325 workflow adj

NAMESPACE

@@ -1,8 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(Add_model,epi_workflow)
+S3method(Add_model,workflow)
 S3method(Math,dist_quantiles)
 S3method(Ops,dist_quantiles)
-S3method(add_model,epi_workflow)
+S3method(Remove_model,epi_workflow)
+S3method(Remove_model,workflow)
+S3method(Update_model,epi_workflow)
+S3method(Update_model,workflow)
 S3method(adjust_epi_recipe,epi_recipe)
 S3method(adjust_epi_recipe,epi_workflow)
 S3method(adjust_frosting,epi_workflow)
@@ -92,7 +97,6 @@ S3method(print,step_population_scaling)
 S3method(print,step_training_window)
 S3method(quantile,dist_quantiles)
 S3method(refresh_blueprint,default_epi_recipe_blueprint)
-S3method(remove_model,epi_workflow)
 S3method(residuals,flatline)
 S3method(run_mold,default_epi_recipe_blueprint)
 S3method(slather,layer_add_forecast_date)
@@ -115,10 +119,12 @@ S3method(tidy,check_enough_train_data)
 S3method(tidy,frosting)
 S3method(tidy,layer)
 S3method(update,layer)
-S3method(update_model,epi_workflow)
 S3method(vec_ptype_abbr,dist_quantiles)
 S3method(vec_ptype_full,dist_quantiles)
 export("%>%")
+export(Add_model)
+export(Remove_model)
+export(Update_model)
 export(add_epi_recipe)
 export(add_frosting)
 export(add_layer)

R/epi_workflow.R

@@ -59,107 +59,6 @@ is_epi_workflow <- function(x) {
 }
 
 
-#' Add a model to an `epi_workflow`
-#'
-#' @seealso [workflows::add_model()]
-#' - `add_model()` adds a parsnip model to the `epi_workflow`.
-#'
-#' - `remove_model()` removes the model specification as well as any fitted
-#'   model object. Any extra formulas are also removed.
-#'
-#' - `update_model()` first removes the model then adds the new
-#' specification to the workflow.
-#'
-#' @details
-#' Has the same behaviour as [workflows::add_model()] but also ensures
-#' that the returned object is an `epi_workflow`.
-#'
-#' @inheritParams workflows::add_model
-#'
-#' @param x An `epi_workflow`.
-#'
-#' @param spec A parsnip model specification.
-#'
-#' @param ... Not used.
-#'
-#' @return
-#' `x`, updated with a new, updated, or removed model.
-#'
-#' @export
-#' @examples
-#' jhu <- case_death_rate_subset %>%
-#'   dplyr::filter(
-#'     time_value > "2021-11-01",
-#'     geo_value %in% c("ak", "ca", "ny")
-#'   )
-#'
-#' r <- epi_recipe(jhu) %>%
-#'   step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
-#'   step_epi_ahead(death_rate, ahead = 7)
-#'
-#' rf_model <- rand_forest(mode = "regression")
-#'
-#' wf <- epi_workflow(r)
-#'
-#' wf <- wf %>% add_model(rf_model)
-#' wf
-#'
-#' lm_model <- parsnip::linear_reg()
-#'
-#' wf <- update_model(wf, lm_model)
-#' wf
-#'
-#' wf <- remove_model(wf)
-#' wf
-#' @export
-add_model <- function(x, spec, ..., formula = NULL) {
-  UseMethod("add_model")
-}
-
-#' @rdname add_model
-#' @export
-remove_model <- function(x) {
-  UseMethod("remove_model")
-}
-
-#' @rdname add_model
-#' @export
-update_model <- function(x, spec, ..., formula = NULL) {
-  UseMethod("update_model")
-}
-
-#' @rdname add_model
-#' @export
-add_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
-  workflows::add_model(x, spec, ..., formula = formula)
-}
-
-#' @rdname add_model
-#' @export
-remove_model.epi_workflow <- function(x) {
-  workflows:::validate_is_workflow(x)
-
-  if (!workflows:::has_spec(x)) {
-    rlang::warn("The workflow has no model to remove.")
-  }
-
-  new_epi_workflow(
-    pre = x$pre,
-    fit = workflows:::new_stage_fit(),
-    post = x$post,
-    trained = FALSE
-  )
-}
-
-#' @rdname add_model
-#' @export
-update_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
-  rlang::check_dots_empty()
-  x <- remove_model(x)
-  workflows::add_model(x, spec, ..., formula = formula)
-}
-
-
 #' Fit an `epi_workflow` object
 #'
 #' @description

