||% (args_list$forecast_date + args_list$ahead)
   preds <- forecast(
     wf,
   ) %>%
@@ -136,7 +139,10 @@ arx_class_epi_workflow <- function(
   if (args_list$adjust_latency == "none") {
     forecast_date_default <- max(epi_data$time_value)
     if (!is.null(args_list$forecast_date) && args_list$forecast_date != forecast_date_default) {
-      cli_warn("The specified forecast date {args_list$forecast_date} doesn't match the date from which the forecast is occurring {forecast_date}.")
+      cli_warn(
+        "The specified forecast date {args_list$forecast_date} doesn't match the date from which the
+        forecast is occurring {forecast_date}."
+      )
     }
   } else {
     forecast_date_default <- attributes(epi_data)$metadata$as_of
@@ -209,7 +215,7 @@ arx_class_epi_workflow <- function(
   r <- r %>%
     step_mutate(
       across(
-        matches(ahead_out_name_regex),
+        tidyselect::matches(ahead_out_name_regex),
         ~ cut(.x, breaks = args_list$breaks),
         .names = "outcome_class",
         .unpack = TRUE
@@ -243,15 +249,16 @@ arx_class_epi_workflow <- function(
 #' Constructs a list of arguments for [arx_classifier()].
 #'
 #' @inheritParams arx_args_list
-#' @param outcome_transform Scalar character. Whether the outcome should
-#'   be created using growth rates (as the predictors are) or lagged
-#'   differences. The second case is closer to the requirements for the
-#'   [2022-23 CDC Flusight Hospitalization Experimental Target](https://github.com/cdcepi/Flusight-forecast-data/blob/745511c436923e1dc201dea0f4181f21a8217b52/data-experimental/README.md).
+#' @param outcome_transform Scalar character. Whether the outcome should be
+#'   created using growth rates (as the predictors are) or lagged differences.
+#'   The second case is closer to the requirements for the [2022-23 CDC Flusight
+#'   Hospitalization Experimental
+#'   Target](https://github.com/cdcepi/Flusight-forecast-data/blob/745511c436923e1dc201dea0f4181f21a8217b52/data-experimental/README.md). # nolint: line_length_linter
 #'   See the Classification Vignette for details of how to create a reasonable
 #'   baseline for this case. Selecting `"growth_rate"` (the default) uses
 #'   [epiprocess::growth_rate()] to create the outcome using some of the
-#'   additional arguments below. Choosing `"lag_difference"` instead simply
-#'   uses the change from the value at the selected `horizon`.
+#'   additional arguments below. Choosing `"lag_difference"` instead simply uses
+#'   the change from the value at the selected `horizon`.
 #' @param breaks Vector. A vector of breaks to turn real-valued growth rates
 #'   into discrete classes. The default gives binary upswing classification
 #'   as in [McDonald, Bien, Green, Hu, et al.](https://doi.org/10.1073/pnas.2111453118).

R/arx_forecaster.R

@@ -130,7 +130,8 @@ arx_fcast_epi_workflow <- function(
     forecast_date_default <- max(epi_data$time_value)
     if (!is.null(args_list$forecast_date) && args_list$forecast_date != forecast_date_default) {
       cli_warn(
-        "The specified forecast date {args_list$forecast_date} doesn't match the date from which the forecast is actually occurring {forecast_date_default}.",
+        "The specified forecast date {args_list$forecast_date} doesn't match the date from which the forecast
+        is actually occurring {forecast_date_default}.",
         class = "epipredict__arx_forecaster__forecast_date_defaulting"
       )
     }
@@ -140,7 +141,8 @@ arx_fcast_epi_workflow <- function(
   forecast_date <- args_list$forecast_date %||% forecast_date_default
   target_date <- args_list$target_date %||% (forecast_date + args_list$ahead)
   if (forecast_date + args_list$ahead != target_date) {
-    cli_abort("`forecast_date` {.val {forecast_date}} + `ahead` {.val {ahead}} must equal `target_date` {.val {target_date}}.",
+    cli_abort(
+      "`forecast_date` {.val {forecast_date}} + `ahead` {.val {ahead}} must equal `target_date`{.val {target_date}}.",
       class = "epipredict__arx_forecaster__inconsistent_target_ahead_forecaste_date"
     )
   }
@@ -310,7 +312,9 @@ arx_args_list <- function(
 
   if (!is.null(forecast_date) && !is.null(target_date)) {
     if (forecast_date + ahead != target_date) {
-      cli_abort("`forecast_date` {.val {forecast_date}} + `ahead` {.val {ahead}} must equal `target_date` {.val {target_date}}.",
+      cli_abort(
+        "`forecast_date` {.val {forecast_date}} + `ahead` {.val {ahead}} must equal `target_date`
+        {.val {target_date}}.",
         class = "epipredict__arx_args__inconsistent_target_ahead_forecaste_date"
       )
     }

