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wip lint: maybe bug fix #403

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wip lint: maybe bug fix #403

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3 changes: 2 additions & 1 deletion .lintr
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Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,6 @@ linters: linters_with_defaults(
)
exclusions: list(
"renv",
"venv"
"venv",
"instr/templates/"
)
29 changes: 18 additions & 11 deletions R/arx_classifier.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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$ahead)
preds <- forecast(
wf,
) %>%
Expand Down Expand Up @@ -136,7 +139,10 @@ arx_class_epi_workflow <- function(
if (args_list$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$as_of
Expand Down Expand Up @@ -209,7 +215,7 @@ arx_class_epi_workflow <- function(
r <- r %>%
step_mutate(
across(
matches(ahead_out_name_regex),
tidyselect::matches(ahead_out_name_regex),
~ cut(.x, breaks = args_list$breaks),
.names = "outcome_class",
.unpack = TRUE
Expand Down Expand Up @@ -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).
Expand Down
10 changes: 7 additions & 3 deletions R/arx_forecaster.R
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Expand Up @@ -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$forecast_date} doesn't match the date from which the forecast
is actually occurring {forecast_date_default}.",
class = "epipredict__arx_forecaster__forecast_date_defaulting"
)
}
Expand All @@ -140,7 +141,8 @@ arx_fcast_epi_workflow <- function(
forecast_date <- args_list$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"
)
}
Expand Down Expand Up @@ -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"
)
}
Expand Down
13 changes: 0 additions & 13 deletions R/blueprint-epi_recipe-default.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
# }
5 changes: 5 additions & 0 deletions R/epipredict-package.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
))
12 changes: 6 additions & 6 deletions R/utils-arg.R
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
11 changes: 5 additions & 6 deletions man/arx_class_args_list.Rd
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4 changes: 2 additions & 2 deletions man/step_adjust_latency.Rd
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