R/model-methods.R

@@ -0,0 +1,133 @@
+#' Add a model to an `epi_workflow`
+#'
+#' @seealso [workflows::add_model()]
+#' - `Add_model()` adds a parsnip model to the `epi_workflow`.
+#'
+#' - `Remove_model()` removes the model specification as well as any fitted
+#'   model object. Any extra formulas are also removed.
+#'
+#' - `Update_model()` first removes the model then adds the new
+#' specification to the workflow.
+#'
+#' @details
+#' Has the same behaviour as [workflows::add_model()] but also ensures
+#' that the returned object is an `epi_workflow`.
+#'
+#' This family is called `Add_*` / `Update_*` / `Remove_*` to avoid
+#' masking the related functions in `{workflows}`. We also provide
+#' aliases with the lower-case names. However, in the event that
+#' `{workflows}` is loaded after `{epipredict}`, these may fail to function
+#' properly.
+#'
+#' @inheritParams workflows::add_model
+#'
+#' @param x An `epi_workflow`.
+#'
+#' @param spec A parsnip model specification.
+#'
+#' @param ... Not used.
+#'
+#' @return
+#' `x`, updated with a new, updated, or removed model.
+#'
+#' @export
+#' @examples
+#' jhu <- case_death_rate_subset %>%
+#'   dplyr::filter(
+#'     time_value > "2021-11-01",
+#'     geo_value %in% c("ak", "ca", "ny")
+#'   )
+#'
+#' r <- epi_recipe(jhu) %>%
+#'   step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
+#'   step_epi_ahead(death_rate, ahead = 7)
+#'
+#' rf_model <- rand_forest(mode = "regression")
+#'
+#' wf <- epi_workflow(r)
+#'
+#' wf <- wf %>% Add_model(rf_model)
+#' wf
+#'
+#' lm_model <- parsnip::linear_reg()
+#'
+#' wf <- Update_model(wf, lm_model)
+#' wf
+#'
+#' wf <- Remove_model(wf)
+#' wf
+#' @export
+Add_model <- function(x, spec, ..., formula = NULL) {
+  UseMethod("Add_model")
+}
+
+#' @rdname Add_model
+#' @export
+Remove_model <- function(x) {
+  UseMethod("Remove_model")
+}
+
+#' @rdname Add_model
+#' @export
+Update_model <- function(x, spec, ..., formula = NULL) {
+  UseMethod("Update_model")
+}
+
+#' @rdname Add_model
+#' @export
+Add_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
+  workflows::add_model(x, spec, ..., formula = formula)
+}
+
+#' @rdname Add_model
+#' @export
+Remove_model.epi_workflow <- function(x) {
+  workflows:::validate_is_workflow(x)
+
+  if (!workflows:::has_spec(x)) {
+    rlang::warn("The workflow has no model to remove.")
+  }
+
+  new_epi_workflow(
+    pre = x$pre,
+    fit = workflows:::new_stage_fit(),
+    post = x$post,
+    trained = FALSE
+  )
+}
+
+#' @rdname Add_model
+#' @export
+Update_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
+  rlang::check_dots_empty()
+  x <- Remove_model(x)
+  Add_model(x, spec, ..., formula = formula)
+}
+
+
+#' @rdname Add_model
+#' @export
+Add_model.workflow <- workflows::add_model
+
+#' @rdname Add_model
+#' @export
+Remove_model.workflow <- workflows::remove_model
+
+#' @rdname Add_model
+#' @export
+Update_model.workflow <- workflows::update_model
+
+
+# Aliases -----------------------------------------------------------------
+
+#' @rdname Add_model
+#' @export
+add_model <- Add_model
+
+#' @rdname Add_model
+#' @export
+remove_model <- Remove_model
+
+#' @rdname Add_model
+#' @export
+update_model <- Update_model

_pkgdown.yml

@@ -22,20 +22,20 @@ navbar:
   type: light
 
 articles:
-  - title: Get started
-    navbar: ~
-    contents:
-      - epipredict
-      - preprocessing-and-models
-      - arx-classifier
-      - articles/update
+- title: Get started
+  navbar: ~
+  contents:
+  - epipredict
+  - preprocessing-and-models
+  - arx-classifier
+  - update
 
-  - title: Advanced methods
-    contents:
-      - articles/sliding
-      - articles/smooth-qr
-      - articles/symptom-surveys
-      - panel-data
+- title: Advanced methods
+  contents:
+  - articles/sliding
+  - articles/smooth-qr
+  - articles/symptom-surveys
+  - panel-data
 
 repo:
   url:
@@ -78,15 +78,16 @@ reference:
       - smooth_quantile_reg
   - title: Custom panel data forecasting workflows
     contents:
-      - epi_recipe
-      - epi_workflow
-      - add_epi_recipe
-      - adjust_epi_recipe
-      - add_model
-      - predict.epi_workflow
-      - fit.epi_workflow
-      - augment.epi_workflow
-      - forecast.epi_workflow
+    - epi_recipe
+    - epi_workflow
+    - add_epi_recipe
+    - adjust_epi_recipe
+    - Add_model
+    - predict.epi_workflow
+    - fit.epi_workflow
+    - augment.epi_workflow
+    - forecast.epi_workflow
+
   - title: Epi recipe preprocessing steps
     contents:
       - starts_with("step_")