R/blueprint-epi_recipe-default.R

@@ -79,7 +79,6 @@ new_default_epi_recipe_blueprint <-
 #' @export
 run_mold.default_epi_recipe_blueprint <- function(blueprint, ..., data) {
   rlang::check_dots_empty0(...)
-  # blueprint <- hardhat:::patch_recipe_default_blueprint(blueprint)
   cleaned <- mold_epi_recipe_default_clean(blueprint = blueprint, data = data)
   blueprint <- cleaned$blueprint
   data <- cleaned$data
@@ -97,15 +96,3 @@ mold_epi_recipe_default_clean <- function(blueprint, data) {
 refresh_blueprint.default_epi_recipe_blueprint <- function(blueprint) {
   do.call(new_default_epi_recipe_blueprint, as.list(blueprint))
 }
-
-
-## removing this function?
-# er_check_is_data_like <- function(.x, .x_nm) {
-#   if (rlang::is_missing(.x_nm)) {
-#     .x_nm <- rlang::as_label(rlang::enexpr(.x))
-#   }
-#   if (!hardhat:::is_new_data_like(.x)) {
-#     hardhat:::glubort("`{.x_nm}` must be a data.frame or a matrix, not a {class1(.x)}.")
-#   }
-#   .x
-# }

R/epipredict-package.R

@@ -15,3 +15,8 @@
 na_chr <- NA_character_
 ## usethis namespace: end
 NULL
+utils::globalVariables(c(
+  ".x", ".group_key", ".ref_time_value", "resid",
+  "fitted", ".response", "geo_value", "time_value",
+  "value", ".data", ".env"
+))

R/utils-arg.R

@@ -66,7 +66,7 @@ arg_is_pos <- function(..., allow_null = FALSE, call = caller_env()) {
       null.ok = allow_null, any.missing = FALSE
     )
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} strictly positive number{?s}.",
         call = call
@@ -79,7 +79,7 @@ arg_is_nonneg <- function(..., allow_null = FALSE, call = caller_env()) {
   handle_arg_list(..., .tests = function(name, value) {
     ok <- test_numeric(value, lower = 0, null.ok = allow_null, any.missing = FALSE)
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} non-negative number{?s}.",
         call = call
@@ -92,7 +92,7 @@ arg_is_int <- function(..., allow_null = FALSE, call = caller_env()) {
   handle_arg_list(..., .tests = function(name, value) {
     ok <- test_integerish(value, null.ok = allow_null)
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} integer{?s}.",
         call = call
@@ -105,7 +105,7 @@ arg_is_pos_int <- function(..., allow_null = FALSE, call = caller_env()) {
   handle_arg_list(..., .tests = function(name, value) {
     ok <- test_integerish(value, null.ok = allow_null, lower = 1, any.missing = FALSE)
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} positive integer{?s}.",
         call = call
@@ -118,7 +118,7 @@ arg_is_nonneg_int <- function(..., allow_null = FALSE, call = caller_env()) {
   handle_arg_list(..., .tests = function(name, value) {
     ok <- test_integerish(value, null.ok = allow_null, lower = 0, any.missing = FALSE)
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} non-negative integer{?s}.",
         call = call
@@ -131,7 +131,7 @@ arg_is_date <- function(..., allow_null = FALSE, call = caller_env()) {
   handle_arg_list(..., .tests = function(name, value) {
     ok <- test_date(value, null.ok = allow_null)
     if (!ok) {
-      len <- length(value)
+      len <- length(value) # nolint: object_usage_linter
       cli_abort(
         "{.arg {name}} must be {cli::qty(len)} {?a/} date{?s}.",
         call = call